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15
.github/workflows/c-cpp.yml
vendored
15
.github/workflows/c-cpp.yml
vendored
@@ -15,9 +15,14 @@ jobs:
|
||||
run: sudo apt-get install libnetcdf-dev
|
||||
- name: make
|
||||
run: make fpocket
|
||||
- name: Set up Python 3.7
|
||||
uses: actions/setup-python@v2
|
||||
with:
|
||||
python-version: 3.7
|
||||
- name: create conda environment
|
||||
run: conda env update -f ./tests/environment.yml
|
||||
- name: activate conda environment
|
||||
run: conda activate fpocket_test
|
||||
- name: Run pytest
|
||||
run: pytest
|
||||
run: conda env update -f ./tests/environment.yml
|
||||
- name : activate
|
||||
run : |
|
||||
eval "$(conda shell.bash hook)"
|
||||
conda activate fpocket_test
|
||||
pytest
|
||||
|
||||
@@ -30,7 +30,7 @@ jobs:
|
||||
|
||||
- job: build_and_test_mac
|
||||
pool:
|
||||
vmImage: 'macOS-10.14'
|
||||
vmImage: 'macOS-10.15'
|
||||
steps:
|
||||
- bash: sudo chown -R $USER $CONDA
|
||||
- script: conda env create --file tests/environment.yml --name fpocket_test
|
||||
|
||||
413
data/all_pdb_test.txt
Normal file
413
data/all_pdb_test.txt
Normal file
@@ -0,0 +1,413 @@
|
||||
data/bio_assembly/NO_BIRD/6FMP.pdb data/bio_assembly/NO_BIRD/6FMP.pdb C
|
||||
data/bio_assembly/NO_BIRD/6QWN.pdb data/bio_assembly/NO_BIRD/6QWN.pdb F
|
||||
data/bio_assembly/NO_BIRD/4D2D.pdb data/bio_assembly/NO_BIRD/4D2D.pdb B
|
||||
data/bio_assembly/NO_BIRD/6QXP.pdb data/bio_assembly/NO_BIRD/6QXP.pdb I
|
||||
data/bio_assembly/NO_BIRD/2OBH.pdb data/bio_assembly/NO_BIRD/2OBH.pdb C
|
||||
data/bio_assembly/NO_BIRD/1YK1.pdb data/bio_assembly/NO_BIRD/1YK1.pdb E
|
||||
data/bio_assembly/NO_BIRD/3KD7.pdb data/bio_assembly/NO_BIRD/3KD7.pdb G
|
||||
data/bio_assembly/NO_BIRD/1YC5.pdb data/bio_assembly/NO_BIRD/1YC5.pdb B
|
||||
data/bio_assembly/NO_BIRD/2H4F.pdb data/bio_assembly/NO_BIRD/2H4F.pdb D
|
||||
data/bio_assembly/NO_BIRD/6F0Y.pdb data/bio_assembly/NO_BIRD/6F0Y.pdb B
|
||||
data/bio_assembly/NO_BIRD/5OJ5.pdb data/bio_assembly/NO_BIRD/5OJ5.pdb B
|
||||
data/bio_assembly/NO_BIRD/5OJR.pdb data/bio_assembly/NO_BIRD/5OJR.pdb E
|
||||
data/bio_assembly/NO_BIRD/2QBX.pdb data/bio_assembly/NO_BIRD/2QBX.pdb D
|
||||
data/bio_assembly/NO_BIRD/5D0J.pdb data/bio_assembly/NO_BIRD/5D0J.pdb L
|
||||
data/bio_assembly/NO_BIRD/3FBR.pdb data/bio_assembly/NO_BIRD/3FBR.pdb B
|
||||
data/bio_assembly/NO_BIRD/3JR3.pdb data/bio_assembly/NO_BIRD/3JR3.pdb D
|
||||
data/bio_assembly/NO_BIRD/3SVM.pdb data/bio_assembly/NO_BIRD/3SVM.pdb P
|
||||
data/bio_assembly/NO_BIRD/4Z5W.pdb data/bio_assembly/NO_BIRD/4Z5W.pdb P
|
||||
data/bio_assembly/NO_BIRD/5E1D.pdb data/bio_assembly/NO_BIRD/5E1D.pdb D
|
||||
data/bio_assembly/NO_BIRD/6Q1U.pdb data/bio_assembly/NO_BIRD/6Q1U.pdb C
|
||||
data/bio_assembly/NO_BIRD/6WZZ.pdb data/bio_assembly/NO_BIRD/6WZZ.pdb B
|
||||
data/bio_assembly/NO_BIRD/1A1R.pdb data/bio_assembly/NO_BIRD/1A1R.pdb C
|
||||
data/bio_assembly/NO_BIRD/1EJH.pdb data/bio_assembly/NO_BIRD/1EJH.pdb E
|
||||
data/bio_assembly/NO_BIRD/1BZH.pdb data/bio_assembly/NO_BIRD/1BZH.pdb I
|
||||
data/bio_assembly/NO_BIRD/1AQC.pdb data/bio_assembly/NO_BIRD/1AQC.pdb C
|
||||
data/bio_assembly/NO_BIRD/6TWQ.pdb data/bio_assembly/NO_BIRD/6TWQ.pdb C
|
||||
data/bio_assembly/NO_BIRD/1YTJ.pdb data/bio_assembly/NO_BIRD/1YTJ.pdb I
|
||||
data/bio_assembly/NO_BIRD/1YTH.pdb data/bio_assembly/NO_BIRD/1YTH.pdb I
|
||||
data/bio_assembly/NO_BIRD/1YTG.pdb data/bio_assembly/NO_BIRD/1YTG.pdb I
|
||||
data/bio_assembly/NO_BIRD/6CD9.pdb data/bio_assembly/NO_BIRD/6CD9.pdb B
|
||||
data/bio_assembly/NO_BIRD/6C4U.pdb data/bio_assembly/NO_BIRD/6C4U.pdb G
|
||||
data/bio_assembly/NO_BIRD/5H6Y.pdb data/bio_assembly/NO_BIRD/5H6Y.pdb B
|
||||
data/bio_assembly/NO_BIRD/5I3L.pdb data/bio_assembly/NO_BIRD/5I3L.pdb C
|
||||
data/bio_assembly/NO_BIRD/6SEO.pdb data/bio_assembly/NO_BIRD/6SEO.pdb L
|
||||
data/bio_assembly/NO_BIRD/6SEN.pdb data/bio_assembly/NO_BIRD/6SEN.pdb L
|
||||
data/bio_assembly/NO_BIRD/2ITK.pdb data/bio_assembly/NO_BIRD/2ITK.pdb B
|
||||
data/bio_assembly/NO_BIRD/2Q5A.pdb data/bio_assembly/NO_BIRD/2Q5A.pdb B
|
||||
data/bio_assembly/NO_BIRD/3UKW.pdb data/bio_assembly/NO_BIRD/3UKW.pdb C
|
||||
data/bio_assembly/NO_BIRD/3UKX.pdb data/bio_assembly/NO_BIRD/3UKX.pdb C
|
||||
data/bio_assembly/NO_BIRD/2VAY.pdb data/bio_assembly/NO_BIRD/2VAY.pdb B
|
||||
data/bio_assembly/NO_BIRD/5UW3.pdb data/bio_assembly/NO_BIRD/5UW3.pdb E
|
||||
data/bio_assembly/NO_BIRD/5U1Q.pdb data/bio_assembly/NO_BIRD/5U1Q.pdb L
|
||||
data/bio_assembly/NO_BIRD/4ZRT.pdb data/bio_assembly/NO_BIRD/4ZRT.pdb B
|
||||
data/bio_assembly/NO_BIRD/5EEL.pdb data/bio_assembly/NO_BIRD/5EEL.pdb L
|
||||
data/bio_assembly/NO_BIRD/5W4E.pdb data/bio_assembly/NO_BIRD/5W4E.pdb A
|
||||
data/bio_assembly/NO_BIRD/4NY3.pdb data/bio_assembly/NO_BIRD/4NY3.pdb C
|
||||
data/bio_assembly/NO_BIRD/4AKT.pdb data/bio_assembly/NO_BIRD/4AKT.pdb C
|
||||
data/bio_assembly/NO_BIRD/5XWR.pdb data/bio_assembly/NO_BIRD/5XWR.pdb C
|
||||
data/bio_assembly/NO_BIRD/2H4H.pdb data/bio_assembly/NO_BIRD/2H4H.pdb B
|
||||
data/bio_assembly/NO_BIRD/3AGY.pdb data/bio_assembly/NO_BIRD/3AGY.pdb C
|
||||
data/bio_assembly/NO_BIRD/3AGZ.pdb data/bio_assembly/NO_BIRD/3AGZ.pdb C
|
||||
data/bio_assembly/NO_BIRD/3TWS.pdb data/bio_assembly/NO_BIRD/3TWS.pdb E
|
||||
data/bio_assembly/NO_BIRD/3TWT.pdb data/bio_assembly/NO_BIRD/3TWT.pdb E
|
||||
data/bio_assembly/NO_BIRD/3TWV.pdb data/bio_assembly/NO_BIRD/3TWV.pdb E
|
||||
data/bio_assembly/NO_BIRD/4DRW.pdb data/bio_assembly/NO_BIRD/4DRW.pdb E
|
||||
data/bio_assembly/NO_BIRD/1EJ4.pdb data/bio_assembly/NO_BIRD/1EJ4.pdb B
|
||||
data/bio_assembly/NO_BIRD/6TWX.pdb data/bio_assembly/NO_BIRD/6TWX.pdb C
|
||||
data/bio_assembly/NO_BIRD/5K4F.pdb data/bio_assembly/NO_BIRD/5K4F.pdb C
|
||||
data/bio_assembly/NO_BIRD/1XJ7.pdb data/bio_assembly/NO_BIRD/1XJ7.pdb B
|
||||
data/bio_assembly/NO_BIRD/1WBP.pdb data/bio_assembly/NO_BIRD/1WBP.pdb B
|
||||
data/bio_assembly/NO_BIRD/1KA6.pdb data/bio_assembly/NO_BIRD/1KA6.pdb B
|
||||
data/bio_assembly/NO_BIRD/6CDG.pdb data/bio_assembly/NO_BIRD/6CDG.pdb B
|
||||
data/bio_assembly/NO_BIRD/5N7F.pdb data/bio_assembly/NO_BIRD/5N7F.pdb C
|
||||
data/bio_assembly/NO_BIRD/6CD8.pdb data/bio_assembly/NO_BIRD/6CD8.pdb C
|
||||
data/bio_assembly/NO_BIRD/5N7D.pdb data/bio_assembly/NO_BIRD/5N7D.pdb C
|
||||
data/bio_assembly/NO_BIRD/2IG0.pdb data/bio_assembly/NO_BIRD/2IG0.pdb B
|
||||
data/bio_assembly/NO_BIRD/2RLY.pdb data/bio_assembly/NO_BIRD/2RLY.pdb P
|
||||
data/bio_assembly/NO_BIRD/5D94.pdb data/bio_assembly/NO_BIRD/5D94.pdb B
|
||||
data/bio_assembly/NO_BIRD/5IC3.pdb data/bio_assembly/NO_BIRD/5IC3.pdb C
|
||||
data/bio_assembly/NO_BIRD/3HS8.pdb data/bio_assembly/NO_BIRD/3HS8.pdb P
|
||||
data/bio_assembly/NO_BIRD/3HS9.pdb data/bio_assembly/NO_BIRD/3HS9.pdb P
|
||||
data/bio_assembly/NO_BIRD/3EG6.pdb data/bio_assembly/NO_BIRD/3EG6.pdb C
|
||||
data/bio_assembly/NO_BIRD/3L3Q.pdb data/bio_assembly/NO_BIRD/3L3Q.pdb B
|
||||
data/bio_assembly/NO_BIRD/3O71.pdb data/bio_assembly/NO_BIRD/3O71.pdb B
|
||||
data/bio_assembly/NO_BIRD/3RZ9.pdb data/bio_assembly/NO_BIRD/3RZ9.pdb B
|
||||
data/bio_assembly/NO_BIRD/3RZ2.pdb data/bio_assembly/NO_BIRD/3RZ2.pdb C
|
||||
data/bio_assembly/NO_BIRD/3RZX.pdb data/bio_assembly/NO_BIRD/3RZX.pdb B
|
||||
data/bio_assembly/NO_BIRD/4HH6.pdb data/bio_assembly/NO_BIRD/4HH6.pdb Z
|
||||
data/bio_assembly/NO_BIRD/4GQ6.pdb data/bio_assembly/NO_BIRD/4GQ6.pdb B
|
||||
data/bio_assembly/NO_BIRD/3WA4.pdb data/bio_assembly/NO_BIRD/3WA4.pdb B
|
||||
data/bio_assembly/NO_BIRD/3ZMP.pdb data/bio_assembly/NO_BIRD/3ZMP.pdb C
|
||||
data/bio_assembly/NO_BIRD/3UL1.pdb data/bio_assembly/NO_BIRD/3UL1.pdb A
|
||||
data/bio_assembly/NO_BIRD/5GG4.pdb data/bio_assembly/NO_BIRD/5GG4.pdb E
|
||||
data/bio_assembly/NO_BIRD/5GJH.pdb data/bio_assembly/NO_BIRD/5GJH.pdb B
|
||||
data/bio_assembly/NO_BIRD/4QE8.pdb data/bio_assembly/NO_BIRD/4QE8.pdb C
|
||||
data/bio_assembly/NO_BIRD/4QE6.pdb data/bio_assembly/NO_BIRD/4QE6.pdb B
|
||||
data/bio_assembly/NO_BIRD/5E6Q.pdb data/bio_assembly/NO_BIRD/5E6Q.pdb A
|
||||
data/bio_assembly/NO_BIRD/5EOD.pdb data/bio_assembly/NO_BIRD/5EOD.pdb B
|
||||
data/bio_assembly/NO_BIRD/4LP9.pdb data/bio_assembly/NO_BIRD/4LP9.pdb I
|
||||
data/bio_assembly/NO_BIRD/4M91.pdb data/bio_assembly/NO_BIRD/4M91.pdb B
|
||||
data/bio_assembly/NO_BIRD/4M92.pdb data/bio_assembly/NO_BIRD/4M92.pdb B
|
||||
data/bio_assembly/NO_BIRD/5W4F.pdb data/bio_assembly/NO_BIRD/5W4F.pdb A
|
||||
data/bio_assembly/NO_BIRD/4O56.pdb data/bio_assembly/NO_BIRD/4O56.pdb B
|
||||
data/bio_assembly/NO_BIRD/4YOS.pdb data/bio_assembly/NO_BIRD/4YOS.pdb E
|
||||
data/bio_assembly/NO_BIRD/4Z63.pdb data/bio_assembly/NO_BIRD/4Z63.pdb P
|
||||
data/bio_assembly/NO_BIRD/2YJD.pdb data/bio_assembly/NO_BIRD/2YJD.pdb C
|
||||
data/bio_assembly/NO_BIRD/4X3O.pdb data/bio_assembly/NO_BIRD/4X3O.pdb C
|
||||
data/bio_assembly/NO_BIRD/4X3P.pdb data/bio_assembly/NO_BIRD/4X3P.pdb C
|
||||
data/bio_assembly/NO_BIRD/2H9P.pdb data/bio_assembly/NO_BIRD/2H9P.pdb B
|
||||
data/bio_assembly/NO_BIRD/2H9N.pdb data/bio_assembly/NO_BIRD/2H9N.pdb B
|
||||
data/bio_assembly/NO_BIRD/1LKL.pdb data/bio_assembly/NO_BIRD/1LKL.pdb B
|
||||
data/bio_assembly/NO_BIRD/1LKK.pdb data/bio_assembly/NO_BIRD/1LKK.pdb B
|
||||
data/bio_assembly/NO_BIRD/3IOL.pdb data/bio_assembly/NO_BIRD/3IOL.pdb B
|
||||
data/bio_assembly/NO_BIRD/5DNJ.pdb data/bio_assembly/NO_BIRD/5DNJ.pdb B
|
||||
data/bio_assembly/NO_BIRD/6P5L.pdb data/bio_assembly/NO_BIRD/6P5L.pdb D
|
||||
data/bio_assembly/NO_BIRD/6Y4Q.pdb data/bio_assembly/NO_BIRD/6Y4Q.pdb C
|
||||
data/bio_assembly/NO_BIRD/1QKB.pdb data/bio_assembly/NO_BIRD/1QKB.pdb B
|
||||
data/bio_assembly/NO_BIRD/1QKA.pdb data/bio_assembly/NO_BIRD/1QKA.pdb B
|
||||
data/bio_assembly/NO_BIRD/1E6I.pdb data/bio_assembly/NO_BIRD/1E6I.pdb P
|
||||
data/bio_assembly/NO_BIRD/6RJP.pdb data/bio_assembly/NO_BIRD/6RJP.pdb C
|
||||
data/bio_assembly/NO_BIRD/1OHE.pdb data/bio_assembly/NO_BIRD/1OHE.pdb B
|
||||
data/bio_assembly/NO_BIRD/1Q1S.pdb data/bio_assembly/NO_BIRD/1Q1S.pdb A
|
||||
data/bio_assembly/NO_BIRD/1G5J.pdb data/bio_assembly/NO_BIRD/1G5J.pdb B
|
||||
data/bio_assembly/NO_BIRD/1JEV.pdb data/bio_assembly/NO_BIRD/1JEV.pdb B
|
||||
data/bio_assembly/NO_BIRD/1JEU.pdb data/bio_assembly/NO_BIRD/1JEU.pdb B
|
||||
data/bio_assembly/NO_BIRD/1JET.pdb data/bio_assembly/NO_BIRD/1JET.pdb B
|
||||
data/bio_assembly/NO_BIRD/1B32.pdb data/bio_assembly/NO_BIRD/1B32.pdb B
|
||||
data/bio_assembly/NO_BIRD/1B46.pdb data/bio_assembly/NO_BIRD/1B46.pdb B
|
||||
data/bio_assembly/NO_BIRD/1B9J.pdb data/bio_assembly/NO_BIRD/1B9J.pdb B
|
||||
data/bio_assembly/NO_BIRD/6JXU.pdb data/bio_assembly/NO_BIRD/6JXU.pdb B
|
||||
data/bio_assembly/NO_BIRD/6EJ8.pdb data/bio_assembly/NO_BIRD/6EJ8.pdb B
|
||||
data/bio_assembly/NO_BIRD/6EJ9.pdb data/bio_assembly/NO_BIRD/6EJ9.pdb B
|
||||
data/bio_assembly/NO_BIRD/1O6P.pdb data/bio_assembly/NO_BIRD/1O6P.pdb C
|
||||
data/bio_assembly/NO_BIRD/5OK6.pdb data/bio_assembly/NO_BIRD/5OK6.pdb C
|
||||
data/bio_assembly/NO_BIRD/2IV8.pdb data/bio_assembly/NO_BIRD/2IV8.pdb P
|
||||
data/bio_assembly/NO_BIRD/2OY2.pdb data/bio_assembly/NO_BIRD/2OY2.pdb W
|
||||
data/bio_assembly/NO_BIRD/2OXW.pdb data/bio_assembly/NO_BIRD/2OXW.pdb X
|
||||
data/bio_assembly/NO_BIRD/2O5G.pdb data/bio_assembly/NO_BIRD/2O5G.pdb B
|
||||
data/bio_assembly/NO_BIRD/3GLU.pdb data/bio_assembly/NO_BIRD/3GLU.pdb B
|
||||
data/bio_assembly/NO_BIRD/2Y1N.pdb data/bio_assembly/NO_BIRD/2Y1N.pdb B
|
||||
data/bio_assembly/NO_BIRD/3FDL.pdb data/bio_assembly/NO_BIRD/3FDL.pdb B
|
||||
data/bio_assembly/NO_BIRD/3JZO.pdb data/bio_assembly/NO_BIRD/3JZO.pdb P
|
||||
data/bio_assembly/NO_BIRD/3PDH.pdb data/bio_assembly/NO_BIRD/3PDH.pdb D
|
||||
data/bio_assembly/NO_BIRD/3RC0.pdb data/bio_assembly/NO_BIRD/3RC0.pdb P
|
||||
data/bio_assembly/NO_BIRD/4FII.pdb data/bio_assembly/NO_BIRD/4FII.pdb B
|
||||
data/bio_assembly/NO_BIRD/3ZMQ.pdb data/bio_assembly/NO_BIRD/3ZMQ.pdb C
|
||||
data/bio_assembly/NO_BIRD/3ZRJ.pdb data/bio_assembly/NO_BIRD/3ZRJ.pdb X
|
||||
data/bio_assembly/NO_BIRD/3SRJ.pdb data/bio_assembly/NO_BIRD/3SRJ.pdb C
|
||||
data/bio_assembly/NO_BIRD/5FOS.pdb data/bio_assembly/NO_BIRD/5FOS.pdb C
|
||||
data/bio_assembly/NO_BIRD/5GH9.pdb data/bio_assembly/NO_BIRD/5GH9.pdb B
|
||||
data/bio_assembly/NO_BIRD/5TWH.pdb data/bio_assembly/NO_BIRD/5TWH.pdb E
|
||||
data/bio_assembly/NO_BIRD/5TYI.pdb data/bio_assembly/NO_BIRD/5TYI.pdb L
|
||||
data/bio_assembly/NO_BIRD/5UW5.pdb data/bio_assembly/NO_BIRD/5UW5.pdb E
|
||||
data/bio_assembly/NO_BIRD/5UW7.pdb data/bio_assembly/NO_BIRD/5UW7.pdb C
|
||||
data/bio_assembly/NO_BIRD/5K9S.pdb data/bio_assembly/NO_BIRD/5K9S.pdb B
|
||||
data/bio_assembly/NO_BIRD/5AFG.pdb data/bio_assembly/NO_BIRD/5AFG.pdb B
|
||||
data/bio_assembly/NO_BIRD/4QSY.pdb data/bio_assembly/NO_BIRD/4QSY.pdb B
|
||||
data/bio_assembly/NO_BIRD/5VLA.pdb data/bio_assembly/NO_BIRD/5VLA.pdb Z
|
||||
data/bio_assembly/NO_BIRD/5VTB.pdb data/bio_assembly/NO_BIRD/5VTB.pdb B
|
||||
data/bio_assembly/NO_BIRD/4O6W.pdb data/bio_assembly/NO_BIRD/4O6W.pdb C
|
||||
data/bio_assembly/NO_BIRD/4Y6L.pdb data/bio_assembly/NO_BIRD/4Y6L.pdb C
|
||||
data/bio_assembly/NO_BIRD/4Z2V.pdb data/bio_assembly/NO_BIRD/4Z2V.pdb C
|
||||
data/bio_assembly/NO_BIRD/2Z3L.pdb data/bio_assembly/NO_BIRD/2Z3L.pdb C
|
||||
data/bio_assembly/NO_BIRD/2Z3N.pdb data/bio_assembly/NO_BIRD/2Z3N.pdb C
|
||||
data/bio_assembly/NO_BIRD/4X6S.pdb data/bio_assembly/NO_BIRD/4X6S.pdb L
|
||||
data/bio_assembly/NO_BIRD/4OKF.pdb data/bio_assembly/NO_BIRD/4OKF.pdb A
|
||||
data/bio_assembly/NO_BIRD/6HON.pdb data/bio_assembly/NO_BIRD/6HON.pdb B
|
||||
data/bio_assembly/NO_BIRD/6HOM.pdb data/bio_assembly/NO_BIRD/6HOM.pdb B
|
||||
data/bio_assembly/NO_BIRD/6HV2.pdb data/bio_assembly/NO_BIRD/6HV2.pdb B
|
||||
data/bio_assembly/NO_BIRD/5X7B.pdb data/bio_assembly/NO_BIRD/5X7B.pdb L
|
||||
data/bio_assembly/BIRD/2R9B.pdb data/bio_assembly/BIRD/2R9B.pdb C
|
||||
data/bio_assembly/BIRD/3URI.pdb data/bio_assembly/BIRD/3URI.pdb B
|
||||
data/bio_assembly/BIRD/3URL.pdb data/bio_assembly/BIRD/3URL.pdb B
|
||||
data/bio_assembly/BIRD/3V3B.pdb data/bio_assembly/BIRD/3V3B.pdb D
|
||||
data/bio_assembly/BIRD/3UQP.pdb data/bio_assembly/BIRD/3UQP.pdb B
|
||||
data/bio_assembly/BIRD/3UQR.pdb data/bio_assembly/BIRD/3UQR.pdb D
|
||||
data/bio_assembly/BIRD/5JXH.pdb data/bio_assembly/BIRD/5JXH.pdb H
|
||||
data/bio_assembly/BIRD/5JXJ.pdb data/bio_assembly/BIRD/5JXJ.pdb H
|
||||
data/bio_assembly/BIRD/4RCP.pdb data/bio_assembly/BIRD/4RCP.pdb B
|
||||
data/bio_assembly/BIRD/4TPG.pdb data/bio_assembly/BIRD/4TPG.pdb E
|
||||
data/bio_assembly/BIRD/4RYD.pdb data/bio_assembly/BIRD/4RYD.pdb H
|
||||
data/bio_assembly/BIRD/4O6W.pdb data/bio_assembly/BIRD/4O6W.pdb C
|
||||
data/bio_assembly/BIRD/4K1E.pdb data/bio_assembly/BIRD/4K1E.pdb B
|
||||
data/bio_assembly/BIRD/4DV9.pdb data/bio_assembly/BIRD/4DV9.pdb B
|
||||
data/bio_assembly/BIRD/4DVF.pdb data/bio_assembly/BIRD/4DVF.pdb C
|
||||
data/bio_assembly/BIRD/4EZP.pdb data/bio_assembly/BIRD/4EZP.pdb D
|
||||
data/bio_assembly/BIRD/4FBX.pdb data/bio_assembly/BIRD/4FBX.pdb B
|
||||
data/bio_assembly/BIRD/4G35.pdb data/bio_assembly/BIRD/4G35.pdb B
|
||||
data/bio_assembly/BIRD/5DNJ.pdb data/bio_assembly/BIRD/5DNJ.pdb B
|
||||
data/bio_assembly/BIRD/4WHH.pdb data/bio_assembly/BIRD/4WHH.pdb B
|
||||
data/bio_assembly/BIRD/4WHK.pdb data/bio_assembly/BIRD/4WHK.pdb B
|
||||
data/bio_assembly/BIRD/4WHL.pdb data/bio_assembly/BIRD/4WHL.pdb B
|
||||
data/bio_assembly/BIRD/1SFI.pdb data/bio_assembly/BIRD/1SFI.pdb I
|
||||
data/bio_assembly/BIRD/3RQ7.pdb data/bio_assembly/BIRD/3RQ7.pdb B
|
||||
data/bio_assembly/BIRD/3SNA.pdb data/bio_assembly/BIRD/3SNA.pdb H
|
||||
data/bio_assembly/BIRD/3SNB.pdb data/bio_assembly/BIRD/3SNB.pdb H
|
||||
data/bio_assembly/BIRD/3SNC.pdb data/bio_assembly/BIRD/3SNC.pdb H
|
||||
data/bio_assembly/BIRD/3SND.pdb data/bio_assembly/BIRD/3SND.pdb C
|
||||
data/bio_assembly/BIRD/3SNE.pdb data/bio_assembly/BIRD/3SNE.pdb H
|
||||
data/bio_assembly/BIRD/3S70.pdb data/bio_assembly/BIRD/3S70.pdb B
|
||||
data/bio_assembly/BIRD/1OKX.pdb data/bio_assembly/BIRD/1OKX.pdb C
|
||||
data/bio_assembly/BIRD/6VXY.pdb data/bio_assembly/BIRD/6VXY.pdb C
|
||||
data/bio_assembly/BIRD/3VFK.pdb data/bio_assembly/BIRD/3VFK.pdb G
|
||||
data/bio_assembly/BIRD/3VFJ.pdb data/bio_assembly/BIRD/3VFJ.pdb G
|
||||
data/bio_assembly/BIRD/2XAD.pdb data/bio_assembly/BIRD/2XAD.pdb E
|
||||
data/bio_assembly/BIRD/4MFL.pdb data/bio_assembly/BIRD/4MFL.pdb B
|
||||
data/bio_assembly/BIRD/4MFP.pdb data/bio_assembly/BIRD/4MFP.pdb B
|
||||
data/bio_assembly/BIRD/4MFQ.pdb data/bio_assembly/BIRD/4MFQ.pdb B
|
||||
data/bio_assembly/BIRD/4PJZ.pdb data/bio_assembly/BIRD/4PJZ.pdb B
|
||||
data/bio_assembly/BIRD/4PK0.pdb data/bio_assembly/BIRD/4PK0.pdb B
|
||||
data/bio_assembly/BIRD/4EEC.pdb data/bio_assembly/BIRD/4EEC.pdb C
|
||||
data/bio_assembly/BIRD/4JNA.pdb data/bio_assembly/BIRD/4JNA.pdb I
|
||||
data/bio_assembly/BIRD/4NEC.pdb data/bio_assembly/BIRD/4NEC.pdb E
|
||||
data/bio_assembly/BIRD/3AH8.pdb data/bio_assembly/BIRD/3AH8.pdb Y
|
||||
data/bio_assembly/BIRD/3RQD.pdb data/bio_assembly/BIRD/3RQD.pdb C
|
||||
data/bio_assembly/BIRD/2CV3.pdb data/bio_assembly/BIRD/2CV3.pdb B
|
||||
data/bio_assembly/BIRD/2RMC.pdb data/bio_assembly/BIRD/2RMC.pdb B
|
||||
data/bio_assembly/BIRD/4TOT.pdb data/bio_assembly/BIRD/4TOT.pdb E
|
||||
data/bio_assembly/BIRD/6O21.pdb data/bio_assembly/BIRD/6O21.pdb B
|
||||
data/bio_assembly/BIRD/6C1Q.pdb data/bio_assembly/BIRD/6C1Q.pdb L
|
||||
data/bio_assembly/BIRD/6C1R.pdb data/bio_assembly/BIRD/6C1R.pdb L
|
||||
data/bio_assembly/BIRD/1MF8.pdb data/bio_assembly/BIRD/1MF8.pdb D
|
||||
data/bio_assembly/BIRD/3WDC.pdb data/bio_assembly/BIRD/3WDC.pdb B
|
||||
data/bio_assembly/BIRD/3WDD.pdb data/bio_assembly/BIRD/3WDD.pdb B
|
||||
data/bio_assembly/BIRD/3WDE.pdb data/bio_assembly/BIRD/3WDE.pdb B
|
||||
data/bio_assembly/BIRD/3WMG.pdb data/bio_assembly/BIRD/3WMG.pdb B
|
||||
data/bio_assembly/BIRD/3WNE.pdb data/bio_assembly/BIRD/3WNE.pdb C
|
||||
data/bio_assembly/BIRD/3WNF.pdb data/bio_assembly/BIRD/3WNF.pdb C
|
||||
data/bio_assembly/BIRD/3WNG.pdb data/bio_assembly/BIRD/3WNG.pdb C
|
||||
data/bio_assembly/BIRD/2Z6W.pdb data/bio_assembly/BIRD/2Z6W.pdb M
|
||||
data/bio_assembly/BIRD/4MNW.pdb data/bio_assembly/BIRD/4MNW.pdb B
|
||||
data/bio_assembly/BIRD/4MNX.pdb data/bio_assembly/BIRD/4MNX.pdb B
|
||||
data/bio_assembly/BIRD/4MNY.pdb data/bio_assembly/BIRD/4MNY.pdb C
|
||||
data/bio_assembly/BIRD/4OS1.pdb data/bio_assembly/BIRD/4OS1.pdb B
|
||||
data/bio_assembly/BIRD/4OS2.pdb data/bio_assembly/BIRD/4OS2.pdb B
|
||||
data/bio_assembly/BIRD/4OS4.pdb data/bio_assembly/BIRD/4OS4.pdb B
|
||||
data/bio_assembly/BIRD/4OS5.pdb data/bio_assembly/BIRD/4OS5.pdb B
|
||||
data/bio_assembly/BIRD/4OS6.pdb data/bio_assembly/BIRD/4OS6.pdb B
|
||||
data/bio_assembly/BIRD/4OS7.pdb data/bio_assembly/BIRD/4OS7.pdb B
|
||||
data/bio_assembly/BIRD/4IPZ.pdb data/bio_assembly/BIRD/4IPZ.pdb B
|
||||
data/bio_assembly/BIRD/4JJM.pdb data/bio_assembly/BIRD/4JJM.pdb F
|
||||
data/bio_assembly/BIRD/4JK5.pdb data/bio_assembly/BIRD/4JK5.pdb B
|
||||
data/bio_assembly/BIRD/4JK6.pdb data/bio_assembly/BIRD/4JK6.pdb B
|
||||
data/bio_assembly/BIRD/4DGC.pdb data/bio_assembly/BIRD/4DGC.pdb F
|
||||
data/bio_assembly/BIRD/4GLY.pdb data/bio_assembly/BIRD/4GLY.pdb B
|
||||
data/bio_assembly/BIRD/4YV9.pdb data/bio_assembly/BIRD/4YV9.pdb E
|
||||
data/bio_assembly/BIRD/4ZJX.pdb data/bio_assembly/BIRD/4ZJX.pdb B
|
||||
data/bio_assembly/BIRD/4ZQW.pdb data/bio_assembly/BIRD/4ZQW.pdb A
|
||||
data/bio_assembly/BIRD/3BO7.pdb data/bio_assembly/BIRD/3BO7.pdb E
|
||||
data/bio_assembly/BIRD/3EOV.pdb data/bio_assembly/BIRD/3EOV.pdb C
|
||||
data/bio_assembly/BIRD/4GUX.pdb data/bio_assembly/BIRD/4GUX.pdb D
|
||||
data/bio_assembly/BIRD/4GVU.pdb data/bio_assembly/BIRD/4GVU.pdb B
|
||||
data/bio_assembly/BIRD/4HGC.pdb data/bio_assembly/BIRD/4HGC.pdb I
|
||||
data/bio_assembly/BIRD/4HY7.pdb data/bio_assembly/BIRD/4HY7.pdb B
|
||||
data/bio_assembly/BIRD/2WFJ.pdb data/bio_assembly/BIRD/2WFJ.pdb B
|
||||
data/bio_assembly/BIRD/2X7K.pdb data/bio_assembly/BIRD/2X7K.pdb B
|
||||
data/bio_assembly/BIRD/4KEL.pdb data/bio_assembly/BIRD/4KEL.pdb B
|
||||
data/bio_assembly/BIRD/4L3O.pdb data/bio_assembly/BIRD/4L3O.pdb E
|
||||
data/bio_assembly/BIRD/4KTU.pdb data/bio_assembly/BIRD/4KTU.pdb B
|
||||
data/bio_assembly/BIRD/4KTS.pdb data/bio_assembly/BIRD/4KTS.pdb B
|
||||
data/bio_assembly/BIRD/4KTC.pdb data/bio_assembly/BIRD/4KTC.pdb B
|
||||
data/bio_assembly/BIRD/3AVA.pdb data/bio_assembly/BIRD/3AVA.pdb X
|
||||
data/bio_assembly/BIRD/3AVB.pdb data/bio_assembly/BIRD/3AVB.pdb X
|
||||
data/bio_assembly/BIRD/3AV9.pdb data/bio_assembly/BIRD/3AV9.pdb X
|
||||
data/bio_assembly/BIRD/3AVI.pdb data/bio_assembly/BIRD/3AVI.pdb D
|
||||
data/bio_assembly/BIRD/3AVJ.pdb data/bio_assembly/BIRD/3AVJ.pdb D
|
||||
data/bio_assembly/BIRD/3AVK.pdb data/bio_assembly/BIRD/3AVK.pdb D
|
||||
data/bio_assembly/BIRD/3AVL.pdb data/bio_assembly/BIRD/3AVL.pdb E
|
||||
data/bio_assembly/BIRD/3AVM.pdb data/bio_assembly/BIRD/3AVM.pdb D
|
||||
data/bio_assembly/BIRD/3AVN.pdb data/bio_assembly/BIRD/3AVN.pdb G
|
||||
data/bio_assembly/BIRD/5XN3.pdb data/bio_assembly/BIRD/5XN3.pdb B
|
||||
data/bio_assembly/BIRD/6CN8.pdb data/bio_assembly/BIRD/6CN8.pdb B
|
||||
data/bio_assembly/BIRD/6DN8.pdb data/bio_assembly/BIRD/6DN8.pdb B
|
||||
data/bio_assembly/BIRD/6DN5.pdb data/bio_assembly/BIRD/6DN5.pdb B
|
||||
data/bio_assembly/BIRD/6DN7.pdb data/bio_assembly/BIRD/6DN7.pdb D
|
||||
data/bio_assembly/BIRD/6DN6.pdb data/bio_assembly/BIRD/6DN6.pdb B
|
||||
data/bio_assembly/BIRD/5VI6.pdb data/bio_assembly/BIRD/5VI6.pdb B
|
||||
data/bio_assembly/BIRD/4WVT.pdb data/bio_assembly/BIRD/4WVT.pdb C
|
||||
data/bio_assembly/BIRD/4WVU.pdb data/bio_assembly/BIRD/4WVU.pdb B
|
||||
data/bio_assembly/BIRD/2POY.pdb data/bio_assembly/BIRD/2POY.pdb T
|
||||
data/bio_assembly/BIRD/2OJU.pdb data/bio_assembly/BIRD/2OJU.pdb D
|
||||
data/bio_assembly/BIRD/1BCK.pdb data/bio_assembly/BIRD/1BCK.pdb C
|
||||
data/bio_assembly/BIRD/1CWC.pdb data/bio_assembly/BIRD/1CWC.pdb C
|
||||
data/bio_assembly/BIRD/1CWB.pdb data/bio_assembly/BIRD/1CWB.pdb C
|
||||
data/bio_assembly/BIRD/1CWA.pdb data/bio_assembly/BIRD/1CWA.pdb C
|
||||
data/bio_assembly/BIRD/1CYN.pdb data/bio_assembly/BIRD/1CYN.pdb C
|
||||
data/bio_assembly/BIRD/1IKF.pdb data/bio_assembly/BIRD/1IKF.pdb C
|
||||
data/bio_assembly/BIRD/6J67.pdb data/bio_assembly/BIRD/6J67.pdb C
|
||||
data/bio_assembly/BIRD/3PMP.pdb data/bio_assembly/BIRD/3PMP.pdb C
|
||||
data/bio_assembly/BIRD/1MIK.pdb data/bio_assembly/BIRD/1MIK.pdb B
|
||||
data/bio_assembly/BIRD/1QNH.pdb data/bio_assembly/BIRD/1QNH.pdb C
|
||||
data/bio_assembly/BIRD/1QNG.pdb data/bio_assembly/BIRD/1QNG.pdb D
|
||||
data/bio_assembly/BIRD/1TK2.pdb data/bio_assembly/BIRD/1TK2.pdb B
|
||||
data/bio_assembly/BIRD/1TMB.pdb data/bio_assembly/BIRD/1TMB.pdb T
|
||||
data/bio_assembly/BIRD/1W9U.pdb data/bio_assembly/BIRD/1W9U.pdb C
|
||||
data/bio_assembly/BIRD/1WAW.pdb data/bio_assembly/BIRD/1WAW.pdb B
|
||||
data/bio_assembly/BIRD/1XQ7.pdb data/bio_assembly/BIRD/1XQ7.pdb D
|
||||
data/bio_assembly/BIRD/2BCD.pdb data/bio_assembly/BIRD/2BCD.pdb B
|
||||
data/bio_assembly/BIRD/3SM1.pdb data/bio_assembly/BIRD/3SM1.pdb J
|
||||
data/bio_assembly/BIRD/6DNO.pdb data/bio_assembly/BIRD/6DNO.pdb C
|
||||
data/bio_assembly/BIRD/6DTN.pdb data/bio_assembly/BIRD/6DTN.pdb A
|
||||
data/bio_assembly/BIRD/6M9D.pdb data/bio_assembly/BIRD/6M9D.pdb B
|
||||
data/bio_assembly/BIRD/6APR.pdb data/bio_assembly/BIRD/6APR.pdb I
|
||||
data/bio_assembly/BIRD/6V2D.pdb data/bio_assembly/BIRD/6V2D.pdb B
|
||||
data/bio_assembly/BIRD/6V2S.pdb data/bio_assembly/BIRD/6V2S.pdb C
|
||||
data/bio_assembly/BIRD/6V2R.pdb data/bio_assembly/BIRD/6V2R.pdb B
|
||||
data/bio_assembly/BIRD/5U66.pdb data/bio_assembly/BIRD/5U66.pdb B
|
||||
data/bio_assembly/BIRD/1M21.pdb data/bio_assembly/BIRD/1M21.pdb C
|
||||
data/bio_assembly/BIRD/1LS5.pdb data/bio_assembly/BIRD/1LS5.pdb C
|
||||
data/bio_assembly/BIRD/1M43.pdb data/bio_assembly/BIRD/1M43.pdb C
|
||||
data/bio_assembly/BIRD/2CF9.pdb data/bio_assembly/BIRD/2CF9.pdb I
|
||||
data/bio_assembly/BIRD/2CF8.pdb data/bio_assembly/BIRD/2CF8.pdb I
|
||||
data/bio_assembly/BIRD/2CN0.pdb data/bio_assembly/BIRD/2CN0.pdb I
|
||||
data/bio_assembly/BIRD/2F9N.pdb data/bio_assembly/BIRD/2F9N.pdb E
|
||||
data/bio_assembly/BIRD/2F9P.pdb data/bio_assembly/BIRD/2F9P.pdb E
|
||||
data/bio_assembly/BIRD/2FES.pdb data/bio_assembly/BIRD/2FES.pdb D
|
||||
data/bio_assembly/BIRD/2FEQ.pdb data/bio_assembly/BIRD/2FEQ.pdb D
|
||||
data/bio_assembly/BIRD/1APU.pdb data/bio_assembly/BIRD/1APU.pdb I
|
||||
data/bio_assembly/BIRD/1AQ7.pdb data/bio_assembly/BIRD/1AQ7.pdb B
|
||||
data/bio_assembly/BIRD/1O0D.pdb data/bio_assembly/BIRD/1O0D.pdb D
|
||||
data/bio_assembly/BIRD/2AGI.pdb data/bio_assembly/BIRD/2AGI.pdb A
|
||||
data/bio_assembly/BIRD/2ANK.pdb data/bio_assembly/BIRD/2ANK.pdb P
|
||||
data/bio_assembly/BIRD/1WB0.pdb data/bio_assembly/BIRD/1WB0.pdb B
|
||||
data/bio_assembly/BIRD/1W9V.pdb data/bio_assembly/BIRD/1W9V.pdb C
|
||||
data/bio_assembly/BIRD/1W6I.pdb data/bio_assembly/BIRD/1W6I.pdb B
|
||||
data/bio_assembly/BIRD/1QS8.pdb data/bio_assembly/BIRD/1QS8.pdb C
|
||||
data/bio_assembly/BIRD/1PSO.pdb data/bio_assembly/BIRD/1PSO.pdb I
|
||||
data/bio_assembly/BIRD/1POP.pdb data/bio_assembly/BIRD/1POP.pdb B
|
||||
data/bio_assembly/BIRD/1OYT.pdb data/bio_assembly/BIRD/1OYT.pdb I
|
||||
data/bio_assembly/BIRD/1NZQ.pdb data/bio_assembly/BIRD/1NZQ.pdb D
|
||||
data/bio_assembly/BIRD/1WVM.pdb data/bio_assembly/BIRD/1WVM.pdb C
|
||||
data/bio_assembly/BIRD/1XDH.pdb data/bio_assembly/BIRD/1XDH.pdb C
|
||||
data/bio_assembly/BIRD/1WKR.pdb data/bio_assembly/BIRD/1WKR.pdb I
|
||||
data/bio_assembly/BIRD/1BCS.pdb data/bio_assembly/BIRD/1BCS.pdb C
|
||||
data/bio_assembly/BIRD/1BCR.pdb data/bio_assembly/BIRD/1BCR.pdb C
|
||||
data/bio_assembly/BIRD/6OBR.pdb data/bio_assembly/BIRD/6OBR.pdb D
|
||||
data/bio_assembly/BIRD/6OBQ.pdb data/bio_assembly/BIRD/6OBQ.pdb C
|
||||
data/bio_assembly/BIRD/6OBU.pdb data/bio_assembly/BIRD/6OBU.pdb C
|
||||
data/bio_assembly/BIRD/1H0I.pdb data/bio_assembly/BIRD/1H0I.pdb C
|
||||
data/bio_assembly/BIRD/6XA4.pdb data/bio_assembly/BIRD/6XA4.pdb B
|
||||
data/bio_assembly/BIRD/6YZ6.pdb data/bio_assembly/BIRD/6YZ6.pdb C
|
||||
data/bio_assembly/BIRD/1FJM.pdb data/bio_assembly/BIRD/1FJM.pdb M
|
||||
data/bio_assembly/BIRD/6BKJ.pdb data/bio_assembly/BIRD/6BKJ.pdb F
|
||||
data/bio_assembly/BIRD/5WGQ.pdb data/bio_assembly/BIRD/5WGQ.pdb E
|
||||
data/bio_assembly/BIRD/4IMQ.pdb data/bio_assembly/BIRD/4IMQ.pdb B
|
||||
data/bio_assembly/BIRD/4INH.pdb data/bio_assembly/BIRD/4INH.pdb M
|
||||
data/bio_assembly/BIRD/4IMZ.pdb data/bio_assembly/BIRD/4IMZ.pdb B
|
||||
data/bio_assembly/BIRD/1TL9.pdb data/bio_assembly/BIRD/1TL9.pdb B
|
||||
data/bio_assembly/BIRD/1SGC.pdb data/bio_assembly/BIRD/1SGC.pdb B
|
||||
data/bio_assembly/BIRD/1IZE.pdb data/bio_assembly/BIRD/1IZE.pdb B
|
||||
data/bio_assembly/BIRD/1JRT.pdb data/bio_assembly/BIRD/1JRT.pdb B
|
||||
data/bio_assembly/BIRD/1JRS.pdb data/bio_assembly/BIRD/1JRS.pdb B
|
||||
data/bio_assembly/BIRD/4Y9W.pdb data/bio_assembly/BIRD/4Y9W.pdb B
|
||||
data/bio_assembly/BIRD/4NMT.pdb data/bio_assembly/BIRD/4NMT.pdb C
|
||||
data/bio_assembly/BIRD/4NMS.pdb data/bio_assembly/BIRD/4NMS.pdb C
|
||||
data/bio_assembly/BIRD/4NMR.pdb data/bio_assembly/BIRD/4NMR.pdb C
|
||||
data/bio_assembly/BIRD/4NMQ.pdb data/bio_assembly/BIRD/4NMQ.pdb C
|
||||
data/bio_assembly/BIRD/4NMP.pdb data/bio_assembly/BIRD/4NMP.pdb C
|
||||
data/bio_assembly/BIRD/4NMO.pdb data/bio_assembly/BIRD/4NMO.pdb C
|
||||
data/bio_assembly/BIRD/4MZJ.pdb data/bio_assembly/BIRD/4MZJ.pdb T
|
||||
data/bio_assembly/BIRD/3P72.pdb data/bio_assembly/BIRD/3P72.pdb B
|
||||
data/bio_assembly/BIRD/3OE0.pdb data/bio_assembly/BIRD/3OE0.pdb I
|
||||
data/bio_assembly/BIRD/4I7D.pdb data/bio_assembly/BIRD/4I7D.pdb B
|
||||
data/bio_assembly/BIRD/4I7C.pdb data/bio_assembly/BIRD/4I7C.pdb B
|
||||
data/bio_assembly/BIRD/4I7B.pdb data/bio_assembly/BIRD/4I7B.pdb B
|
||||
data/bio_assembly/BIRD/4I5N.pdb data/bio_assembly/BIRD/4I5N.pdb G
|
||||
data/bio_assembly/BIRD/4I5L.pdb data/bio_assembly/BIRD/4I5L.pdb G
|
||||
data/bio_assembly/BIRD/2P0R.pdb data/bio_assembly/BIRD/2P0R.pdb D
|
||||
data/bio_assembly/BIRD/2NYL.pdb data/bio_assembly/BIRD/2NYL.pdb G
|
||||
data/bio_assembly/BIRD/2NYM.pdb data/bio_assembly/BIRD/2NYM.pdb G
|
||||
data/bio_assembly/BIRD/2NQA.pdb data/bio_assembly/BIRD/2NQA.pdb D
|
||||
data/bio_assembly/BIRD/2NPP.pdb data/bio_assembly/BIRD/2NPP.pdb Y
|
||||
data/bio_assembly/BIRD/2QZX.pdb data/bio_assembly/BIRD/2QZX.pdb C
|
||||
data/bio_assembly/BIRD/2RMP.pdb data/bio_assembly/BIRD/2RMP.pdb B
|
||||
data/bio_assembly/BIRD/2PSX.pdb data/bio_assembly/BIRD/2PSX.pdb B
|
||||
data/bio_assembly/BIRD/2PSY.pdb data/bio_assembly/BIRD/2PSY.pdb B
|
||||
data/bio_assembly/BIRD/4ER2.pdb data/bio_assembly/BIRD/4ER2.pdb I
|
||||
data/bio_assembly/BIRD/4NMV.pdb data/bio_assembly/BIRD/4NMV.pdb C
|
||||
data/bio_assembly/BIRD/4EJK.pdb data/bio_assembly/BIRD/4EJK.pdb N
|
||||
data/bio_assembly/BIRD/4EJD.pdb data/bio_assembly/BIRD/4EJD.pdb C
|
||||
data/bio_assembly/BIRD/4EXH.pdb data/bio_assembly/BIRD/4EXH.pdb J
|
||||
data/bio_assembly/BIRD/4G5G.pdb data/bio_assembly/BIRD/4G5G.pdb I
|
||||
data/bio_assembly/BIRD/4BP9.pdb data/bio_assembly/BIRD/4BP9.pdb G
|
||||
data/bio_assembly/BIRD/3V4L.pdb data/bio_assembly/BIRD/3V4L.pdb B
|
||||
data/bio_assembly/BIRD/3V4O.pdb data/bio_assembly/BIRD/3V4O.pdb B
|
||||
data/bio_assembly/BIRD/3UOA.pdb data/bio_assembly/BIRD/3UOA.pdb L
|
||||
data/bio_assembly/BIRD/3UO8.pdb data/bio_assembly/BIRD/3UO8.pdb L
|
||||
data/bio_assembly/BIRD/3BPM.pdb data/bio_assembly/BIRD/3BPM.pdb D
|
||||
data/bio_assembly/BIRD/5LW1.pdb data/bio_assembly/BIRD/5LW1.pdb C
|
||||
data/bio_assembly/BIRD/5MS4.pdb data/bio_assembly/BIRD/5MS4.pdb E
|
||||
data/bio_assembly/BIRD/5K99.pdb data/bio_assembly/BIRD/5K99.pdb C
|
||||
data/bio_assembly/BIRD/5JPF.pdb data/bio_assembly/BIRD/5JPF.pdb M
|
||||
data/bio_assembly/BIRD/5N7Q.pdb data/bio_assembly/BIRD/5N7Q.pdb I
|
||||
data/bio_assembly/BIRD/5I70.pdb data/bio_assembly/BIRD/5I70.pdb D
|
||||
data/bio_assembly/BIRD/5HVP.pdb data/bio_assembly/BIRD/5HVP.pdb C
|
||||
data/bio_assembly/BIRD/5FC3.pdb data/bio_assembly/BIRD/5FC3.pdb A
|
||||
data/bio_assembly/BIRD/5FC2.pdb data/bio_assembly/BIRD/5FC2.pdb A
|
||||
data/bio_assembly/BIRD/5EPK.pdb data/bio_assembly/BIRD/5EPK.pdb B
|
||||
data/bio_assembly/BIRD/5EPJ.pdb data/bio_assembly/BIRD/5EPJ.pdb B
|
||||
data/bio_assembly/BIRD/5EQ0.pdb data/bio_assembly/BIRD/5EQ0.pdb B
|
||||
data/bio_assembly/BIRD/2XE4.pdb data/bio_assembly/BIRD/2XE4.pdb B
|
||||
data/bio_assembly/BIRD/2Z2P.pdb data/bio_assembly/BIRD/2Z2P.pdb C
|
||||
data/bio_assembly/BIRD/3E7A.pdb data/bio_assembly/BIRD/3E7A.pdb C
|
||||
data/bio_assembly/BIRD/3DW8.pdb data/bio_assembly/BIRD/3DW8.pdb G
|
||||
data/bio_assembly/BIRD/3EGH.pdb data/bio_assembly/BIRD/3EGH.pdb E
|
||||
data/bio_assembly/BIRD/3EMY.pdb data/bio_assembly/BIRD/3EMY.pdb B
|
||||
data/bio_assembly/BIRD/3MGB.pdb data/bio_assembly/BIRD/3MGB.pdb C
|
||||
data/bio_assembly/BIRD/3MG9.pdb data/bio_assembly/BIRD/3MG9.pdb B
|
||||
data/bio_assembly/BIRD/3FGA.pdb data/bio_assembly/BIRD/3FGA.pdb E
|
||||
data/bio_assembly/BIRD/3FNT.pdb data/bio_assembly/BIRD/3FNT.pdb I
|
||||
data/bio_assembly/BIRD/3FV3.pdb data/bio_assembly/BIRD/3FV3.pdb J
|
||||
data/bio_assembly/BIRD/2V3H.pdb data/bio_assembly/BIRD/2V3H.pdb I
|
||||
data/bio_assembly/BIRD/2V3O.pdb data/bio_assembly/BIRD/2V3O.pdb I
|
||||
data/bio_assembly/BIRD/4YV8.pdb data/bio_assembly/BIRD/4YV8.pdb B
|
||||
data/bio_assembly/BIRD/3Q4K.pdb data/bio_assembly/BIRD/3Q4K.pdb C
|
||||
data/bio_assembly/BIRD/3Q4L.pdb data/bio_assembly/BIRD/3Q4L.pdb C
|
||||
data/bio_assembly/BIRD/4TVG.pdb data/bio_assembly/BIRD/4TVG.pdb C
|
||||
data/bio_assembly/BIRD/5D13.pdb data/bio_assembly/BIRD/5D13.pdb E
|
||||
data/bio_assembly/BIRD/1A2C.pdb data/bio_assembly/BIRD/1A2C.pdb I
|
||||
data/bio_assembly/BIRD/2IAE.pdb data/bio_assembly/BIRD/2IAE.pdb M
|
||||
data/bio_assembly/BIRD/2IE3.pdb data/bio_assembly/BIRD/2IE3.pdb I
|
||||
data/bio_assembly/BIRD/2H6T.pdb data/bio_assembly/BIRD/2H6T.pdb B
|
||||
data/bio_assembly/BIRD/2FO5.pdb data/bio_assembly/BIRD/2FO5.pdb E
|
||||
253
data/bird_test.txt
Normal file
253
data/bird_test.txt
Normal file
@@ -0,0 +1,253 @@
|
||||
data/bio_assembly/BIRD/2R9B.pdb data/bio_assembly/BIRD/2R9B.pdb C
|
||||
data/bio_assembly/BIRD/3URI.pdb data/bio_assembly/BIRD/3URI.pdb B
|
||||
data/bio_assembly/BIRD/3URL.pdb data/bio_assembly/BIRD/3URL.pdb B
|
||||
data/bio_assembly/BIRD/3V3B.pdb data/bio_assembly/BIRD/3V3B.pdb D
|
||||
data/bio_assembly/BIRD/3UQP.pdb data/bio_assembly/BIRD/3UQP.pdb B
|
||||
data/bio_assembly/BIRD/3UQR.pdb data/bio_assembly/BIRD/3UQR.pdb D
|
||||
data/bio_assembly/BIRD/5JXH.pdb data/bio_assembly/BIRD/5JXH.pdb H
|
||||
data/bio_assembly/BIRD/5JXJ.pdb data/bio_assembly/BIRD/5JXJ.pdb H
|
||||
data/bio_assembly/BIRD/4RCP.pdb data/bio_assembly/BIRD/4RCP.pdb B
|
||||
data/bio_assembly/BIRD/4TPG.pdb data/bio_assembly/BIRD/4TPG.pdb E
|
||||
data/bio_assembly/BIRD/4RYD.pdb data/bio_assembly/BIRD/4RYD.pdb H
|
||||
data/bio_assembly/BIRD/4O6W.pdb data/bio_assembly/BIRD/4O6W.pdb C
|
||||
data/bio_assembly/BIRD/4K1E.pdb data/bio_assembly/BIRD/4K1E.pdb B
|
||||
data/bio_assembly/BIRD/4DV9.pdb data/bio_assembly/BIRD/4DV9.pdb B
|
||||
data/bio_assembly/BIRD/4DVF.pdb data/bio_assembly/BIRD/4DVF.pdb C
|
||||
data/bio_assembly/BIRD/4EZP.pdb data/bio_assembly/BIRD/4EZP.pdb D
|
||||
data/bio_assembly/BIRD/4FBX.pdb data/bio_assembly/BIRD/4FBX.pdb B
|
||||
data/bio_assembly/BIRD/4G35.pdb data/bio_assembly/BIRD/4G35.pdb B
|
||||
data/bio_assembly/BIRD/5DNJ.pdb data/bio_assembly/BIRD/5DNJ.pdb B
|
||||
data/bio_assembly/BIRD/4WHH.pdb data/bio_assembly/BIRD/4WHH.pdb B
|
||||
data/bio_assembly/BIRD/4WHK.pdb data/bio_assembly/BIRD/4WHK.pdb B
|
||||
data/bio_assembly/BIRD/4WHL.pdb data/bio_assembly/BIRD/4WHL.pdb B
|
||||
data/bio_assembly/BIRD/1SFI.pdb data/bio_assembly/BIRD/1SFI.pdb I
|
||||
data/bio_assembly/BIRD/3RQ7.pdb data/bio_assembly/BIRD/3RQ7.pdb B
|
||||
data/bio_assembly/BIRD/3SNA.pdb data/bio_assembly/BIRD/3SNA.pdb H
|
||||
data/bio_assembly/BIRD/3SNB.pdb data/bio_assembly/BIRD/3SNB.pdb H
|
||||
data/bio_assembly/BIRD/3SNC.pdb data/bio_assembly/BIRD/3SNC.pdb H
|
||||
data/bio_assembly/BIRD/3SND.pdb data/bio_assembly/BIRD/3SND.pdb C
|
||||
data/bio_assembly/BIRD/3SNE.pdb data/bio_assembly/BIRD/3SNE.pdb H
|
||||
data/bio_assembly/BIRD/3S70.pdb data/bio_assembly/BIRD/3S70.pdb B
|
||||
data/bio_assembly/BIRD/1OKX.pdb data/bio_assembly/BIRD/1OKX.pdb C
|
||||
data/bio_assembly/BIRD/6VXY.pdb data/bio_assembly/BIRD/6VXY.pdb C
|
||||
data/bio_assembly/BIRD/3VFK.pdb data/bio_assembly/BIRD/3VFK.pdb G
|
||||
data/bio_assembly/BIRD/3VFJ.pdb data/bio_assembly/BIRD/3VFJ.pdb G
|
||||
data/bio_assembly/BIRD/2XAD.pdb data/bio_assembly/BIRD/2XAD.pdb E
|
||||
data/bio_assembly/BIRD/4MFL.pdb data/bio_assembly/BIRD/4MFL.pdb B
|
||||
data/bio_assembly/BIRD/4MFP.pdb data/bio_assembly/BIRD/4MFP.pdb B
|
||||
data/bio_assembly/BIRD/4MFQ.pdb data/bio_assembly/BIRD/4MFQ.pdb B
|
||||
data/bio_assembly/BIRD/4PJZ.pdb data/bio_assembly/BIRD/4PJZ.pdb B
|
||||
data/bio_assembly/BIRD/4PK0.pdb data/bio_assembly/BIRD/4PK0.pdb B
|
||||
data/bio_assembly/BIRD/4EEC.pdb data/bio_assembly/BIRD/4EEC.pdb C
|
||||
data/bio_assembly/BIRD/4JNA.pdb data/bio_assembly/BIRD/4JNA.pdb I
|
||||
data/bio_assembly/BIRD/4NEC.pdb data/bio_assembly/BIRD/4NEC.pdb E
|
||||
data/bio_assembly/BIRD/3AH8.pdb data/bio_assembly/BIRD/3AH8.pdb Y
|
||||
data/bio_assembly/BIRD/3RQD.pdb data/bio_assembly/BIRD/3RQD.pdb C
|
||||
data/bio_assembly/BIRD/2CV3.pdb data/bio_assembly/BIRD/2CV3.pdb B
|
||||
data/bio_assembly/BIRD/2RMC.pdb data/bio_assembly/BIRD/2RMC.pdb B
|
||||
data/bio_assembly/BIRD/4TOT.pdb data/bio_assembly/BIRD/4TOT.pdb E
|
||||
data/bio_assembly/BIRD/6O21.pdb data/bio_assembly/BIRD/6O21.pdb B
|
||||
data/bio_assembly/BIRD/6C1Q.pdb data/bio_assembly/BIRD/6C1Q.pdb L
|
||||
data/bio_assembly/BIRD/6C1R.pdb data/bio_assembly/BIRD/6C1R.pdb L
|
||||
data/bio_assembly/BIRD/1MF8.pdb data/bio_assembly/BIRD/1MF8.pdb D
|
||||
data/bio_assembly/BIRD/3WDC.pdb data/bio_assembly/BIRD/3WDC.pdb B
|
||||
data/bio_assembly/BIRD/3WDD.pdb data/bio_assembly/BIRD/3WDD.pdb B
|
||||
data/bio_assembly/BIRD/3WDE.pdb data/bio_assembly/BIRD/3WDE.pdb B
|
||||
data/bio_assembly/BIRD/3WMG.pdb data/bio_assembly/BIRD/3WMG.pdb B
|
||||
data/bio_assembly/BIRD/3WNE.pdb data/bio_assembly/BIRD/3WNE.pdb C
|
||||
data/bio_assembly/BIRD/3WNF.pdb data/bio_assembly/BIRD/3WNF.pdb C
|
||||
data/bio_assembly/BIRD/3WNG.pdb data/bio_assembly/BIRD/3WNG.pdb C
|
||||
data/bio_assembly/BIRD/2Z6W.pdb data/bio_assembly/BIRD/2Z6W.pdb M
|
||||
data/bio_assembly/BIRD/4MNW.pdb data/bio_assembly/BIRD/4MNW.pdb B
|
||||
data/bio_assembly/BIRD/4MNX.pdb data/bio_assembly/BIRD/4MNX.pdb B
|
||||
data/bio_assembly/BIRD/4MNY.pdb data/bio_assembly/BIRD/4MNY.pdb C
|
||||
data/bio_assembly/BIRD/4OS1.pdb data/bio_assembly/BIRD/4OS1.pdb B
|
||||
data/bio_assembly/BIRD/4OS2.pdb data/bio_assembly/BIRD/4OS2.pdb B
|
||||
data/bio_assembly/BIRD/4OS4.pdb data/bio_assembly/BIRD/4OS4.pdb B
|
||||
data/bio_assembly/BIRD/4OS5.pdb data/bio_assembly/BIRD/4OS5.pdb B
|
||||
data/bio_assembly/BIRD/4OS6.pdb data/bio_assembly/BIRD/4OS6.pdb B
|
||||
data/bio_assembly/BIRD/4OS7.pdb data/bio_assembly/BIRD/4OS7.pdb B
|
||||
data/bio_assembly/BIRD/4IPZ.pdb data/bio_assembly/BIRD/4IPZ.pdb B
|
||||
data/bio_assembly/BIRD/4JJM.pdb data/bio_assembly/BIRD/4JJM.pdb F
|
||||
data/bio_assembly/BIRD/4JK5.pdb data/bio_assembly/BIRD/4JK5.pdb B
|
||||
data/bio_assembly/BIRD/4JK6.pdb data/bio_assembly/BIRD/4JK6.pdb B
|
||||
data/bio_assembly/BIRD/4DGC.pdb data/bio_assembly/BIRD/4DGC.pdb F
|
||||
data/bio_assembly/BIRD/4GLY.pdb data/bio_assembly/BIRD/4GLY.pdb B
|
||||
data/bio_assembly/BIRD/4YV9.pdb data/bio_assembly/BIRD/4YV9.pdb E
|
||||
data/bio_assembly/BIRD/4ZJX.pdb data/bio_assembly/BIRD/4ZJX.pdb B
|
||||
data/bio_assembly/BIRD/4ZQW.pdb data/bio_assembly/BIRD/4ZQW.pdb A
|
||||
data/bio_assembly/BIRD/3BO7.pdb data/bio_assembly/BIRD/3BO7.pdb E
|
||||
data/bio_assembly/BIRD/3EOV.pdb data/bio_assembly/BIRD/3EOV.pdb C
|
||||
data/bio_assembly/BIRD/4GUX.pdb data/bio_assembly/BIRD/4GUX.pdb D
|
||||
data/bio_assembly/BIRD/4GVU.pdb data/bio_assembly/BIRD/4GVU.pdb B
|
||||
data/bio_assembly/BIRD/4HGC.pdb data/bio_assembly/BIRD/4HGC.pdb I
|
||||
data/bio_assembly/BIRD/4HY7.pdb data/bio_assembly/BIRD/4HY7.pdb B
|
||||
data/bio_assembly/BIRD/2WFJ.pdb data/bio_assembly/BIRD/2WFJ.pdb B
|
||||
data/bio_assembly/BIRD/2X7K.pdb data/bio_assembly/BIRD/2X7K.pdb B
|
||||
data/bio_assembly/BIRD/4KEL.pdb data/bio_assembly/BIRD/4KEL.pdb B
|
||||
data/bio_assembly/BIRD/4L3O.pdb data/bio_assembly/BIRD/4L3O.pdb E
|
||||
data/bio_assembly/BIRD/4KTU.pdb data/bio_assembly/BIRD/4KTU.pdb B
|
||||
data/bio_assembly/BIRD/4KTS.pdb data/bio_assembly/BIRD/4KTS.pdb B
|
||||
data/bio_assembly/BIRD/4KTC.pdb data/bio_assembly/BIRD/4KTC.pdb B
|
||||
data/bio_assembly/BIRD/3AVA.pdb data/bio_assembly/BIRD/3AVA.pdb X
|
||||
data/bio_assembly/BIRD/3AVB.pdb data/bio_assembly/BIRD/3AVB.pdb X
|
||||
data/bio_assembly/BIRD/3AV9.pdb data/bio_assembly/BIRD/3AV9.pdb X
|
||||
data/bio_assembly/BIRD/3AVI.pdb data/bio_assembly/BIRD/3AVI.pdb D
|
||||
data/bio_assembly/BIRD/3AVJ.pdb data/bio_assembly/BIRD/3AVJ.pdb D
|
||||
data/bio_assembly/BIRD/3AVK.pdb data/bio_assembly/BIRD/3AVK.pdb D
|
||||
data/bio_assembly/BIRD/3AVL.pdb data/bio_assembly/BIRD/3AVL.pdb E
|
||||
data/bio_assembly/BIRD/3AVM.pdb data/bio_assembly/BIRD/3AVM.pdb D
|
||||
data/bio_assembly/BIRD/3AVN.pdb data/bio_assembly/BIRD/3AVN.pdb G
|
||||
data/bio_assembly/BIRD/5XN3.pdb data/bio_assembly/BIRD/5XN3.pdb B
|
||||
data/bio_assembly/BIRD/6CN8.pdb data/bio_assembly/BIRD/6CN8.pdb B
|
||||
data/bio_assembly/BIRD/6DN8.pdb data/bio_assembly/BIRD/6DN8.pdb B
|
||||
data/bio_assembly/BIRD/6DN5.pdb data/bio_assembly/BIRD/6DN5.pdb B
|
||||
data/bio_assembly/BIRD/6DN7.pdb data/bio_assembly/BIRD/6DN7.pdb D
|
||||
data/bio_assembly/BIRD/6DN6.pdb data/bio_assembly/BIRD/6DN6.pdb B
|
||||
data/bio_assembly/BIRD/5VI6.pdb data/bio_assembly/BIRD/5VI6.pdb B
|
||||
data/bio_assembly/BIRD/4WVT.pdb data/bio_assembly/BIRD/4WVT.pdb C
|
||||
data/bio_assembly/BIRD/4WVU.pdb data/bio_assembly/BIRD/4WVU.pdb B
|
||||
data/bio_assembly/BIRD/2POY.pdb data/bio_assembly/BIRD/2POY.pdb T
|
||||
data/bio_assembly/BIRD/2OJU.pdb data/bio_assembly/BIRD/2OJU.pdb D
|
||||
data/bio_assembly/BIRD/1BCK.pdb data/bio_assembly/BIRD/1BCK.pdb C
|
||||
data/bio_assembly/BIRD/1CWC.pdb data/bio_assembly/BIRD/1CWC.pdb C
|
||||
data/bio_assembly/BIRD/1CWB.pdb data/bio_assembly/BIRD/1CWB.pdb C
|
||||
data/bio_assembly/BIRD/1CWA.pdb data/bio_assembly/BIRD/1CWA.pdb C
|
||||
data/bio_assembly/BIRD/1CYN.pdb data/bio_assembly/BIRD/1CYN.pdb C
|
||||
data/bio_assembly/BIRD/1IKF.pdb data/bio_assembly/BIRD/1IKF.pdb C
|
||||
data/bio_assembly/BIRD/6J67.pdb data/bio_assembly/BIRD/6J67.pdb C
|
||||
data/bio_assembly/BIRD/3PMP.pdb data/bio_assembly/BIRD/3PMP.pdb C
|
||||
data/bio_assembly/BIRD/1MIK.pdb data/bio_assembly/BIRD/1MIK.pdb B
|
||||
data/bio_assembly/BIRD/1QNH.pdb data/bio_assembly/BIRD/1QNH.pdb C
|
||||
data/bio_assembly/BIRD/1QNG.pdb data/bio_assembly/BIRD/1QNG.pdb D
|
||||
data/bio_assembly/BIRD/1TK2.pdb data/bio_assembly/BIRD/1TK2.pdb B
|
||||
data/bio_assembly/BIRD/1TMB.pdb data/bio_assembly/BIRD/1TMB.pdb T
|
||||
data/bio_assembly/BIRD/1W9U.pdb data/bio_assembly/BIRD/1W9U.pdb C
|
||||
data/bio_assembly/BIRD/1WAW.pdb data/bio_assembly/BIRD/1WAW.pdb B
|
||||
data/bio_assembly/BIRD/1XQ7.pdb data/bio_assembly/BIRD/1XQ7.pdb D
|
||||
data/bio_assembly/BIRD/2BCD.pdb data/bio_assembly/BIRD/2BCD.pdb B
|
||||
data/bio_assembly/BIRD/3SM1.pdb data/bio_assembly/BIRD/3SM1.pdb J
|
||||
data/bio_assembly/BIRD/6DNO.pdb data/bio_assembly/BIRD/6DNO.pdb C
|
||||
data/bio_assembly/BIRD/6DTN.pdb data/bio_assembly/BIRD/6DTN.pdb A
|
||||
data/bio_assembly/BIRD/6M9D.pdb data/bio_assembly/BIRD/6M9D.pdb B
|
||||
data/bio_assembly/BIRD/6APR.pdb data/bio_assembly/BIRD/6APR.pdb I
|
||||
data/bio_assembly/BIRD/6V2D.pdb data/bio_assembly/BIRD/6V2D.pdb B
|
||||
data/bio_assembly/BIRD/6V2S.pdb data/bio_assembly/BIRD/6V2S.pdb C
|
||||
data/bio_assembly/BIRD/6V2R.pdb data/bio_assembly/BIRD/6V2R.pdb B
|
||||
data/bio_assembly/BIRD/5U66.pdb data/bio_assembly/BIRD/5U66.pdb B
|
||||
data/bio_assembly/BIRD/1M21.pdb data/bio_assembly/BIRD/1M21.pdb C
|
||||
data/bio_assembly/BIRD/1LS5.pdb data/bio_assembly/BIRD/1LS5.pdb C
|
||||
data/bio_assembly/BIRD/1M43.pdb data/bio_assembly/BIRD/1M43.pdb C
|
||||
data/bio_assembly/BIRD/2CF9.pdb data/bio_assembly/BIRD/2CF9.pdb I
|
||||
data/bio_assembly/BIRD/2CF8.pdb data/bio_assembly/BIRD/2CF8.pdb I
|
||||
data/bio_assembly/BIRD/2CN0.pdb data/bio_assembly/BIRD/2CN0.pdb I
|
||||
data/bio_assembly/BIRD/2F9N.pdb data/bio_assembly/BIRD/2F9N.pdb E
|
||||
data/bio_assembly/BIRD/2F9P.pdb data/bio_assembly/BIRD/2F9P.pdb E
|
||||
data/bio_assembly/BIRD/2FES.pdb data/bio_assembly/BIRD/2FES.pdb D
|
||||
data/bio_assembly/BIRD/2FEQ.pdb data/bio_assembly/BIRD/2FEQ.pdb D
|
||||
data/bio_assembly/BIRD/1APU.pdb data/bio_assembly/BIRD/1APU.pdb I
|
||||
data/bio_assembly/BIRD/1AQ7.pdb data/bio_assembly/BIRD/1AQ7.pdb B
|
||||
data/bio_assembly/BIRD/1O0D.pdb data/bio_assembly/BIRD/1O0D.pdb D
|
||||
data/bio_assembly/BIRD/2AGI.pdb data/bio_assembly/BIRD/2AGI.pdb A
|
||||
data/bio_assembly/BIRD/2ANK.pdb data/bio_assembly/BIRD/2ANK.pdb P
|
||||
data/bio_assembly/BIRD/1WB0.pdb data/bio_assembly/BIRD/1WB0.pdb B
|
||||
data/bio_assembly/BIRD/1W9V.pdb data/bio_assembly/BIRD/1W9V.pdb C
|
||||
data/bio_assembly/BIRD/1W6I.pdb data/bio_assembly/BIRD/1W6I.pdb B
|
||||
data/bio_assembly/BIRD/1QS8.pdb data/bio_assembly/BIRD/1QS8.pdb C
|
||||
data/bio_assembly/BIRD/1PSO.pdb data/bio_assembly/BIRD/1PSO.pdb I
|
||||
data/bio_assembly/BIRD/1POP.pdb data/bio_assembly/BIRD/1POP.pdb B
|
||||
data/bio_assembly/BIRD/1OYT.pdb data/bio_assembly/BIRD/1OYT.pdb I
|
||||
data/bio_assembly/BIRD/1NZQ.pdb data/bio_assembly/BIRD/1NZQ.pdb D
|
||||
data/bio_assembly/BIRD/1WVM.pdb data/bio_assembly/BIRD/1WVM.pdb C
|
||||
data/bio_assembly/BIRD/1XDH.pdb data/bio_assembly/BIRD/1XDH.pdb C
|
||||
data/bio_assembly/BIRD/1WKR.pdb data/bio_assembly/BIRD/1WKR.pdb I
|
||||
data/bio_assembly/BIRD/1BCS.pdb data/bio_assembly/BIRD/1BCS.pdb C
|
||||
data/bio_assembly/BIRD/1BCR.pdb data/bio_assembly/BIRD/1BCR.pdb C
|
||||
data/bio_assembly/BIRD/6OBR.pdb data/bio_assembly/BIRD/6OBR.pdb D
|
||||
data/bio_assembly/BIRD/6OBQ.pdb data/bio_assembly/BIRD/6OBQ.pdb C
|
||||
data/bio_assembly/BIRD/6OBU.pdb data/bio_assembly/BIRD/6OBU.pdb C
|
||||
data/bio_assembly/BIRD/1H0I.pdb data/bio_assembly/BIRD/1H0I.pdb C
|
||||
data/bio_assembly/BIRD/6XA4.pdb data/bio_assembly/BIRD/6XA4.pdb B
|
||||
data/bio_assembly/BIRD/6YZ6.pdb data/bio_assembly/BIRD/6YZ6.pdb C
|
||||
data/bio_assembly/BIRD/1FJM.pdb data/bio_assembly/BIRD/1FJM.pdb M
|
||||
data/bio_assembly/BIRD/6BKJ.pdb data/bio_assembly/BIRD/6BKJ.pdb F
|
||||
data/bio_assembly/BIRD/5WGQ.pdb data/bio_assembly/BIRD/5WGQ.pdb E
|
||||
data/bio_assembly/BIRD/4IMQ.pdb data/bio_assembly/BIRD/4IMQ.pdb B
|
||||
data/bio_assembly/BIRD/4INH.pdb data/bio_assembly/BIRD/4INH.pdb M
|
||||
data/bio_assembly/BIRD/4IMZ.pdb data/bio_assembly/BIRD/4IMZ.pdb B
|
||||
data/bio_assembly/BIRD/1TL9.pdb data/bio_assembly/BIRD/1TL9.pdb B
|
||||
data/bio_assembly/BIRD/1SGC.pdb data/bio_assembly/BIRD/1SGC.pdb B
|
||||
data/bio_assembly/BIRD/1IZE.pdb data/bio_assembly/BIRD/1IZE.pdb B
|
||||
data/bio_assembly/BIRD/1JRT.pdb data/bio_assembly/BIRD/1JRT.pdb B
|
||||
data/bio_assembly/BIRD/1JRS.pdb data/bio_assembly/BIRD/1JRS.pdb B
|
||||
data/bio_assembly/BIRD/4Y9W.pdb data/bio_assembly/BIRD/4Y9W.pdb B
|
||||
data/bio_assembly/BIRD/4NMT.pdb data/bio_assembly/BIRD/4NMT.pdb C
|
||||
data/bio_assembly/BIRD/4NMS.pdb data/bio_assembly/BIRD/4NMS.pdb C
|
||||
data/bio_assembly/BIRD/4NMR.pdb data/bio_assembly/BIRD/4NMR.pdb C
|
||||
data/bio_assembly/BIRD/4NMQ.pdb data/bio_assembly/BIRD/4NMQ.pdb C
|
||||
data/bio_assembly/BIRD/4NMP.pdb data/bio_assembly/BIRD/4NMP.pdb C
|
||||
data/bio_assembly/BIRD/4NMO.pdb data/bio_assembly/BIRD/4NMO.pdb C
|
||||
data/bio_assembly/BIRD/4MZJ.pdb data/bio_assembly/BIRD/4MZJ.pdb T
|
||||
data/bio_assembly/BIRD/3P72.pdb data/bio_assembly/BIRD/3P72.pdb B
|
||||
data/bio_assembly/BIRD/3OE0.pdb data/bio_assembly/BIRD/3OE0.pdb I
|
||||
data/bio_assembly/BIRD/4I7D.pdb data/bio_assembly/BIRD/4I7D.pdb B
|
||||
data/bio_assembly/BIRD/4I7C.pdb data/bio_assembly/BIRD/4I7C.pdb B
|
||||
data/bio_assembly/BIRD/4I7B.pdb data/bio_assembly/BIRD/4I7B.pdb B
|
||||
data/bio_assembly/BIRD/4I5N.pdb data/bio_assembly/BIRD/4I5N.pdb G
|
||||
data/bio_assembly/BIRD/4I5L.pdb data/bio_assembly/BIRD/4I5L.pdb G
|
||||
data/bio_assembly/BIRD/2P0R.pdb data/bio_assembly/BIRD/2P0R.pdb D
|
||||
data/bio_assembly/BIRD/2NYL.pdb data/bio_assembly/BIRD/2NYL.pdb G
|
||||
data/bio_assembly/BIRD/2NYM.pdb data/bio_assembly/BIRD/2NYM.pdb G
|
||||
data/bio_assembly/BIRD/2NQA.pdb data/bio_assembly/BIRD/2NQA.pdb D
|
||||
data/bio_assembly/BIRD/2NPP.pdb data/bio_assembly/BIRD/2NPP.pdb Y
|
||||
data/bio_assembly/BIRD/2QZX.pdb data/bio_assembly/BIRD/2QZX.pdb C
|
||||
data/bio_assembly/BIRD/2RMP.pdb data/bio_assembly/BIRD/2RMP.pdb B
|
||||
data/bio_assembly/BIRD/2PSX.pdb data/bio_assembly/BIRD/2PSX.pdb B
|
||||
data/bio_assembly/BIRD/2PSY.pdb data/bio_assembly/BIRD/2PSY.pdb B
|
||||
data/bio_assembly/BIRD/4ER2.pdb data/bio_assembly/BIRD/4ER2.pdb I
|
||||
data/bio_assembly/BIRD/4NMV.pdb data/bio_assembly/BIRD/4NMV.pdb C
|
||||
data/bio_assembly/BIRD/4EJK.pdb data/bio_assembly/BIRD/4EJK.pdb N
|
||||
data/bio_assembly/BIRD/4EJD.pdb data/bio_assembly/BIRD/4EJD.pdb C
|
||||
data/bio_assembly/BIRD/4EXH.pdb data/bio_assembly/BIRD/4EXH.pdb J
|
||||
data/bio_assembly/BIRD/4G5G.pdb data/bio_assembly/BIRD/4G5G.pdb I
|
||||
data/bio_assembly/BIRD/4BP9.pdb data/bio_assembly/BIRD/4BP9.pdb G
|
||||
data/bio_assembly/BIRD/3V4L.pdb data/bio_assembly/BIRD/3V4L.pdb B
|
||||
data/bio_assembly/BIRD/3V4O.pdb data/bio_assembly/BIRD/3V4O.pdb B
|
||||
data/bio_assembly/BIRD/3UOA.pdb data/bio_assembly/BIRD/3UOA.pdb L
|
||||
data/bio_assembly/BIRD/3UO8.pdb data/bio_assembly/BIRD/3UO8.pdb L
|
||||
data/bio_assembly/BIRD/3BPM.pdb data/bio_assembly/BIRD/3BPM.pdb D
|
||||
data/bio_assembly/BIRD/5LW1.pdb data/bio_assembly/BIRD/5LW1.pdb C
|
||||
data/bio_assembly/BIRD/5MS4.pdb data/bio_assembly/BIRD/5MS4.pdb E
|
||||
data/bio_assembly/BIRD/5K99.pdb data/bio_assembly/BIRD/5K99.pdb C
|
||||
data/bio_assembly/BIRD/5JPF.pdb data/bio_assembly/BIRD/5JPF.pdb M
|
||||
data/bio_assembly/BIRD/5N7Q.pdb data/bio_assembly/BIRD/5N7Q.pdb I
|
||||
data/bio_assembly/BIRD/5I70.pdb data/bio_assembly/BIRD/5I70.pdb D
|
||||
data/bio_assembly/BIRD/5HVP.pdb data/bio_assembly/BIRD/5HVP.pdb C
|
||||
data/bio_assembly/BIRD/5FC3.pdb data/bio_assembly/BIRD/5FC3.pdb A
|
||||
data/bio_assembly/BIRD/5FC2.pdb data/bio_assembly/BIRD/5FC2.pdb A
|
||||
data/bio_assembly/BIRD/5EPK.pdb data/bio_assembly/BIRD/5EPK.pdb B
|
||||
data/bio_assembly/BIRD/5EPJ.pdb data/bio_assembly/BIRD/5EPJ.pdb B
|
||||
data/bio_assembly/BIRD/5EQ0.pdb data/bio_assembly/BIRD/5EQ0.pdb B
|
||||
data/bio_assembly/BIRD/2XE4.pdb data/bio_assembly/BIRD/2XE4.pdb B
|
||||
data/bio_assembly/BIRD/2Z2P.pdb data/bio_assembly/BIRD/2Z2P.pdb C
|
||||
data/bio_assembly/BIRD/3E7A.pdb data/bio_assembly/BIRD/3E7A.pdb C
|
||||
data/bio_assembly/BIRD/3DW8.pdb data/bio_assembly/BIRD/3DW8.pdb G
|
||||
data/bio_assembly/BIRD/3EGH.pdb data/bio_assembly/BIRD/3EGH.pdb E
|
||||
data/bio_assembly/BIRD/3EMY.pdb data/bio_assembly/BIRD/3EMY.pdb B
|
||||
data/bio_assembly/BIRD/3MGB.pdb data/bio_assembly/BIRD/3MGB.pdb C
|
||||
data/bio_assembly/BIRD/3MG9.pdb data/bio_assembly/BIRD/3MG9.pdb B
|
||||
data/bio_assembly/BIRD/3FGA.pdb data/bio_assembly/BIRD/3FGA.pdb E
|
||||
data/bio_assembly/BIRD/3FNT.pdb data/bio_assembly/BIRD/3FNT.pdb I
|
||||
data/bio_assembly/BIRD/3FV3.pdb data/bio_assembly/BIRD/3FV3.pdb J
|
||||
data/bio_assembly/BIRD/2V3H.pdb data/bio_assembly/BIRD/2V3H.pdb I
|
||||
data/bio_assembly/BIRD/2V3O.pdb data/bio_assembly/BIRD/2V3O.pdb I
|
||||
data/bio_assembly/BIRD/4YV8.pdb data/bio_assembly/BIRD/4YV8.pdb B
|
||||
data/bio_assembly/BIRD/3Q4K.pdb data/bio_assembly/BIRD/3Q4K.pdb C
|
||||
data/bio_assembly/BIRD/3Q4L.pdb data/bio_assembly/BIRD/3Q4L.pdb C
|
||||
data/bio_assembly/BIRD/4TVG.pdb data/bio_assembly/BIRD/4TVG.pdb C
|
||||
data/bio_assembly/BIRD/5D13.pdb data/bio_assembly/BIRD/5D13.pdb E
|
||||
data/bio_assembly/BIRD/1A2C.pdb data/bio_assembly/BIRD/1A2C.pdb I
|
||||
data/bio_assembly/BIRD/2IAE.pdb data/bio_assembly/BIRD/2IAE.pdb M
|
||||
data/bio_assembly/BIRD/2IE3.pdb data/bio_assembly/BIRD/2IE3.pdb I
|
||||
data/bio_assembly/BIRD/2H6T.pdb data/bio_assembly/BIRD/2H6T.pdb B
|
||||
data/bio_assembly/BIRD/2FO5.pdb data/bio_assembly/BIRD/2FO5.pdb E
|
||||
253
data/data_fpocket.csv
Normal file
253
data/data_fpocket.csv
Normal file
@@ -0,0 +1,253 @@
|
||||
2R9B;C,D;PLM2_PLAFA;;;;
|
||||
3URI;B;CARP_CRYPA;;;;
|
||||
3URL;B;CARP_CRYPA;;;;
|
||||
3V3B;C,D;MDM2_HUMAN;;;;
|
||||
3UQP;B;BACE1_HUMAN;;;;
|
||||
3UQR;D,E,F;BACE1_HUMAN;;;;
|
||||
5JXH;H;FURIN_HUMAN;;;;
|
||||
5JXJ;H;FURIN_HUMAN;;;;
|
||||
4RCP;B;PLK1_HUMAN;;;;
|
||||
4TPG;E;Q8EHE6_SHEON;;;;
|
||||
4RYD;H, I, J, K, L, N;FURIN_HUMAN;;;;
|
||||
4O6W;C;PLK1_HUMAN;;;;
|
||||
4K1E;B;KLK4_HUMAN;;;;
|
||||
4DV9;B;BACE1_HUMAN;;;;
|
||||
4DVF;C,D;BACE1_HUMAN;;;;
|
||||
4EZP;C,D;DNAK_ECOLI;;;;
|
||||
4FBX;B;CSK21_HUMAN;;;;
|
||||
4G35;B;MCL1_MOUSE;-----;;;
|
||||
5DNJ;B;PLK1_MOUSE;;;;
|
||||
4WHH;B;PLK1_HUMAN;;;;
|
||||
4WHK;B;PLK1_HUMAN;;;;
|
||||
4WHL;B;PLK1_HUMAN;;;;
|
||||
1SFI;I;TRY1_BOVIN;;;;
|
||||
3RQ7;B;PLK1_HUMAN;;;;
|
||||
3SNA;H;R1AB_CVHSA;;;;
|
||||
3SNB;H;R1A_CVHSA;;;;
|
||||
3SNC;H;R1A_CVHSA;-----;;;
|
||||
3SND;C,D;R1A_CVHSA;;;;
|
||||
3SNE;H;R1A_CVHSA;;;;
|
||||
3S70;B,D;CASP6_HUMAN;;;;
|
||||
1OKX;C,D;CELA1_PIG;------------;;;
|
||||
6VXY;C;TRY1_BOVIN;;;;
|
||||
3VFK;G;UBC_HUMAN;;;;
|
||||
3VFJ;G;MALE_ECOLI;;;;
|
||||
2XAD;E,F,G,H;Q6ZZJ1_ACTTI;;;;
|
||||
4MFL;B;Q6F275_MESFL;;;;
|
||||
4MFP;B;A0A2Z5FPF1_9MUSC;;;;
|
||||
4MFQ;B;Q70AY4_ACTTI;;;;
|
||||
4PJZ;B;D9IEF7_BPT4;;;;
|
||||
4PK0;B;D9IEF7_BPT4;;;;
|
||||
4EEC;C;STAL_STRTO;;;;
|
||||
4JNA;H,I;A4ZPY8_CHRVL;;;;
|
||||
4NEC;E,F,G,H;PCSK4_MOUSE;;;;
|
||||
3AH8;Y;GNAI1_RAT;;;;
|
||||
3RQD;C,D;HDAC8_HUMAN;;;;
|
||||
2CV3;B;CELA1_PIG;;;;
|
||||
2RMC;B,D,F,H;PPIC_MOUSE;;;;
|
||||
4TOT;E,F,G,H;PPIF_RAT;;;;
|
||||
6O21;B;KLK4_HUMAN;;;;
|
||||
6C1Q;L;C5AR1_HUMAN;;;;
|
||||
6C1R;L;C5AR1_HUMAN;;;;
|
||||
1MF8;D;CANB1_HUMAN;;;;
|
||||
3WDC;B;CLPC1_MYCTU;;;;
|
||||
3WDD;B;CLPC1_MYCTU;;;;
|
||||
3WDE;B;CLPC1_MYCTU;;;;
|
||||
3WMG;B;M1VAN7_CYAM1;;;;
|
||||
3WNE;C,D;POL_HV1N5;;;;
|
||||
3WNF;C,D;POL_HV1N5;;;;
|
||||
3WNG;C,D;POL_HV1N5;;;;
|
||||
2Z6W;M,N;PPIF_HUMAN;;;;
|
||||
4MNW;B;UROK_HUMAN;;;;
|
||||
4MNX;B;UROK_HUMAN;;;;
|
||||
4MNY;C,D;UROK_HUMAN;;;;
|
||||
4OS1;B;UROK_HUMAN;;;;
|
||||
4OS2;B;UROK_HUMAN;;;;
|
||||
4OS4;B;UROK_HUMAN;;;;
|
||||
4OS5;B;UROK_HUMAN;;;;
|
||||
4OS6;B;UROK_HUMAN;;;;
|
||||
4OS7;B;UROK_HUMAN;;;;
|
||||
4IPZ;B;PPIA_HUMAN;;;;
|
||||
4JJM;E,F;D0ELH5_CITSI;;;;
|
||||
4JK5;B;UROK_HUMAN;;;;
|
||||
4JK6;B;UROK_HUMAN;;;;
|
||||
4DGC;F,G,H,I,J;PPIA_MACMU;;;;
|
||||
4GLY;B;UROK_HUMAN;;;;
|
||||
4YV9;E,F,G,H;A0A0J9X288_STRDY;;;;
|
||||
4ZJX;B;BXA1_CLOBH;;;;
|
||||
4ZQW;A,C;CDIA4_ECO5C;;;;
|
||||
3BO7;E,F,G,H;D0VWS5_TOXGO;;;;
|
||||
3EOV;C,D;Q9U9R3_LEIDO;;;;
|
||||
4GUX;D,E,F;TRY1_BOVIN;;;;
|
||||
4GVU;D,E,F;CELA1_PIG;;;;
|
||||
4HGC;I;TRY1_BOVIN;;;;
|
||||
4HY7;B;Q93W25_WHEAT;;;;
|
||||
2WFJ;B;PPIG_HUMAN;;;;
|
||||
2X7K;B;PPIL1_HUMAN;;;;
|
||||
4KEL;B;KLK4_HUMAN;;;;
|
||||
4L3O;E,F,G,H;SIR2_HUMAN;;;;
|
||||
4KTU;B;TRY1_BOVIN;;;;
|
||||
4KTS;B;TRY1_BOVIN;;;;
|
||||
4KTC;B,D;POLG_HCVJA;;;;
|
||||
3AVA;X,Y;POL_HV1N5;;;;
|
||||
3AVB;X,Y;POL_HV1N5;;;;
|
||||
3AV9;X,Y;POL_HV1N5;;;;
|
||||
3AVI;D,F;POL_HV1B1;;;;
|
||||
3AVJ;D,F;POL_HV1N5;;;;
|
||||
3AVK;D,F;POL_HV1N5;;;;
|
||||
3AVL;E,F;POL_HV1N5;;;;
|
||||
3AVM;D,F;POL_HV1N5;;;;
|
||||
3AVN;G,H;POL_HV1N5;;;;
|
||||
5XN3;B;NOS2_HUMAN;;;;
|
||||
6CN8;B;CLPC1_MYCTU;;;;
|
||||
6DN8;B,D,F;SPSB4_HUMAN;;;;
|
||||
6DN5;B;SPSB2_HUMAN;;;;
|
||||
6DN7;B,D;SPSB4_HUMAN;;;;
|
||||
6DN6;B;SPSB2_HUMAN;;;;
|
||||
5VI6;B;HDAC8_HUMAN;;;;
|
||||
4WVT;C,D;XIAP_HUMAN;;;;
|
||||
4WVU;B;XIAP_HUMAN;;;;
|
||||
2POY;T,U,V;A3FQA7_CRYPI;;;;
|
||||
2OJU;C,D;PPIL3_HUMAN;;;;
|
||||
1BCK;C;PPIA_HUMAN;;;;
|
||||
1CWC;C;PPIA_HUMAN;;;;
|
||||
1CWB;C;PPIA_HUMAN;;;;
|
||||
1CWA;C;PPIA_HUMAN;;;;
|
||||
1CYN;C;PPIB_HUMAN;Enzyme;;;
|
||||
1IKF;C;?;;;;
|
||||
6J67;C;TERF2_HUMAN;;;;
|
||||
3PMP;C,D;PMP22_HUMAN;;;;
|
||||
1MIK;B;PPIA_HUMAN;;;;
|
||||
1QNH;C,D;Q25756_PLAFA;;;;
|
||||
1QNG;D;Q25756_PLAFA;;;;
|
||||
1TK2;B;NEP4_DROME;;;;
|
||||
1TMB;T;THRB_HUMAN;;;;
|
||||
1W9U;C,D;CHIB1_ASPFM;;;;
|
||||
1WAW;B;CHIT1_HUMAN;;;;
|
||||
1XQ7;D,E,F;Q4DPB9_TRYCC;;;;
|
||||
2BCD;B;PP1G_HUMAN;;;;
|
||||
3SM1;J,M;Q9E7M1_9GAMR;;;;
|
||||
6DNO;C;PP1A_HUMAN;;;;
|
||||
6DTN;A,C;NTM1A_HUMAN;;;;
|
||||
6M9D;B;PICP_PSESR;;;;
|
||||
6APR;I;CARP_RHICH;;;;
|
||||
6V2D;B, D, F, H, J, L;CDYL2_HUMAN;;;;
|
||||
6V2S;C,D;MPP8_HUMAN;;;;
|
||||
6V2R;B;CBX7_HUMAN;;;;
|
||||
5U66;B;IGHG1_HUMAN;;;;
|
||||
1M21;C,D;Q8RJN5_STEMA;;;;
|
||||
1LS5;C,D;Q8IM16_PLAF7;;;;
|
||||
1M43;C,D;PLM2_PLAFA;;;;
|
||||
2CF9;I;THRB_HUMAN;;;;
|
||||
2CF8;I;THRB_HUMAN;;;;
|
||||
2CN0;I;THRB_HUMAN;;;;
|
||||
2F9N;E, F, G, H;TRYB1_HUMAN;;;;
|
||||
2F9P;E, F, G, H;TRYB1_HUMAN;;;;
|
||||
2FES;D;THRB_HUMAN;;;;
|
||||
2FEQ;D;THRB_HUMAN;;;;
|
||||
1APU;I;PEPA1_PENJA;;;;
|
||||
1AQ7;B;TRY1_BOVIN;;;;
|
||||
1O0D;D;THRB_HUMAN;;;;
|
||||
2AGI;A;TRY1_BOVIN;;;;
|
||||
2ANK;P;THRB_HUMAN;;;;
|
||||
1WB0;B;CHIT1_HUMAN;;;;
|
||||
1W9V;C,D;CHIB1_ASPFU;;;;
|
||||
1W6I;B,D;PLM2_PLAFA;;;;
|
||||
1QS8;C,D;O60989_PLAVI;;;;
|
||||
1PSO;I;PEPA4_HUMAN;;;;
|
||||
1POP;B;PAPA1_CARPA;;;;
|
||||
1OYT;I;HIR2B_HIRME;;;;
|
||||
1NZQ;D;THRB_HUMAN;;;;
|
||||
1WVM;C,D;Q65Z69_9GAMM;;;;
|
||||
1XDH;C,D;PLM2_PLAFA;;;;
|
||||
1WKR;I;CARP_IRPLA;;;;
|
||||
1BCS;C;CBP2_WHEAT;;;;
|
||||
1BCR;C;CBP2_WHEAT;;;;
|
||||
6OBR;D,E;PP1A_HUMAN;;;;
|
||||
6OBQ;C,D;PP1A_HUMAN;;;;
|
||||
6OBU;C,D;PP1A_HUMAN;;;;
|
||||
1H0I;C,D;CHIB_SERMA;;;;
|
||||
6XA4;B;R1AB_SARS2;;;;
|
||||
6YZ6;C;R1AB_SARS2;;;;
|
||||
1FJM;M,N;PP1A_RABIT;;;;
|
||||
6BKJ;F, G, H, I;CAN3_HUMAN;;;;
|
||||
5WGQ;E,F;ESR1_HUMAN;;;;
|
||||
4IMQ;B;POLG_NVN68;;;;
|
||||
4INH;J, M, N, O, P, Q, S, T;POLG_NVN68;;;;
|
||||
4IMZ;B;POLG_NVN68;;;;
|
||||
1TL9;B;CAN1_RAT;;;;
|
||||
1SGC;B;PRTA_STRGR;;;;
|
||||
1IZE;B;PEPA_ASPOZ;;;;
|
||||
1JRT;B;TRY1_BOVIN;;;;
|
||||
1JRS;B;TRY1_BOVIN;;;;
|
||||
4Y9W;B;G8B6Y8_CANPC;;;;
|
||||
4NMT;C,D;GOPC_HUMAN;;;;
|
||||
4NMS;C,D;GOPC_HUMAN;;;;
|
||||
4NMR;C,D;GOPC_HUMAN;;;;
|
||||
4NMQ;C,D;GOPC_HUMAN;;;;
|
||||
4NMP;C,D;GOPC_HUMAN;;;;
|
||||
4NMO;C,D;GOPC_HUMAN;;;;
|
||||
4MZJ;T;Q8I4W8_PLAF7;;;;
|
||||
3P72;B;GP1BA_HUMAN;;;;
|
||||
3OE0;I;CXCR4_HUMAN;;;;
|
||||
4I7D;B,D;SIAH1_HUMAN;;;;
|
||||
4I7C;B,D;SIAH1_HUMAN;;;;
|
||||
4I7B;B,D;SIAH1_HUMAN;;;;
|
||||
4I5N;G,H;2AAA_HUMAN;;;;
|
||||
4I5L;G,H;PP2AA_HUMAN;;;;
|
||||
2P0R;D,E;CAN9_HUMAN;;;;
|
||||
2NYL;G,H;2A5G_HUMAN;;;;
|
||||
2NYM;G,H;2A5G_HUMAN;;;;
|
||||
2NQA;D,E;CAN8_HUMAN;;;;
|
||||
2NPP;X,Y;PP2AA_HUMAN;;;;
|
||||
2QZX;C,D;CARP5_CANAL;;;;
|
||||
2RMP;B;CARP_RHIMI;;;;
|
||||
2PSX;B;KLK5_HUMAN;;;;
|
||||
2PSY;B;KLK5_HUMAN;;;;
|
||||
4ER2;I;CARP_CRYPA;;;;
|
||||
4NMV;C,D;GOPC_HUMAN;;;;
|
||||
4EJK;N;POL_HV1Z2;;;;
|
||||
4EJD;C;POL_HV1Z2;;;;
|
||||
4EXH;J, M, P;Q9E7M1_9GAMR;;;;
|
||||
4G5G;I;EFTU1_ECOLI;;;;
|
||||
4BP9;G, H, I, J, K, L;O76728_TRYBB;;;;
|
||||
3V4L;B;MALT1_MOUSE;;;;
|
||||
3V4O;B;MALT1_HUMAN;;;;
|
||||
3UOA;L, M;MALT1_HUMAN;;;;
|
||||
3UO8;L, M;MALT1_HUMAN;;;;
|
||||
3BPM;C,D;Q9NAW4_PLAFA;;;;
|
||||
5LW1;C, F, I;MK08_HUMAN;;;;
|
||||
5MS4;E, F, G, H;KLK8_HUMAN;;;;
|
||||
5K99;C, D;A0A0F7RFM6_BACAN;;;;
|
||||
5JPF;M,N;C4YM68_CANAW;;;;
|
||||
5N7Q;I,J;V5HCK7_IXORI;;;;
|
||||
5I70;C,D;W7FF86_PLAF8;;;;
|
||||
5HVP;C;POL_HV1N5;;;;
|
||||
5FC3;A;G0SHM3_CHATD;;;;
|
||||
5FC2;A;G0SHM3_CHATD;;;;
|
||||
5EPK;B;CBX2_HUMAN;;;;
|
||||
5EPJ;B;CBX7_HUMAN;;;;
|
||||
5EQ0;B;CBX8_HUMAN;;;;
|
||||
2XE4;B;Q4QHU7_LEIMA;;;;
|
||||
2Z2P;C,D;VGB_STAAU;;;;
|
||||
3E7A;C,D;PP1A_HUMAN;;;;
|
||||
3DW8;G,H;PP2AA_HUMAN;;;;
|
||||
3EGH;E, F;NEB2_RAT;;;;
|
||||
3EMY;B;Q2WBH2_HYPJE;;;;
|
||||
3MGB;C,D;B7T1D7_9BACT;;;;
|
||||
3MG9;B, C;B7T1D7_9BACT;;;;
|
||||
3FGA;E;PP2AA_HUMAN;;;;
|
||||
3FNT;I;Q8IM15_PLAF7;;;;
|
||||
3FV3;I, J, K, L, M, N, O, P;CARP1_CANPA;;;;
|
||||
2V3H;I;THRB_HUMAN;;;;
|
||||
2V3O;I;THRB_HUMAN;;;;
|
||||
4YV8;B;CATK_HUMAN;;;;
|
||||
3Q4K;C,D;DPO3B_ECOLI;;;;
|
||||
3Q4L;C,D;DPO3B_ECOLI;;;;
|
||||
4TVG;C;Q90EA1_9HIV1;;;;
|
||||
5D13;E, F, G, H;DLG4_RAT;;;;
|
||||
1A2C;I;THRB_HUMAN;;;;
|
||||
2IAE;M,N;PP2AA_HUMAN;;;;
|
||||
2IE3;I;PP2AA_HUMAN;;;;
|
||||
2H6T;B;CARP3_CANAL;;;;
|
||||
2FO5;E, F, G, H;CYSP2_HORVU;;;;
|
||||
|
160
data/non_BIRD.csv
Normal file
160
data/non_BIRD.csv
Normal file
@@ -0,0 +1,160 @@
|
||||
6FMP;C;KEAP1_HUMAN
|
||||
6QWN;F, G, H, I, J;PLRX1_ARATH
|
||||
4D2D;B;Q5M4H8_STRT2
|
||||
6QXP;I, J, K, L, M, N, O, P;LRX2_ARATH
|
||||
2OBH;C,D;CETN2_HUMAN
|
||||
1YK1;E;ANPRC_HUMAN
|
||||
3KD7;G, H, I, J, K;
|
||||
1YC5;B;NPD_THEMA
|
||||
2H4F;D;NPD_THEMA
|
||||
6F0Y;B;ASF1_YEAST
|
||||
5OJ5;B;YC48L_THEEB
|
||||
5OJR;E, F;YC48L_THEEB
|
||||
2QBX;D, P;EPHB2_HUMAN
|
||||
5D0J;L, M;GRB7_HUMAN
|
||||
3FBR;B;
|
||||
3JR3;D;NPD_THEMA
|
||||
3SVM;P;MPP8_HUMAN
|
||||
4Z5W;P, Q;PSKR1_DAUCA
|
||||
5E1D;D, E;NTM1A_HUMAN
|
||||
6Q1U;C,D;PLMN_HUMAN
|
||||
6WZZ;B;GID4_HUMAN
|
||||
1A1R;C,D;POLG_HCVH
|
||||
1EJH;E, F, G, H;IF4E_MOUSE
|
||||
1BZH;I, J, K, L, M, N, O, P;PTN1_HUMAN
|
||||
1AQC;C,D;APBA1_HUMAN
|
||||
6TWQ;C,D;ANXA2_HUMAN
|
||||
1YTJ;I;POL_SIVM1
|
||||
1YTH;I;POL_HV1A2
|
||||
1YTG;I;POL_HV1A2
|
||||
6CD9;B;GID4_HUMAN
|
||||
6C4U;G, H, I, J, K, L;RAD53_YEAST
|
||||
5H6Y;B;BPTF_HUMAN
|
||||
5I3L;C;DPF3_HUMAN
|
||||
6SEO;L;TEAD4_HUMAN
|
||||
6SEN;L, M;TEAD4_HUMAN
|
||||
2ITK;B;PIN1_HUMAN
|
||||
2Q5A;B;PIN1_HUMAN
|
||||
3UKW;C;IMA1_MOUSE
|
||||
3UKX;C;IMA1_MOUSE
|
||||
2VAY;B;CALM1_HUMAN
|
||||
5UW3;E, F, G, H;R4P353_9CARY
|
||||
5U1Q;L, M, N, P;GRB7_HUMAN
|
||||
4ZRT;B;PTN1_HUMAN
|
||||
5EEL;L, M, N, P, Q, R;GRB7_HUMAN
|
||||
5W4E;A, D;A0A2R2JFW7_9BASI
|
||||
4NY3;C,D;PTPA_HUMAN
|
||||
4AKT;C;Q52QJ1_PRODI
|
||||
5XWR;C,D;RBBP4_HUMAN
|
||||
2H4H;B;NPD_THEMA
|
||||
3AGY;C, D, F;DNJB1_HUMAN
|
||||
3AGZ;C, D, E, F;DNJB1_HUMAN
|
||||
3TWS;E, F, G, H;TNKS2_HUMAN
|
||||
3TWT;E, F, G, H;TNKS2_HUMAN
|
||||
3TWV;E, F, G, H;TNKS2_HUMAN
|
||||
4DRW;E, F;S10AA_HUMAN
|
||||
1EJ4;B;IF4E_MOUSE
|
||||
6TWX;C, D;MAGI1_HUMAN
|
||||
5K4F;C, D;GOPC_HUMAN
|
||||
1XJ7;B;ANDR_HUMAN
|
||||
1WBP;B;SRPK1_HUMAN
|
||||
1KA6;B;SH21A_HUMAN
|
||||
6CDG;B;GID4_HUMAN
|
||||
5N7F;C;MAGI1_HUMAN
|
||||
6CD8;C,D;GID4_HUMAN
|
||||
5N7D;C;MAGI1_HUMAN
|
||||
2IG0;B;TP53B_HUMAN
|
||||
2RLY;P;TCRG1_MOUSE
|
||||
5D94;B;MLP3B_HUMAN
|
||||
5IC3;C,D;GOPC_HUMAN
|
||||
3HS8;P;AP2A2_MOUSE
|
||||
3HS9;P;AP2B1_RAT
|
||||
3EG6;C;WDR5_HUMAN
|
||||
3L3Q;B, C;IMA1_MOUSE
|
||||
3O71;B;MK01_RAT
|
||||
3RZ9;B;IMA1_MOUSE
|
||||
3RZ2;C,D;TP4A1_RAT
|
||||
3RZX;B;IMA1_MOUSE
|
||||
4HH6;Z;D3GUW1_ECO44
|
||||
4GQ6;B;MEN1_HUMAN
|
||||
3WA4;B;GRB2_HUMAN
|
||||
3ZMP;C,D;PTN1_HUMAN
|
||||
3UL1;A;IMA1_MOUSE
|
||||
5GG4;E, F, G, H;UBP7_HUMAN
|
||||
5GJH;B, D;GRAP2_HUMAN
|
||||
4QE8;C, D;NR1H4_HUMAN
|
||||
4QE6;B;NR1H4_HUMAN
|
||||
5E6Q;A;IMA1_MOUSE
|
||||
5EOD;B;FA11_HUMAN
|
||||
4LP9;I;CARP_CRYPA
|
||||
4M91;B;TUSC3_HUMAN
|
||||
4M92;B;TUSC3_HUMAN
|
||||
5W4F;A, D;IMA1_MOUSE
|
||||
4O56;B;PLK1_HUMAN
|
||||
4YOS;E;RBL1_HUMAN
|
||||
4Z63;P;PSKR1_ARATH
|
||||
2YJD;C, D;ESR2_HUMAN
|
||||
4X3O;C;SIR2_HUMAN
|
||||
4X3P;C;SIR2_HUMAN
|
||||
2H9P;B;WDR5_HUMAN
|
||||
2H9N;B,D;WDR5_HUMAN
|
||||
1LKL;B;LCK_HUMAN
|
||||
1LKK;B;LCK_HUMAN
|
||||
3IOL;B;GLP1R_HUMAN
|
||||
5DNJ;B;PLK1_MOUSE
|
||||
6P5L;D;UBP7_HUMAN
|
||||
6Y4Q;C, D;MDM2_HUMAN
|
||||
1QKB;B;OPPA_SALTY
|
||||
1QKA;B;OPPA_SALTY
|
||||
1E6I;P;GCN5_YEAST
|
||||
6RJP;C,D;B2LA1_HUMAN
|
||||
1OHE;B;CC14B_HUMAN
|
||||
1Q1S;A,B;LT_SV40
|
||||
1G5J;B;B2CL1_HUMAN
|
||||
1JEV;B;OPPA_SALTY
|
||||
1JEU;B;OPPA_SALTY
|
||||
1JET;B;OPPA_SALTY
|
||||
1B32;B;OPPA_SALTY
|
||||
1B46;B;OPPA_SALTY
|
||||
1B9J;B;OPPA_SALTY
|
||||
6JXU;B;SUMO1_HUMAN
|
||||
6EJ8;B;XYLT1_HUMAN
|
||||
6EJ9;B;XYLT1_HUMAN
|
||||
1O6P;C, D, E, F;IMB1_HUMAN
|
||||
5OK6;C, D;UBP11_HUMAN
|
||||
2IV8;P, Q;AP2B1_HUMAN
|
||||
2OY2;W,Y;MMP8_HUMAN
|
||||
2OXW;X;MMP12_HUMAN
|
||||
2O5G;B;CALM_CHICK
|
||||
3GLU;B;SIR3_HUMAN
|
||||
2Y1N;B, D;CBL_HUMAN
|
||||
3FDL;B;B2CL1_HUMAN
|
||||
3JZO;P;MDM4_HUMAN
|
||||
3PDH;D;NPD_THEMA
|
||||
3RC0;P, Q;SETD6_HUMAN
|
||||
4FII;B;PAK4_HUMAN
|
||||
3ZMQ;C;PTN1_HUMAN
|
||||
3ZRJ;X,Y;
|
||||
3SRJ;C, D, E, F;Q7KQK5_PLAF7
|
||||
5FOS;C;RADA_PYRFU
|
||||
5GH9;B;CBP_HUMAN
|
||||
5TWH;E;MOB1A_HUMAN
|
||||
5TYI;L, M, N, P;GRB7_HUMAN
|
||||
5UW5;E, F, G, H;R4P353_9CARY
|
||||
5UW7;C, D;R4P353_9CARY
|
||||
5K9S;B, C;IMA1_MOUSE
|
||||
5AFG;B;MDM2_HUMAN
|
||||
4QSY;B;PTN11_HUMAN
|
||||
5VLA;Z;PCSK9_HUMAN
|
||||
5VTB;B;RBBP4_HUMAN
|
||||
4O6W;C;PLK1_HUMAN
|
||||
4Y6L;C, D;SIR2_HUMAN
|
||||
4Z2V;C, P;HOAVI_HOEPD
|
||||
2Z3L;C, D;LFTR_ECOLI
|
||||
2Z3N;C, D;LFTR_ECOLI
|
||||
4X6S;L, M;GRB7_HUMAN
|
||||
4OKF;A;RNAS1_BOVIN
|
||||
6HON;B, D;CNOT9_HUMAN
|
||||
6HOM;B, D;CNOT9_HUMAN
|
||||
6HV2;B;MMP13_HUMAN
|
||||
5X7B;L, N;PTN11_HUMAN
|
||||
|
160
data/non_bird_test.txt
Normal file
160
data/non_bird_test.txt
Normal file
@@ -0,0 +1,160 @@
|
||||
data/bio_assembly/NO_BIRD/6FMP.pdb data/bio_assembly/NO_BIRD/6FMP.pdb C
|
||||
data/bio_assembly/NO_BIRD/6QWN.pdb data/bio_assembly/NO_BIRD/6QWN.pdb F
|
||||
data/bio_assembly/NO_BIRD/4D2D.pdb data/bio_assembly/NO_BIRD/4D2D.pdb B
|
||||
data/bio_assembly/NO_BIRD/6QXP.pdb data/bio_assembly/NO_BIRD/6QXP.pdb I
|
||||
data/bio_assembly/NO_BIRD/2OBH.pdb data/bio_assembly/NO_BIRD/2OBH.pdb C
|
||||
data/bio_assembly/NO_BIRD/1YK1.pdb data/bio_assembly/NO_BIRD/1YK1.pdb E
|
||||
data/bio_assembly/NO_BIRD/3KD7.pdb data/bio_assembly/NO_BIRD/3KD7.pdb G
|
||||
data/bio_assembly/NO_BIRD/1YC5.pdb data/bio_assembly/NO_BIRD/1YC5.pdb B
|
||||
data/bio_assembly/NO_BIRD/2H4F.pdb data/bio_assembly/NO_BIRD/2H4F.pdb D
|
||||
data/bio_assembly/NO_BIRD/6F0Y.pdb data/bio_assembly/NO_BIRD/6F0Y.pdb B
|
||||
data/bio_assembly/NO_BIRD/5OJ5.pdb data/bio_assembly/NO_BIRD/5OJ5.pdb B
|
||||
data/bio_assembly/NO_BIRD/5OJR.pdb data/bio_assembly/NO_BIRD/5OJR.pdb E
|
||||
data/bio_assembly/NO_BIRD/2QBX.pdb data/bio_assembly/NO_BIRD/2QBX.pdb D
|
||||
data/bio_assembly/NO_BIRD/5D0J.pdb data/bio_assembly/NO_BIRD/5D0J.pdb L
|
||||
data/bio_assembly/NO_BIRD/3FBR.pdb data/bio_assembly/NO_BIRD/3FBR.pdb B
|
||||
data/bio_assembly/NO_BIRD/3JR3.pdb data/bio_assembly/NO_BIRD/3JR3.pdb D
|
||||
data/bio_assembly/NO_BIRD/3SVM.pdb data/bio_assembly/NO_BIRD/3SVM.pdb P
|
||||
data/bio_assembly/NO_BIRD/4Z5W.pdb data/bio_assembly/NO_BIRD/4Z5W.pdb P
|
||||
data/bio_assembly/NO_BIRD/5E1D.pdb data/bio_assembly/NO_BIRD/5E1D.pdb D
|
||||
data/bio_assembly/NO_BIRD/6Q1U.pdb data/bio_assembly/NO_BIRD/6Q1U.pdb C
|
||||
data/bio_assembly/NO_BIRD/6WZZ.pdb data/bio_assembly/NO_BIRD/6WZZ.pdb B
|
||||
data/bio_assembly/NO_BIRD/1A1R.pdb data/bio_assembly/NO_BIRD/1A1R.pdb C
|
||||
data/bio_assembly/NO_BIRD/1EJH.pdb data/bio_assembly/NO_BIRD/1EJH.pdb E
|
||||
data/bio_assembly/NO_BIRD/1BZH.pdb data/bio_assembly/NO_BIRD/1BZH.pdb I
|
||||
data/bio_assembly/NO_BIRD/1AQC.pdb data/bio_assembly/NO_BIRD/1AQC.pdb C
|
||||
data/bio_assembly/NO_BIRD/6TWQ.pdb data/bio_assembly/NO_BIRD/6TWQ.pdb C
|
||||
data/bio_assembly/NO_BIRD/1YTJ.pdb data/bio_assembly/NO_BIRD/1YTJ.pdb I
|
||||
data/bio_assembly/NO_BIRD/1YTH.pdb data/bio_assembly/NO_BIRD/1YTH.pdb I
|
||||
data/bio_assembly/NO_BIRD/1YTG.pdb data/bio_assembly/NO_BIRD/1YTG.pdb I
|
||||
data/bio_assembly/NO_BIRD/6CD9.pdb data/bio_assembly/NO_BIRD/6CD9.pdb B
|
||||
data/bio_assembly/NO_BIRD/6C4U.pdb data/bio_assembly/NO_BIRD/6C4U.pdb G
|
||||
data/bio_assembly/NO_BIRD/5H6Y.pdb data/bio_assembly/NO_BIRD/5H6Y.pdb B
|
||||
data/bio_assembly/NO_BIRD/5I3L.pdb data/bio_assembly/NO_BIRD/5I3L.pdb C
|
||||
data/bio_assembly/NO_BIRD/6SEO.pdb data/bio_assembly/NO_BIRD/6SEO.pdb L
|
||||
data/bio_assembly/NO_BIRD/6SEN.pdb data/bio_assembly/NO_BIRD/6SEN.pdb L
|
||||
data/bio_assembly/NO_BIRD/2ITK.pdb data/bio_assembly/NO_BIRD/2ITK.pdb B
|
||||
data/bio_assembly/NO_BIRD/2Q5A.pdb data/bio_assembly/NO_BIRD/2Q5A.pdb B
|
||||
data/bio_assembly/NO_BIRD/3UKW.pdb data/bio_assembly/NO_BIRD/3UKW.pdb C
|
||||
data/bio_assembly/NO_BIRD/3UKX.pdb data/bio_assembly/NO_BIRD/3UKX.pdb C
|
||||
data/bio_assembly/NO_BIRD/2VAY.pdb data/bio_assembly/NO_BIRD/2VAY.pdb B
|
||||
data/bio_assembly/NO_BIRD/5UW3.pdb data/bio_assembly/NO_BIRD/5UW3.pdb E
|
||||
data/bio_assembly/NO_BIRD/5U1Q.pdb data/bio_assembly/NO_BIRD/5U1Q.pdb L
|
||||
data/bio_assembly/NO_BIRD/4ZRT.pdb data/bio_assembly/NO_BIRD/4ZRT.pdb B
|
||||
data/bio_assembly/NO_BIRD/5EEL.pdb data/bio_assembly/NO_BIRD/5EEL.pdb L
|
||||
data/bio_assembly/NO_BIRD/5W4E.pdb data/bio_assembly/NO_BIRD/5W4E.pdb A
|
||||
data/bio_assembly/NO_BIRD/4NY3.pdb data/bio_assembly/NO_BIRD/4NY3.pdb C
|
||||
data/bio_assembly/NO_BIRD/4AKT.pdb data/bio_assembly/NO_BIRD/4AKT.pdb C
|
||||
data/bio_assembly/NO_BIRD/5XWR.pdb data/bio_assembly/NO_BIRD/5XWR.pdb C
|
||||
data/bio_assembly/NO_BIRD/2H4H.pdb data/bio_assembly/NO_BIRD/2H4H.pdb B
|
||||
data/bio_assembly/NO_BIRD/3AGY.pdb data/bio_assembly/NO_BIRD/3AGY.pdb C
|
||||
data/bio_assembly/NO_BIRD/3AGZ.pdb data/bio_assembly/NO_BIRD/3AGZ.pdb C
|
||||
data/bio_assembly/NO_BIRD/3TWS.pdb data/bio_assembly/NO_BIRD/3TWS.pdb E
|
||||
data/bio_assembly/NO_BIRD/3TWT.pdb data/bio_assembly/NO_BIRD/3TWT.pdb E
|
||||
data/bio_assembly/NO_BIRD/3TWV.pdb data/bio_assembly/NO_BIRD/3TWV.pdb E
|
||||
data/bio_assembly/NO_BIRD/4DRW.pdb data/bio_assembly/NO_BIRD/4DRW.pdb E
|
||||
data/bio_assembly/NO_BIRD/1EJ4.pdb data/bio_assembly/NO_BIRD/1EJ4.pdb B
|
||||
data/bio_assembly/NO_BIRD/6TWX.pdb data/bio_assembly/NO_BIRD/6TWX.pdb C
|
||||
data/bio_assembly/NO_BIRD/5K4F.pdb data/bio_assembly/NO_BIRD/5K4F.pdb C
|
||||
data/bio_assembly/NO_BIRD/1XJ7.pdb data/bio_assembly/NO_BIRD/1XJ7.pdb B
|
||||
data/bio_assembly/NO_BIRD/1WBP.pdb data/bio_assembly/NO_BIRD/1WBP.pdb B
|
||||
data/bio_assembly/NO_BIRD/1KA6.pdb data/bio_assembly/NO_BIRD/1KA6.pdb B
|
||||
data/bio_assembly/NO_BIRD/6CDG.pdb data/bio_assembly/NO_BIRD/6CDG.pdb B
|
||||
data/bio_assembly/NO_BIRD/5N7F.pdb data/bio_assembly/NO_BIRD/5N7F.pdb C
|
||||
data/bio_assembly/NO_BIRD/6CD8.pdb data/bio_assembly/NO_BIRD/6CD8.pdb C
|
||||
data/bio_assembly/NO_BIRD/5N7D.pdb data/bio_assembly/NO_BIRD/5N7D.pdb C
|
||||
data/bio_assembly/NO_BIRD/2IG0.pdb data/bio_assembly/NO_BIRD/2IG0.pdb B
|
||||
data/bio_assembly/NO_BIRD/2RLY.pdb data/bio_assembly/NO_BIRD/2RLY.pdb P
|
||||
data/bio_assembly/NO_BIRD/5D94.pdb data/bio_assembly/NO_BIRD/5D94.pdb B
|
||||
data/bio_assembly/NO_BIRD/5IC3.pdb data/bio_assembly/NO_BIRD/5IC3.pdb C
|
||||
data/bio_assembly/NO_BIRD/3HS8.pdb data/bio_assembly/NO_BIRD/3HS8.pdb P
|
||||
data/bio_assembly/NO_BIRD/3HS9.pdb data/bio_assembly/NO_BIRD/3HS9.pdb P
|
||||
data/bio_assembly/NO_BIRD/3EG6.pdb data/bio_assembly/NO_BIRD/3EG6.pdb C
|
||||
data/bio_assembly/NO_BIRD/3L3Q.pdb data/bio_assembly/NO_BIRD/3L3Q.pdb B
|
||||
data/bio_assembly/NO_BIRD/3O71.pdb data/bio_assembly/NO_BIRD/3O71.pdb B
|
||||
data/bio_assembly/NO_BIRD/3RZ9.pdb data/bio_assembly/NO_BIRD/3RZ9.pdb B
|
||||
data/bio_assembly/NO_BIRD/3RZ2.pdb data/bio_assembly/NO_BIRD/3RZ2.pdb C
|
||||
data/bio_assembly/NO_BIRD/3RZX.pdb data/bio_assembly/NO_BIRD/3RZX.pdb B
|
||||
data/bio_assembly/NO_BIRD/4HH6.pdb data/bio_assembly/NO_BIRD/4HH6.pdb Z
|
||||
data/bio_assembly/NO_BIRD/4GQ6.pdb data/bio_assembly/NO_BIRD/4GQ6.pdb B
|
||||
data/bio_assembly/NO_BIRD/3WA4.pdb data/bio_assembly/NO_BIRD/3WA4.pdb B
|
||||
data/bio_assembly/NO_BIRD/3ZMP.pdb data/bio_assembly/NO_BIRD/3ZMP.pdb C
|
||||
data/bio_assembly/NO_BIRD/3UL1.pdb data/bio_assembly/NO_BIRD/3UL1.pdb A
|
||||
data/bio_assembly/NO_BIRD/5GG4.pdb data/bio_assembly/NO_BIRD/5GG4.pdb E
|
||||
data/bio_assembly/NO_BIRD/5GJH.pdb data/bio_assembly/NO_BIRD/5GJH.pdb B
|
||||
data/bio_assembly/NO_BIRD/4QE8.pdb data/bio_assembly/NO_BIRD/4QE8.pdb C
|
||||
data/bio_assembly/NO_BIRD/4QE6.pdb data/bio_assembly/NO_BIRD/4QE6.pdb B
|
||||
data/bio_assembly/NO_BIRD/5E6Q.pdb data/bio_assembly/NO_BIRD/5E6Q.pdb A
|
||||
data/bio_assembly/NO_BIRD/5EOD.pdb data/bio_assembly/NO_BIRD/5EOD.pdb B
|
||||
data/bio_assembly/NO_BIRD/4LP9.pdb data/bio_assembly/NO_BIRD/4LP9.pdb I
|
||||
data/bio_assembly/NO_BIRD/4M91.pdb data/bio_assembly/NO_BIRD/4M91.pdb B
|
||||
data/bio_assembly/NO_BIRD/4M92.pdb data/bio_assembly/NO_BIRD/4M92.pdb B
|
||||
data/bio_assembly/NO_BIRD/5W4F.pdb data/bio_assembly/NO_BIRD/5W4F.pdb A
|
||||
data/bio_assembly/NO_BIRD/4O56.pdb data/bio_assembly/NO_BIRD/4O56.pdb B
|
||||
data/bio_assembly/NO_BIRD/4YOS.pdb data/bio_assembly/NO_BIRD/4YOS.pdb E
|
||||
data/bio_assembly/NO_BIRD/4Z63.pdb data/bio_assembly/NO_BIRD/4Z63.pdb P
|
||||
data/bio_assembly/NO_BIRD/2YJD.pdb data/bio_assembly/NO_BIRD/2YJD.pdb C
|
||||
data/bio_assembly/NO_BIRD/4X3O.pdb data/bio_assembly/NO_BIRD/4X3O.pdb C
|
||||
data/bio_assembly/NO_BIRD/4X3P.pdb data/bio_assembly/NO_BIRD/4X3P.pdb C
|
||||
data/bio_assembly/NO_BIRD/2H9P.pdb data/bio_assembly/NO_BIRD/2H9P.pdb B
|
||||
data/bio_assembly/NO_BIRD/2H9N.pdb data/bio_assembly/NO_BIRD/2H9N.pdb B
|
||||
data/bio_assembly/NO_BIRD/1LKL.pdb data/bio_assembly/NO_BIRD/1LKL.pdb B
|
||||
data/bio_assembly/NO_BIRD/1LKK.pdb data/bio_assembly/NO_BIRD/1LKK.pdb B
|
||||
data/bio_assembly/NO_BIRD/3IOL.pdb data/bio_assembly/NO_BIRD/3IOL.pdb B
|
||||
data/bio_assembly/NO_BIRD/5DNJ.pdb data/bio_assembly/NO_BIRD/5DNJ.pdb B
|
||||
data/bio_assembly/NO_BIRD/6P5L.pdb data/bio_assembly/NO_BIRD/6P5L.pdb D
|
||||
data/bio_assembly/NO_BIRD/6Y4Q.pdb data/bio_assembly/NO_BIRD/6Y4Q.pdb C
|
||||
data/bio_assembly/NO_BIRD/1QKB.pdb data/bio_assembly/NO_BIRD/1QKB.pdb B
|
||||
data/bio_assembly/NO_BIRD/1QKA.pdb data/bio_assembly/NO_BIRD/1QKA.pdb B
|
||||
data/bio_assembly/NO_BIRD/1E6I.pdb data/bio_assembly/NO_BIRD/1E6I.pdb P
|
||||
data/bio_assembly/NO_BIRD/6RJP.pdb data/bio_assembly/NO_BIRD/6RJP.pdb C
|
||||
data/bio_assembly/NO_BIRD/1OHE.pdb data/bio_assembly/NO_BIRD/1OHE.pdb B
|
||||
data/bio_assembly/NO_BIRD/1Q1S.pdb data/bio_assembly/NO_BIRD/1Q1S.pdb A
|
||||
data/bio_assembly/NO_BIRD/1G5J.pdb data/bio_assembly/NO_BIRD/1G5J.pdb B
|
||||
data/bio_assembly/NO_BIRD/1JEV.pdb data/bio_assembly/NO_BIRD/1JEV.pdb B
|
||||
data/bio_assembly/NO_BIRD/1JEU.pdb data/bio_assembly/NO_BIRD/1JEU.pdb B
|
||||
data/bio_assembly/NO_BIRD/1JET.pdb data/bio_assembly/NO_BIRD/1JET.pdb B
|
||||
data/bio_assembly/NO_BIRD/1B32.pdb data/bio_assembly/NO_BIRD/1B32.pdb B
|
||||
data/bio_assembly/NO_BIRD/1B46.pdb data/bio_assembly/NO_BIRD/1B46.pdb B
|
||||
data/bio_assembly/NO_BIRD/1B9J.pdb data/bio_assembly/NO_BIRD/1B9J.pdb B
|
||||
data/bio_assembly/NO_BIRD/6JXU.pdb data/bio_assembly/NO_BIRD/6JXU.pdb B
|
||||
data/bio_assembly/NO_BIRD/6EJ8.pdb data/bio_assembly/NO_BIRD/6EJ8.pdb B
|
||||
data/bio_assembly/NO_BIRD/6EJ9.pdb data/bio_assembly/NO_BIRD/6EJ9.pdb B
|
||||
data/bio_assembly/NO_BIRD/1O6P.pdb data/bio_assembly/NO_BIRD/1O6P.pdb C
|
||||
data/bio_assembly/NO_BIRD/5OK6.pdb data/bio_assembly/NO_BIRD/5OK6.pdb C
|
||||
data/bio_assembly/NO_BIRD/2IV8.pdb data/bio_assembly/NO_BIRD/2IV8.pdb P
|
||||
data/bio_assembly/NO_BIRD/2OY2.pdb data/bio_assembly/NO_BIRD/2OY2.pdb W
|
||||
data/bio_assembly/NO_BIRD/2OXW.pdb data/bio_assembly/NO_BIRD/2OXW.pdb X
|
||||
data/bio_assembly/NO_BIRD/2O5G.pdb data/bio_assembly/NO_BIRD/2O5G.pdb B
|
||||
data/bio_assembly/NO_BIRD/3GLU.pdb data/bio_assembly/NO_BIRD/3GLU.pdb B
|
||||
data/bio_assembly/NO_BIRD/2Y1N.pdb data/bio_assembly/NO_BIRD/2Y1N.pdb B
|
||||
data/bio_assembly/NO_BIRD/3FDL.pdb data/bio_assembly/NO_BIRD/3FDL.pdb B
|
||||
data/bio_assembly/NO_BIRD/3JZO.pdb data/bio_assembly/NO_BIRD/3JZO.pdb P
|
||||
data/bio_assembly/NO_BIRD/3PDH.pdb data/bio_assembly/NO_BIRD/3PDH.pdb D
|
||||
data/bio_assembly/NO_BIRD/3RC0.pdb data/bio_assembly/NO_BIRD/3RC0.pdb P
|
||||
data/bio_assembly/NO_BIRD/4FII.pdb data/bio_assembly/NO_BIRD/4FII.pdb B
|
||||
data/bio_assembly/NO_BIRD/3ZMQ.pdb data/bio_assembly/NO_BIRD/3ZMQ.pdb C
|
||||
data/bio_assembly/NO_BIRD/3ZRJ.pdb data/bio_assembly/NO_BIRD/3ZRJ.pdb X
|
||||
data/bio_assembly/NO_BIRD/3SRJ.pdb data/bio_assembly/NO_BIRD/3SRJ.pdb C
|
||||
data/bio_assembly/NO_BIRD/5FOS.pdb data/bio_assembly/NO_BIRD/5FOS.pdb C
|
||||
data/bio_assembly/NO_BIRD/5GH9.pdb data/bio_assembly/NO_BIRD/5GH9.pdb B
|
||||
data/bio_assembly/NO_BIRD/5TWH.pdb data/bio_assembly/NO_BIRD/5TWH.pdb E
|
||||
data/bio_assembly/NO_BIRD/5TYI.pdb data/bio_assembly/NO_BIRD/5TYI.pdb L
|
||||
data/bio_assembly/NO_BIRD/5UW5.pdb data/bio_assembly/NO_BIRD/5UW5.pdb E
|
||||
data/bio_assembly/NO_BIRD/5UW7.pdb data/bio_assembly/NO_BIRD/5UW7.pdb C
|
||||
data/bio_assembly/NO_BIRD/5K9S.pdb data/bio_assembly/NO_BIRD/5K9S.pdb B
|
||||
data/bio_assembly/NO_BIRD/5AFG.pdb data/bio_assembly/NO_BIRD/5AFG.pdb B
|
||||
data/bio_assembly/NO_BIRD/4QSY.pdb data/bio_assembly/NO_BIRD/4QSY.pdb B
|
||||
data/bio_assembly/NO_BIRD/5VLA.pdb data/bio_assembly/NO_BIRD/5VLA.pdb Z
|
||||
data/bio_assembly/NO_BIRD/5VTB.pdb data/bio_assembly/NO_BIRD/5VTB.pdb B
|
||||
data/bio_assembly/NO_BIRD/4O6W.pdb data/bio_assembly/NO_BIRD/4O6W.pdb C
|
||||
data/bio_assembly/NO_BIRD/4Y6L.pdb data/bio_assembly/NO_BIRD/4Y6L.pdb C
|
||||
data/bio_assembly/NO_BIRD/4Z2V.pdb data/bio_assembly/NO_BIRD/4Z2V.pdb C
|
||||
data/bio_assembly/NO_BIRD/2Z3L.pdb data/bio_assembly/NO_BIRD/2Z3L.pdb C
|
||||
data/bio_assembly/NO_BIRD/2Z3N.pdb data/bio_assembly/NO_BIRD/2Z3N.pdb C
|
||||
data/bio_assembly/NO_BIRD/4X6S.pdb data/bio_assembly/NO_BIRD/4X6S.pdb L
|
||||
data/bio_assembly/NO_BIRD/4OKF.pdb data/bio_assembly/NO_BIRD/4OKF.pdb A
|
||||
data/bio_assembly/NO_BIRD/6HON.pdb data/bio_assembly/NO_BIRD/6HON.pdb B
|
||||
data/bio_assembly/NO_BIRD/6HOM.pdb data/bio_assembly/NO_BIRD/6HOM.pdb B
|
||||
data/bio_assembly/NO_BIRD/6HV2.pdb data/bio_assembly/NO_BIRD/6HV2.pdb B
|
||||
data/bio_assembly/NO_BIRD/5X7B.pdb data/bio_assembly/NO_BIRD/5X7B.pdb L
|
||||
47
data/pdb_manager.py
Normal file
47
data/pdb_manager.py
Normal file
@@ -0,0 +1,47 @@
|
||||
import os
|
||||
import shutil
|
||||
import fnmatch
|
||||
from os import path
|
||||
import pandas as pd
|
||||
|
||||
def main():
|
||||
|
||||
out_path = "bio_assembly/BIRD"
|
||||
|
||||
doss = "bio_assembly/BIRD"
|
||||
write_path = "data/bio_assembly/NO_BIRD/"
|
||||
# rename the original file
|
||||
#result = find_files("*.pdb",doss)
|
||||
my_cols = [str(i) for i in range(45)]
|
||||
|
||||
data = pd.read_csv('non_BIRD.csv',sep=';|,|\t',names= my_cols,engine='python')
|
||||
|
||||
|
||||
|
||||
write_txt(data,write_path)
|
||||
'''for files in result:
|
||||
os.rename(files,out_path+files[len(doss):-1]) '''
|
||||
|
||||
'''result = find_files("*.pdb*","RCSB_test1")
|
||||
for files in result:
|
||||
os.remove(files)'''
|
||||
|
||||
|
||||
def find_files(pattern, search_path):
|
||||
result = []
|
||||
# Wlaking top-down from the root
|
||||
for root, dir, files in os.walk(search_path):
|
||||
for filename in files:
|
||||
if fnmatch.fnmatch(filename, pattern):
|
||||
result.append(os.path.join(root, filename))
|
||||
return result
|
||||
|
||||
|
||||
def write_txt(data,write_path):
|
||||
file = open('non_bird_test.txt','w+')
|
||||
for i in range(len(data)):
|
||||
file.write(write_path+str(data['0'][i])+'.pdb'+' '+write_path+str(data['0'][i])+'.pdb'+' '+ str(data['1'][i])+'\n')
|
||||
file.close()
|
||||
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
27
data/peptide-test.txt
Normal file
27
data/peptide-test.txt
Normal file
@@ -0,0 +1,27 @@
|
||||
data/peptide_data/3uqp.pdb data/peptide_data/3uqp.pdb B
|
||||
data/peptide_data/3uri.pdb data/peptide_data/3uri.pdb B
|
||||
data/peptide_data/4rcp.pdb data/peptide_data/4rcp.pdb B
|
||||
data/peptide_data/4tpg.pdb data/peptide_data/4tpg.pdb E
|
||||
data/peptide_data/5jxh.pdb data/peptide_data/5jxh.pdb H
|
||||
data/peptide_data/4o6w.pdb data/peptide_data/4o6w.pdb C
|
||||
data/peptide_data/4k1e.pdb data/peptide_data/4k1e.pdb B
|
||||
data/peptide_data/4dv9.pdb data/peptide_data/4dv9.pdb B
|
||||
data/peptide_data/4fbx.pdb data/peptide_data/4fbx.pdb B
|
||||
data/peptide_data/4g35.pdb data/peptide_data/4g35.pdb B
|
||||
data/peptide_data/5dnj.pdb data/peptide_data/5dnj.pdb B
|
||||
data/peptide_data/4whh.pdb data/peptide_data/4whh.pdb B
|
||||
data/peptide_data/4whk.pdb data/peptide_data/4whk.pdb B
|
||||
data/peptide_data/4whl.pdb data/peptide_data/4whl.pdb B
|
||||
data/peptide_data/1sfi.pdb data/peptide_data/1sfi.pdb I
|
||||
data/peptide_data/3rq7.pdb data/peptide_data/3rq7.pdb B
|
||||
data/peptide_data/3sna.pdb data/peptide_data/3sna.pdb H
|
||||
data/peptide_data/3snb.pdb data/peptide_data/3snb.pdb H
|
||||
data/peptide_data/3snc.pdb data/peptide_data/3snc.pdb H
|
||||
data/peptide_data/3snd.pdb data/peptide_data/3snd.pdb C
|
||||
data/peptide_data/1okx.pdb data/peptide_data/1okx.pdb C
|
||||
data/peptide_data/3s70.pdb data/peptide_data/3s70.pdb B
|
||||
data/peptide_data/3snd.pdb data/peptide_data/3snd.pdb D
|
||||
data/peptide_data/1okx.pdb data/peptide_data/1okx.pdb D
|
||||
data/peptide_data/3s70.pdb data/peptide_data/3s70.pdb D
|
||||
data/peptide_data/1okx1.pdb data/peptide_data/1okx1.pdb C
|
||||
data/peptide_data/1okx1.pdb data/peptide_data/1okx1.pdb C
|
||||
4894
data/sample/1QNH.cif
Normal file
4894
data/sample/1QNH.cif
Normal file
File diff suppressed because it is too large
Load Diff
3678
data/sample/1UYD.cif
Normal file
3678
data/sample/1UYD.cif
Normal file
File diff suppressed because it is too large
Load Diff
1969
data/sample/1UYD_wrote.cif
Normal file
1969
data/sample/1UYD_wrote.cif
Normal file
File diff suppressed because it is too large
Load Diff
1952
data/sample/1UYD_wrote.pdb
Normal file
1952
data/sample/1UYD_wrote.pdb
Normal file
File diff suppressed because it is too large
Load Diff
1555
data/sample/1orc.cif
Normal file
1555
data/sample/1orc.cif
Normal file
File diff suppressed because it is too large
Load Diff
877
data/sample/1orc.pdb
Normal file
877
data/sample/1orc.pdb
Normal file
@@ -0,0 +1,877 @@
|
||||
HEADER GENE REGULATING PROTEIN 30-OCT-95 1ORC
|
||||
TITLE CRO REPRESSOR INSERTION MUTANT K56-[DGEVK]
|
||||
COMPND MOL_ID: 1;
|
||||
COMPND 2 MOLECULE: CRO REPRESSOR INSERTION MUTANT K56-[DGEVK];
|
||||
COMPND 3 CHAIN: A;
|
||||
COMPND 4 ENGINEERED: YES;
|
||||
COMPND 5 MUTATION: YES;
|
||||
COMPND 6 OTHER_DETAILS: RESULTS IN A 71-RESIDUE STABLE "MONOMER"
|
||||
COMPND 7 MUTANT
|
||||
SOURCE MOL_ID: 1;
|
||||
SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE LAMBDA;
|
||||
SOURCE 3 ORGANISM_TAXID: 10710;
|
||||
SOURCE 4 GENE: CRO MUTANT K56-[DGEVK];
|
||||
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
|
||||
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
|
||||
SOURCE 7 EXPRESSION_SYSTEM_GENE: CRO MUTANT K56-[DGEVK]
|
||||
KEYWDS GENE REGULATING PROTEIN
|
||||
EXPDTA X-RAY DIFFRACTION
|
||||
AUTHOR R.A.ALBRIGHT,M.C.MOSSING,B.W.MATTHEWS
|
||||
REVDAT 2 24-FEB-09 1ORC 1 VERSN
|
||||
REVDAT 1 23-DEC-96 1ORC 0
|
||||
JRNL AUTH R.A.ALBRIGHT,M.C.MOSSING,B.W.MATTHEWS
|
||||
JRNL TITL HIGH-RESOLUTION STRUCTURE OF AN ENGINEERED CRO
|
||||
JRNL TITL 2 MONOMER SHOWS CHANGES IN CONFORMATION RELATIVE TO
|
||||
JRNL TITL 3 THE NATIVE DIMER.
|
||||
JRNL REF BIOCHEMISTRY V. 35 735 1996
|
||||
JRNL REFN ISSN 0006-2960
|
||||
JRNL PMID 8547253
|
||||
JRNL DOI 10.1021/BI951958N
|
||||
REMARK 1
|
||||
REMARK 1 REFERENCE 1
|
||||
REMARK 1 AUTH M.C.MOSSING,R.T.SAUER
|
||||
REMARK 1 TITL STABLE, MONOMERIC VARIANTS OF LAMBDA CRO OBTAINED
|
||||
REMARK 1 TITL 2 BY INSERTION OF A DESIGNED BETA-HAIRPIN SEQUENCE
|
||||
REMARK 1 REF SCIENCE V. 250 1712 1990
|
||||
REMARK 1 REFN ISSN 0036-8075
|
||||
REMARK 2
|
||||
REMARK 2 RESOLUTION. 1.54 ANGSTROMS.
|
||||
REMARK 3
|
||||
REMARK 3 REFINEMENT.
|
||||
REMARK 3 PROGRAM : TNT
|
||||
REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS
|
||||
REMARK 3
|
||||
REMARK 3 DATA USED IN REFINEMENT.
|
||||
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.54
|
||||
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
|
||||
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
|
||||
REMARK 3 COMPLETENESS FOR RANGE (%) : NULL
|
||||
REMARK 3 NUMBER OF REFLECTIONS : 9834
|
||||
REMARK 3
|
||||
REMARK 3 USING DATA ABOVE SIGMA CUTOFF.
|
||||
REMARK 3 CROSS-VALIDATION METHOD : NULL
|
||||
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
|
||||
REMARK 3 R VALUE (WORKING + TEST SET) : NULL
|
||||
REMARK 3 R VALUE (WORKING SET) : 0.178
|
||||
REMARK 3 FREE R VALUE : NULL
|
||||
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
|
||||
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
|
||||
REMARK 3
|
||||
REMARK 3 USING ALL DATA, NO SIGMA CUTOFF.
|
||||
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL
|
||||
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.1780
|
||||
REMARK 3 FREE R VALUE (NO CUTOFF) : NULL
|
||||
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
|
||||
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL
|
||||
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 9834
|
||||
REMARK 3
|
||||
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
|
||||
REMARK 3 PROTEIN ATOMS : 500
|
||||
REMARK 3 NUCLEIC ACID ATOMS : 0
|
||||
REMARK 3 HETEROGEN ATOMS : 0
|
||||
REMARK 3 SOLVENT ATOMS : 59
|
||||
REMARK 3
|
||||
REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL
|
||||
REMARK 3
|
||||
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT
|
||||
REMARK 3 BOND LENGTHS (A) : 0.015 ; NULL ; NULL
|
||||
REMARK 3 BOND ANGLES (DEGREES) : 2.300 ; NULL ; NULL
|
||||
REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL
|
||||
REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL
|
||||
REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL
|
||||
REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL
|
||||
REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL
|
||||
REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL
|
||||
REMARK 3
|
||||
REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL
|
||||
REMARK 3
|
||||
REMARK 3 BULK SOLVENT MODELING.
|
||||
REMARK 3 METHOD USED : NULL
|
||||
REMARK 3 KSOL : NULL
|
||||
REMARK 3 BSOL : NULL
|
||||
REMARK 3
|
||||
REMARK 3 RESTRAINT LIBRARIES.
|
||||
REMARK 3 STEREOCHEMISTRY : NULL
|
||||
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL
|
||||
REMARK 3
|
||||
REMARK 3 OTHER REFINEMENT REMARKS: BOTH TERMINI OF CRO K56-[DGEVK]ARE
|
||||
REMARK 3 DISORDERED. RESIDUES 1, 2, 62, 63, 64, 65, AND 66 HAVE NO
|
||||
REMARK 3 INTERPRETABLE DENSITY AND ARE NOT INCLUDED IN THE MODEL.
|
||||
REMARK 3 RESIDUES 3 AND 61 EXTEN AWAY FROM THE GLOBULAR PORTION OF THE
|
||||
REMARK 3 MOLECULE AND ARE MOST PROBABLY IN MULTIPLE CONFORMATIONS. THE
|
||||
REMARK 3 GLOBULAR PORTION OF THE MOLECULE (RESIDUES 4 - 59) IS
|
||||
REMARK 3 EXCEPTIONALLY WELL-DEFINED IN THE DENSITY.
|
||||
REMARK 4
|
||||
REMARK 4 1ORC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
|
||||
REMARK 100
|
||||
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
|
||||
REMARK 200
|
||||
REMARK 200 EXPERIMENTAL DETAILS
|
||||
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
|
||||
REMARK 200 DATE OF DATA COLLECTION : 26-SEP-93
|
||||
REMARK 200 TEMPERATURE (KELVIN) : NULL
|
||||
REMARK 200 PH : NULL
|
||||
REMARK 200 NUMBER OF CRYSTALS USED : NULL
|
||||
REMARK 200
|
||||
REMARK 200 SYNCHROTRON (Y/N) : N
|
||||
REMARK 200 RADIATION SOURCE : NULL
|
||||
REMARK 200 BEAMLINE : NULL
|
||||
REMARK 200 X-RAY GENERATOR MODEL : NULL
|
||||
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
|
||||
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
|
||||
REMARK 200 MONOCHROMATOR : NULL
|
||||
REMARK 200 OPTICS : NULL
|
||||
REMARK 200
|
||||
REMARK 200 DETECTOR TYPE : AREA DETECTOR
|
||||
REMARK 200 DETECTOR MANUFACTURER : XUONG-HAMLIN MULTIWIRE
|
||||
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SDMS
|
||||
REMARK 200 DATA SCALING SOFTWARE : NULL
|
||||
REMARK 200
|
||||
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9834
|
||||
REMARK 200 RESOLUTION RANGE HIGH (A) : NULL
|
||||
REMARK 200 RESOLUTION RANGE LOW (A) : NULL
|
||||
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
|
||||
REMARK 200
|
||||
REMARK 200 OVERALL.
|
||||
REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8
|
||||
REMARK 200 DATA REDUNDANCY : 4.600
|
||||
REMARK 200 R MERGE (I) : 0.02900
|
||||
REMARK 200 R SYM (I) : NULL
|
||||
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
|
||||
REMARK 200
|
||||
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
|
||||
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
|
||||
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
|
||||
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
|
||||
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
|
||||
REMARK 200 R MERGE FOR SHELL (I) : NULL
|
||||
REMARK 200 R SYM FOR SHELL (I) : NULL
|
||||
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
|
||||
REMARK 200
|
||||
REMARK 200 DIFFRACTION PROTOCOL: NULL
|
||||
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
|
||||
REMARK 200 SOFTWARE USED: NULL
|
||||
REMARK 200 STARTING MODEL: NULL
|
||||
REMARK 200
|
||||
REMARK 200 REMARK: NULL
|
||||
REMARK 280
|
||||
REMARK 280 CRYSTAL
|
||||
REMARK 280 SOLVENT CONTENT, VS (%): 40.87
|
||||
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08
|
||||
REMARK 280
|
||||
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
|
||||
REMARK 290
|
||||
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
|
||||
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
|
||||
REMARK 290
|
||||
REMARK 290 SYMOP SYMMETRY
|
||||
REMARK 290 NNNMMM OPERATOR
|
||||
REMARK 290 1555 X,Y,Z
|
||||
REMARK 290 2555 -X+1/2,-Y,Z+1/2
|
||||
REMARK 290 3555 -X,Y+1/2,-Z+1/2
|
||||
REMARK 290 4555 X+1/2,-Y+1/2,-Z
|
||||
REMARK 290
|
||||
REMARK 290 WHERE NNN -> OPERATOR NUMBER
|
||||
REMARK 290 MMM -> TRANSLATION VECTOR
|
||||
REMARK 290
|
||||
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
|
||||
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
|
||||
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
|
||||
REMARK 290 RELATED MOLECULES.
|
||||
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
|
||||
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
|
||||
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
|
||||
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 17.38500
|
||||
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
|
||||
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.15500
|
||||
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
|
||||
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.58500
|
||||
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 24.15500
|
||||
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.38500
|
||||
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.58500
|
||||
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
|
||||
REMARK 290
|
||||
REMARK 290 REMARK: NULL
|
||||
REMARK 300
|
||||
REMARK 300 BIOMOLECULE: 1
|
||||
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
|
||||
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
|
||||
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
|
||||
REMARK 300 BURIED SURFACE AREA.
|
||||
REMARK 350
|
||||
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
|
||||
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
|
||||
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
|
||||
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
|
||||
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
|
||||
REMARK 350
|
||||
REMARK 350 BIOMOLECULE: 1
|
||||
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
|
||||
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
|
||||
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
|
||||
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
|
||||
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
|
||||
REMARK 465
|
||||
REMARK 465 MISSING RESIDUES
|
||||
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
|
||||
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
|
||||
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
|
||||
REMARK 465
|
||||
REMARK 465 M RES C SSSEQI
|
||||
REMARK 465 MET A 1
|
||||
REMARK 465 GLU A 2
|
||||
REMARK 465 LYS A 62
|
||||
REMARK 465 LYS A 63
|
||||
REMARK 465 THR A 64
|
||||
REMARK 465 THR A 65
|
||||
REMARK 465 ALA A 66
|
||||
REMARK 470
|
||||
REMARK 470 MISSING ATOM
|
||||
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER;
|
||||
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
|
||||
REMARK 470 I=INSERTION CODE):
|
||||
REMARK 470 M RES CSSEQI ATOMS
|
||||
REMARK 470 LYS A 21 CG CD CE NZ
|
||||
REMARK 500
|
||||
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
|
||||
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
|
||||
REMARK 500
|
||||
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
|
||||
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
|
||||
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
|
||||
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
|
||||
REMARK 500
|
||||
REMARK 500 STANDARD TABLE:
|
||||
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
|
||||
REMARK 500
|
||||
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
|
||||
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
|
||||
REMARK 500
|
||||
REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
|
||||
REMARK 500 GLU A 54 CD GLU A 54 OE2 0.069
|
||||
REMARK 500
|
||||
REMARK 500 REMARK: NULL
|
||||
REMARK 500
|
||||
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
|
||||
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
|
||||
REMARK 500
|
||||
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
|
||||
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
|
||||
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
|
||||
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
|
||||
REMARK 500
|
||||
REMARK 500 STANDARD TABLE:
|
||||
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
|
||||
REMARK 500
|
||||
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
|
||||
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
|
||||
REMARK 500
|
||||
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
|
||||
REMARK 500 ASP A 9 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES
|
||||
REMARK 500 ASP A 47 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES
|
||||
REMARK 500 ASP A 47 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES
|
||||
REMARK 500 ASP A 56A CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES
|
||||
REMARK 500
|
||||
REMARK 500 REMARK: NULL
|
||||
REMARK 525
|
||||
REMARK 525 SOLVENT
|
||||
REMARK 525
|
||||
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
|
||||
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
|
||||
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
|
||||
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
|
||||
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
|
||||
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
|
||||
REMARK 525 NUMBER; I=INSERTION CODE):
|
||||
REMARK 525
|
||||
REMARK 525 M RES CSSEQI
|
||||
REMARK 525 HOH A 148 DISTANCE = 5.42 ANGSTROMS
|
||||
DBREF 1ORC A 1 66 UNP P03040 RCRO_LAMBD 1 66
|
||||
SEQADV 1ORC GLU A 54 UNP P03040 INSERTION
|
||||
SEQADV 1ORC VAL A 55 UNP P03040 INSERTION
|
||||
SEQADV 1ORC LYS A 56 UNP P03040 INSERTION
|
||||
SEQADV 1ORC ASP A 56A UNP P03040 INSERTION
|
||||
SEQADV 1ORC GLY A 56B UNP P03040 INSERTION
|
||||
SEQRES 1 A 71 MET GLU GLN ARG ILE THR LEU LYS ASP TYR ALA MET ARG
|
||||
SEQRES 2 A 71 PHE GLY GLN THR LYS THR ALA LYS ASP LEU GLY VAL TYR
|
||||
SEQRES 3 A 71 GLN SER ALA ILE ASN LYS ALA ILE HIS ALA GLY ARG LYS
|
||||
SEQRES 4 A 71 ILE PHE LEU THR ILE ASN ALA ASP GLY SER VAL TYR ALA
|
||||
SEQRES 5 A 71 GLU GLU VAL LYS ASP GLY GLU VAL LYS PRO PHE PRO SER
|
||||
SEQRES 6 A 71 ASN LYS LYS THR THR ALA
|
||||
FORMUL 2 HOH *57(H2 O)
|
||||
HELIX 1 1 LEU A 7 PHE A 14 1 8
|
||||
HELIX 2 2 GLN A 16 LEU A 23 1 8
|
||||
HELIX 3 3 GLN A 27 HIS A 35 1 9
|
||||
SHEET 1 A 3 LYS A 39 ILE A 44 0
|
||||
SHEET 2 A 3 VAL A 50 LYS A 56 -1 N VAL A 55 O LYS A 39
|
||||
SHEET 3 A 3 GLU A 56C PRO A 57 -1 N LYS A 56E O GLU A 54
|
||||
CISPEP 1 PHE A 58 PRO A 59 0 -0.65
|
||||
CRYST1 34.770 39.170 48.310 90.00 90.00 90.00 P 21 21 21 4
|
||||
ORIGX1 1.000000 0.000000 0.000000 0.00000
|
||||
ORIGX2 0.000000 1.000000 0.000000 0.00000
|
||||
ORIGX3 0.000000 0.000000 1.000000 0.00000
|
||||
SCALE1 0.028760 0.000000 0.000000 0.00000
|
||||
SCALE2 0.000000 0.025530 0.000000 0.00000
|
||||
SCALE3 0.000000 0.000000 0.020700 0.00000
|
||||
ATOM 1 N GLN A 3 12.772 36.309 7.065 1.00100.00 N
|
||||
ATOM 2 CA GLN A 3 12.632 37.265 8.163 1.00 48.14 C
|
||||
ATOM 3 C GLN A 3 13.732 37.165 9.263 1.00 52.27 C
|
||||
ATOM 4 O GLN A 3 14.053 36.101 9.788 1.00 44.13 O
|
||||
ATOM 5 CB GLN A 3 11.223 37.222 8.746 1.00 74.94 C
|
||||
ATOM 6 CG GLN A 3 10.520 38.577 8.616 1.00100.00 C
|
||||
ATOM 7 CD GLN A 3 10.533 39.326 9.931 1.00100.00 C
|
||||
ATOM 8 OE1 GLN A 3 9.824 38.926 10.900 1.00100.00 O
|
||||
ATOM 9 NE2 GLN A 3 11.382 40.376 9.990 1.00 83.72 N
|
||||
ATOM 10 N ARG A 4 14.321 38.294 9.634 1.00 25.53 N
|
||||
ATOM 11 CA ARG A 4 15.360 38.275 10.642 1.00 18.68 C
|
||||
ATOM 12 C ARG A 4 14.763 38.034 12.028 1.00 21.79 C
|
||||
ATOM 13 O ARG A 4 13.620 38.418 12.306 1.00 21.16 O
|
||||
ATOM 14 CB ARG A 4 16.095 39.616 10.699 1.00 18.77 C
|
||||
ATOM 15 CG ARG A 4 16.778 40.003 9.403 1.00 24.51 C
|
||||
ATOM 16 CD ARG A 4 17.273 41.464 9.421 1.00 32.20 C
|
||||
ATOM 17 NE ARG A 4 18.202 41.755 8.324 1.00 36.56 N
|
||||
ATOM 18 CZ ARG A 4 17.806 41.955 7.070 1.00 84.82 C
|
||||
ATOM 19 NH1 ARG A 4 16.515 41.892 6.756 1.00 46.36 N
|
||||
ATOM 20 NH2 ARG A 4 18.690 42.219 6.117 1.00 31.29 N
|
||||
ATOM 21 N ILE A 5 15.549 37.392 12.890 1.00 17.55 N
|
||||
ATOM 22 CA ILE A 5 15.183 37.125 14.284 1.00 14.87 C
|
||||
ATOM 23 C ILE A 5 16.203 37.872 15.172 1.00 16.47 C
|
||||
ATOM 24 O ILE A 5 17.401 37.815 14.843 1.00 17.02 O
|
||||
ATOM 25 CB ILE A 5 15.285 35.595 14.525 1.00 15.08 C
|
||||
ATOM 26 CG1 ILE A 5 14.275 34.892 13.658 1.00 40.26 C
|
||||
ATOM 27 CG2 ILE A 5 15.049 35.246 15.983 1.00 14.47 C
|
||||
ATOM 28 CD1 ILE A 5 14.495 33.386 13.673 1.00 45.11 C
|
||||
ATOM 29 N THR A 6 15.800 38.526 16.285 1.00 13.28 N
|
||||
ATOM 30 CA THR A 6 16.814 39.214 17.093 1.00 11.96 C
|
||||
ATOM 31 C THR A 6 17.671 38.212 17.779 1.00 14.04 C
|
||||
ATOM 32 O THR A 6 17.266 37.055 17.907 1.00 14.20 O
|
||||
ATOM 33 CB THR A 6 16.173 40.127 18.156 1.00 14.58 C
|
||||
ATOM 34 OG1 THR A 6 15.450 39.272 19.028 1.00 17.32 O
|
||||
ATOM 35 CG2 THR A 6 15.146 41.042 17.451 1.00 14.30 C
|
||||
ATOM 36 N LEU A 7 18.849 38.618 18.202 1.00 13.73 N
|
||||
ATOM 37 CA LEU A 7 19.728 37.670 18.894 1.00 13.16 C
|
||||
ATOM 38 C LEU A 7 19.041 37.135 20.139 1.00 15.87 C
|
||||
ATOM 39 O LEU A 7 19.090 35.912 20.454 1.00 12.79 O
|
||||
ATOM 40 CB LEU A 7 21.048 38.383 19.263 1.00 12.68 C
|
||||
ATOM 41 CG LEU A 7 21.982 37.558 20.140 1.00 17.98 C
|
||||
ATOM 42 CD1 LEU A 7 22.427 36.311 19.389 1.00 20.47 C
|
||||
ATOM 43 CD2 LEU A 7 23.218 38.409 20.407 1.00 18.75 C
|
||||
ATOM 44 N LYS A 8 18.371 38.033 20.873 1.00 14.10 N
|
||||
ATOM 45 CA LYS A 8 17.689 37.619 22.103 1.00 14.00 C
|
||||
ATOM 46 C LYS A 8 16.593 36.611 21.795 1.00 19.65 C
|
||||
ATOM 47 O LYS A 8 16.429 35.627 22.507 1.00 19.85 O
|
||||
ATOM 48 CB LYS A 8 17.076 38.822 22.826 1.00 15.93 C
|
||||
ATOM 49 CG LYS A 8 16.367 38.544 24.133 1.00 20.77 C
|
||||
ATOM 50 CD LYS A 8 15.511 39.771 24.498 1.00 38.02 C
|
||||
ATOM 51 CE LYS A 8 15.092 39.901 25.953 1.00 83.24 C
|
||||
ATOM 52 NZ LYS A 8 14.141 41.009 26.161 1.00 99.56 N
|
||||
ATOM 53 N ASP A 9 15.797 36.854 20.746 1.00 12.13 N
|
||||
ATOM 54 CA ASP A 9 14.716 35.901 20.441 1.00 12.04 C
|
||||
ATOM 55 C ASP A 9 15.261 34.577 19.956 1.00 16.77 C
|
||||
ATOM 56 O ASP A 9 14.676 33.565 20.239 1.00 17.35 O
|
||||
ATOM 57 CB ASP A 9 13.754 36.452 19.381 1.00 16.98 C
|
||||
ATOM 58 CG ASP A 9 12.817 37.489 19.951 1.00 30.47 C
|
||||
ATOM 59 OD1 ASP A 9 12.548 37.571 21.130 1.00 29.85 O
|
||||
ATOM 60 OD2 ASP A 9 12.329 38.272 19.045 1.00 30.89 O
|
||||
ATOM 61 N TYR A 10 16.369 34.570 19.227 1.00 13.45 N
|
||||
ATOM 62 CA TYR A 10 16.968 33.316 18.763 1.00 12.08 C
|
||||
ATOM 63 C TYR A 10 17.425 32.470 19.933 1.00 13.52 C
|
||||
ATOM 64 O TYR A 10 17.190 31.235 19.970 1.00 14.35 O
|
||||
ATOM 65 CB TYR A 10 18.152 33.638 17.846 1.00 14.33 C
|
||||
ATOM 66 CG TYR A 10 18.675 32.467 17.052 1.00 13.99 C
|
||||
ATOM 67 CD1 TYR A 10 19.677 31.649 17.566 1.00 14.46 C
|
||||
ATOM 68 CD2 TYR A 10 18.162 32.193 15.781 1.00 15.06 C
|
||||
ATOM 69 CE1 TYR A 10 20.159 30.568 16.820 1.00 14.84 C
|
||||
ATOM 70 CE2 TYR A 10 18.645 31.118 15.037 1.00 17.89 C
|
||||
ATOM 71 CZ TYR A 10 19.654 30.307 15.551 1.00 13.52 C
|
||||
ATOM 72 OH TYR A 10 20.113 29.235 14.810 1.00 18.91 O
|
||||
ATOM 73 N ALA A 11 18.053 33.115 20.912 1.00 14.43 N
|
||||
ATOM 74 CA ALA A 11 18.530 32.389 22.104 1.00 17.07 C
|
||||
ATOM 75 C ALA A 11 17.358 31.828 22.884 1.00 17.90 C
|
||||
ATOM 76 O ALA A 11 17.431 30.725 23.401 1.00 17.23 O
|
||||
ATOM 77 CB ALA A 11 19.353 33.293 23.015 1.00 13.38 C
|
||||
ATOM 78 N MET A 12 16.267 32.569 22.941 1.00 13.72 N
|
||||
ATOM 79 CA MET A 12 15.110 32.087 23.658 1.00 13.95 C
|
||||
ATOM 80 C MET A 12 14.489 30.885 22.958 1.00 16.33 C
|
||||
ATOM 81 O MET A 12 13.821 30.024 23.529 1.00 15.90 O
|
||||
ATOM 82 CB MET A 12 14.085 33.240 23.737 1.00 16.34 C
|
||||
ATOM 83 CG MET A 12 14.166 34.057 24.981 1.00 55.28 C
|
||||
ATOM 84 SD MET A 12 13.007 35.441 24.890 1.00100.00 S
|
||||
ATOM 85 CE MET A 12 13.748 36.594 26.079 1.00 98.88 C
|
||||
ATOM 86 N ARG A 13 14.591 30.843 21.623 1.00 14.91 N
|
||||
ATOM 87 CA ARG A 13 14.011 29.725 20.874 1.00 13.59 C
|
||||
ATOM 88 C ARG A 13 14.894 28.499 20.818 1.00 14.85 C
|
||||
ATOM 89 O ARG A 13 14.377 27.403 20.833 1.00 16.17 O
|
||||
ATOM 90 CB ARG A 13 13.631 30.085 19.422 1.00 13.23 C
|
||||
ATOM 91 CG ARG A 13 12.343 30.937 19.399 1.00 25.46 C
|
||||
ATOM 92 CD ARG A 13 12.232 31.960 18.236 1.00 26.76 C
|
||||
ATOM 93 NE ARG A 13 10.993 32.722 18.331 1.00 32.94 N
|
||||
ATOM 94 CZ ARG A 13 10.675 33.572 19.327 1.00 49.00 C
|
||||
ATOM 95 NH1 ARG A 13 11.504 33.835 20.326 1.00 49.46 N
|
||||
ATOM 96 NH2 ARG A 13 9.491 34.194 19.329 1.00 62.76 N
|
||||
ATOM 97 N PHE A 14 16.201 28.679 20.678 1.00 11.35 N
|
||||
ATOM 98 CA PHE A 14 17.091 27.571 20.478 1.00 12.06 C
|
||||
ATOM 99 C PHE A 14 18.062 27.296 21.591 1.00 16.73 C
|
||||
ATOM 100 O PHE A 14 18.752 26.272 21.544 1.00 17.92 O
|
||||
ATOM 101 CB PHE A 14 17.937 27.839 19.221 1.00 12.10 C
|
||||
ATOM 102 CG PHE A 14 17.051 27.815 18.032 1.00 21.70 C
|
||||
ATOM 103 CD1 PHE A 14 16.447 26.617 17.644 1.00 20.65 C
|
||||
ATOM 104 CD2 PHE A 14 16.771 28.999 17.344 1.00 23.31 C
|
||||
ATOM 105 CE1 PHE A 14 15.616 26.604 16.530 1.00 30.57 C
|
||||
ATOM 106 CE2 PHE A 14 15.924 29.013 16.241 1.00 24.51 C
|
||||
ATOM 107 CZ PHE A 14 15.349 27.803 15.854 1.00 29.75 C
|
||||
ATOM 108 N GLY A 15 18.187 28.213 22.551 1.00 12.81 N
|
||||
ATOM 109 CA GLY A 15 19.126 28.023 23.641 1.00 16.07 C
|
||||
ATOM 110 C GLY A 15 20.448 28.715 23.368 1.00 15.58 C
|
||||
ATOM 111 O GLY A 15 20.833 28.977 22.216 1.00 15.80 O
|
||||
ATOM 112 N GLN A 16 21.160 29.060 24.429 1.00 19.00 N
|
||||
ATOM 113 CA GLN A 16 22.448 29.783 24.302 1.00 23.07 C
|
||||
ATOM 114 C GLN A 16 23.545 28.961 23.693 1.00 19.82 C
|
||||
ATOM 115 O GLN A 16 24.387 29.465 22.952 1.00 22.09 O
|
||||
ATOM 116 CB GLN A 16 22.898 30.455 25.608 1.00 31.37 C
|
||||
ATOM 117 CG GLN A 16 21.973 31.648 25.860 1.00 44.42 C
|
||||
ATOM 118 CD GLN A 16 22.477 32.563 26.928 1.00 89.98 C
|
||||
ATOM 119 OE1 GLN A 16 21.674 33.132 27.677 1.00100.00 O
|
||||
ATOM 120 NE2 GLN A 16 23.797 32.701 27.003 1.00 83.25 N
|
||||
ATOM 121 N THR A 17 23.503 27.676 23.943 1.00 14.81 N
|
||||
ATOM 122 CA THR A 17 24.522 26.836 23.410 1.00 14.49 C
|
||||
ATOM 123 C THR A 17 24.469 26.755 21.886 1.00 18.16 C
|
||||
ATOM 124 O THR A 17 25.485 26.941 21.176 1.00 18.87 O
|
||||
ATOM 125 CB THR A 17 24.387 25.482 24.095 1.00 29.61 C
|
||||
ATOM 126 OG1 THR A 17 24.840 25.669 25.428 1.00 37.58 O
|
||||
ATOM 127 CG2 THR A 17 25.221 24.420 23.405 1.00 37.41 C
|
||||
ATOM 128 N LYS A 18 23.271 26.451 21.353 1.00 15.02 N
|
||||
ATOM 129 CA LYS A 18 23.171 26.378 19.902 1.00 14.97 C
|
||||
ATOM 130 C LYS A 18 23.473 27.761 19.265 1.00 19.02 C
|
||||
ATOM 131 O LYS A 18 24.128 27.857 18.233 1.00 17.30 O
|
||||
ATOM 132 CB LYS A 18 21.799 25.902 19.488 1.00 15.62 C
|
||||
ATOM 133 CG LYS A 18 21.565 26.030 17.979 1.00 17.87 C
|
||||
ATOM 134 CD LYS A 18 20.302 25.331 17.522 1.00 20.77 C
|
||||
ATOM 135 CE LYS A 18 19.938 25.641 16.061 1.00 21.05 C
|
||||
ATOM 136 NZ LYS A 18 21.070 25.348 15.174 1.00 23.25 N
|
||||
ATOM 137 N THR A 19 22.998 28.826 19.929 1.00 13.94 N
|
||||
ATOM 138 CA THR A 19 23.232 30.176 19.408 1.00 15.11 C
|
||||
ATOM 139 C THR A 19 24.728 30.452 19.247 1.00 17.10 C
|
||||
ATOM 140 O THR A 19 25.195 30.883 18.197 1.00 16.28 O
|
||||
ATOM 141 CB THR A 19 22.562 31.204 20.345 1.00 14.30 C
|
||||
ATOM 142 OG1 THR A 19 21.163 30.972 20.435 1.00 16.12 O
|
||||
ATOM 143 CG2 THR A 19 22.748 32.585 19.777 1.00 18.66 C
|
||||
ATOM 144 N ALA A 20 25.504 30.162 20.312 1.00 15.42 N
|
||||
ATOM 145 CA ALA A 20 26.961 30.386 20.308 1.00 16.54 C
|
||||
ATOM 146 C ALA A 20 27.601 29.564 19.216 1.00 18.55 C
|
||||
ATOM 147 O ALA A 20 28.435 30.047 18.448 1.00 16.40 O
|
||||
ATOM 148 CB ALA A 20 27.581 30.040 21.665 1.00 18.19 C
|
||||
ATOM 149 N LYS A 21 27.178 28.327 19.124 1.00 15.87 N
|
||||
ATOM 150 CA LYS A 21 27.755 27.471 18.068 1.00 14.12 C
|
||||
ATOM 151 C LYS A 21 27.417 27.978 16.665 1.00 23.53 C
|
||||
ATOM 152 O LYS A 21 28.261 27.983 15.775 1.00 22.00 O
|
||||
ATOM 153 CB LYS A 21 27.380 25.988 18.165 1.00 19.74 C
|
||||
ATOM 154 N ASP A 22 26.163 28.359 16.428 1.00 13.98 N
|
||||
ATOM 155 CA ASP A 22 25.792 28.797 15.096 1.00 13.60 C
|
||||
ATOM 156 C ASP A 22 26.555 30.021 14.674 1.00 17.42 C
|
||||
ATOM 157 O ASP A 22 26.763 30.257 13.483 1.00 18.55 O
|
||||
ATOM 158 CB ASP A 22 24.285 29.133 15.132 1.00 17.16 C
|
||||
ATOM 159 CG ASP A 22 23.463 27.892 15.121 1.00 21.24 C
|
||||
ATOM 160 OD1 ASP A 22 23.956 26.806 14.917 1.00 21.84 O
|
||||
ATOM 161 OD2 ASP A 22 22.212 28.101 15.342 1.00 21.83 O
|
||||
ATOM 162 N LEU A 23 26.917 30.836 15.671 1.00 16.70 N
|
||||
ATOM 163 CA LEU A 23 27.573 32.091 15.415 1.00 17.48 C
|
||||
ATOM 164 C LEU A 23 29.059 31.985 15.508 1.00 21.83 C
|
||||
ATOM 165 O LEU A 23 29.783 32.927 15.155 1.00 32.31 O
|
||||
ATOM 166 CB LEU A 23 27.082 33.234 16.362 1.00 17.26 C
|
||||
ATOM 167 CG LEU A 23 25.591 33.560 16.187 1.00 21.17 C
|
||||
ATOM 168 CD1 LEU A 23 25.236 34.773 17.030 1.00 23.34 C
|
||||
ATOM 169 CD2 LEU A 23 25.395 33.916 14.721 1.00 27.21 C
|
||||
ATOM 170 N GLY A 24 29.528 30.890 16.014 1.00 19.23 N
|
||||
ATOM 171 CA GLY A 24 30.950 30.717 16.194 1.00 19.43 C
|
||||
ATOM 172 C GLY A 24 31.518 31.656 17.260 1.00 25.53 C
|
||||
ATOM 173 O GLY A 24 32.607 32.153 17.082 1.00 29.65 O
|
||||
ATOM 174 N VAL A 25 30.822 31.922 18.393 1.00 18.56 N
|
||||
ATOM 175 CA VAL A 25 31.348 32.806 19.455 1.00 18.47 C
|
||||
ATOM 176 C VAL A 25 31.227 31.997 20.731 1.00 29.23 C
|
||||
ATOM 177 O VAL A 25 30.609 30.971 20.707 1.00 35.08 O
|
||||
ATOM 178 CB VAL A 25 30.567 34.121 19.584 1.00 20.81 C
|
||||
ATOM 179 CG1 VAL A 25 30.841 34.963 18.347 1.00 28.96 C
|
||||
ATOM 180 CG2 VAL A 25 29.091 33.779 19.602 1.00 30.28 C
|
||||
ATOM 181 N TYR A 26 31.767 32.399 21.827 1.00 16.42 N
|
||||
ATOM 182 CA TYR A 26 31.548 31.539 22.976 1.00 16.61 C
|
||||
ATOM 183 C TYR A 26 30.335 32.063 23.742 1.00 26.02 C
|
||||
ATOM 184 O TYR A 26 29.975 33.190 23.562 1.00 20.21 O
|
||||
ATOM 185 CB TYR A 26 32.816 31.460 23.844 1.00 15.69 C
|
||||
ATOM 186 CG TYR A 26 33.397 32.834 24.133 1.00 15.36 C
|
||||
ATOM 187 CD1 TYR A 26 33.008 33.568 25.261 1.00 19.73 C
|
||||
ATOM 188 CD2 TYR A 26 34.370 33.356 23.286 1.00 20.92 C
|
||||
ATOM 189 CE1 TYR A 26 33.566 34.821 25.529 1.00 22.18 C
|
||||
ATOM 190 CE2 TYR A 26 34.915 34.612 23.529 1.00 20.77 C
|
||||
ATOM 191 CZ TYR A 26 34.528 35.334 24.653 1.00 23.19 C
|
||||
ATOM 192 OH TYR A 26 35.125 36.565 24.868 1.00 37.78 O
|
||||
ATOM 193 N GLN A 27 29.724 31.279 24.636 1.00 15.04 N
|
||||
ATOM 194 CA GLN A 27 28.470 31.644 25.313 1.00 16.50 C
|
||||
ATOM 195 C GLN A 27 28.439 32.914 26.073 1.00 18.25 C
|
||||
ATOM 196 O GLN A 27 27.478 33.680 26.054 1.00 21.76 O
|
||||
ATOM 197 CB GLN A 27 27.876 30.468 26.136 1.00 20.07 C
|
||||
ATOM 198 CG AGLN A 27 27.570 29.232 25.290 0.50 12.45 C
|
||||
ATOM 199 CG BGLN A 27 26.388 30.644 26.494 0.50 28.90 C
|
||||
ATOM 200 CD AGLN A 27 26.956 28.056 26.052 0.50 20.66 C
|
||||
ATOM 201 CD BGLN A 27 26.083 30.009 27.823 0.50 30.43 C
|
||||
ATOM 202 OE1AGLN A 27 27.168 26.882 25.699 0.50 22.61 O
|
||||
ATOM 203 OE1BGLN A 27 25.473 30.610 28.715 0.50 34.69 O
|
||||
ATOM 204 NE2AGLN A 27 26.206 28.365 27.097 0.50 23.95 N
|
||||
ATOM 205 NE2BGLN A 27 26.508 28.766 27.938 0.50 41.63 N
|
||||
ATOM 206 N SER A 28 29.464 33.122 26.809 1.00 15.52 N
|
||||
ATOM 207 CA SER A 28 29.586 34.339 27.606 1.00 16.10 C
|
||||
ATOM 208 C SER A 28 29.401 35.614 26.777 1.00 21.89 C
|
||||
ATOM 209 O SER A 28 28.767 36.563 27.222 1.00 20.41 O
|
||||
ATOM 210 CB SER A 28 30.919 34.313 28.380 1.00 14.82 C
|
||||
ATOM 211 OG SER A 28 30.982 35.513 29.123 1.00 26.67 O
|
||||
ATOM 212 N ALA A 29 29.961 35.637 25.564 1.00 17.59 N
|
||||
ATOM 213 CA ALA A 29 29.883 36.770 24.667 1.00 17.67 C
|
||||
ATOM 214 C ALA A 29 28.484 37.014 24.183 1.00 27.65 C
|
||||
ATOM 215 O ALA A 29 28.089 38.132 23.981 1.00 20.63 O
|
||||
ATOM 216 CB ALA A 29 30.757 36.537 23.465 1.00 21.94 C
|
||||
ATOM 217 N ILE A 30 27.751 35.952 23.955 1.00 23.64 N
|
||||
ATOM 218 CA ILE A 30 26.369 36.053 23.551 1.00 36.96 C
|
||||
ATOM 219 C ILE A 30 25.512 36.766 24.653 1.00 26.56 C
|
||||
ATOM 220 O ILE A 30 24.675 37.683 24.424 1.00 21.49 O
|
||||
ATOM 221 CB ILE A 30 25.777 34.653 23.188 1.00 26.00 C
|
||||
ATOM 222 CG1 ILE A 30 26.348 34.051 21.899 1.00 22.78 C
|
||||
ATOM 223 CG2 ILE A 30 24.260 34.754 23.064 1.00 24.42 C
|
||||
ATOM 224 CD1 ILE A 30 26.113 34.938 20.703 1.00 24.43 C
|
||||
ATOM 225 N ASN A 31 25.684 36.302 25.886 1.00 26.96 N
|
||||
ATOM 226 CA ASN A 31 24.929 36.844 27.012 1.00 24.13 C
|
||||
ATOM 227 C ASN A 31 25.256 38.335 27.274 1.00 17.11 C
|
||||
ATOM 228 O ASN A 31 24.450 39.220 27.547 1.00 18.57 O
|
||||
ATOM 229 CB ASN A 31 25.209 35.902 28.208 1.00 28.18 C
|
||||
ATOM 230 CG ASN A 31 24.270 36.176 29.328 1.00100.00 C
|
||||
ATOM 231 OD1 ASN A 31 24.697 36.533 30.445 1.00 89.90 O
|
||||
ATOM 232 ND2 ASN A 31 22.981 36.068 28.999 1.00 64.11 N
|
||||
ATOM 233 N LYS A 32 26.471 38.639 27.080 1.00 16.17 N
|
||||
ATOM 234 CA LYS A 32 26.812 40.008 27.294 1.00 17.05 C
|
||||
ATOM 235 C LYS A 32 26.216 40.905 26.218 1.00 31.66 C
|
||||
ATOM 236 O LYS A 32 25.732 41.995 26.518 1.00 29.57 O
|
||||
ATOM 237 CB LYS A 32 28.306 40.081 27.162 1.00 21.07 C
|
||||
ATOM 238 CG LYS A 32 28.902 41.412 27.606 1.00 52.04 C
|
||||
ATOM 239 CD LYS A 32 30.396 41.492 27.303 1.00 81.78 C
|
||||
ATOM 240 CE LYS A 32 31.140 42.468 28.196 1.00100.00 C
|
||||
ATOM 241 NZ LYS A 32 30.873 43.865 27.856 1.00 43.46 N
|
||||
ATOM 242 N ALA A 33 26.285 40.437 24.956 1.00 19.80 N
|
||||
ATOM 243 CA ALA A 33 25.747 41.180 23.787 1.00 21.92 C
|
||||
ATOM 244 C ALA A 33 24.297 41.500 23.968 1.00 21.92 C
|
||||
ATOM 245 O ALA A 33 23.806 42.585 23.666 1.00 22.77 O
|
||||
ATOM 246 CB ALA A 33 25.948 40.430 22.479 1.00 18.69 C
|
||||
ATOM 247 N ILE A 34 23.591 40.542 24.444 1.00 18.08 N
|
||||
ATOM 248 CA ILE A 34 22.199 40.740 24.698 1.00 21.87 C
|
||||
ATOM 249 C ILE A 34 22.059 41.741 25.810 1.00 43.97 C
|
||||
ATOM 250 O ILE A 34 21.320 42.721 25.716 1.00 33.65 O
|
||||
ATOM 251 CB ILE A 34 21.594 39.409 25.069 1.00 29.26 C
|
||||
ATOM 252 CG1 ILE A 34 21.436 38.525 23.825 1.00 21.75 C
|
||||
ATOM 253 CG2 ILE A 34 20.239 39.555 25.760 1.00 34.93 C
|
||||
ATOM 254 CD1 ILE A 34 20.948 37.106 24.189 1.00 26.89 C
|
||||
ATOM 255 N HIS A 35 22.822 41.512 26.856 1.00 29.05 N
|
||||
ATOM 256 CA HIS A 35 22.815 42.399 28.012 1.00 39.46 C
|
||||
ATOM 257 C HIS A 35 23.018 43.838 27.625 1.00 23.68 C
|
||||
ATOM 258 O HIS A 35 22.323 44.672 28.118 1.00 38.17 O
|
||||
ATOM 259 CB HIS A 35 23.911 42.003 29.015 1.00 30.65 C
|
||||
ATOM 260 CG HIS A 35 24.280 43.102 29.942 1.00100.00 C
|
||||
ATOM 261 ND1 HIS A 35 25.418 43.879 29.708 1.00 68.44 N
|
||||
ATOM 262 CD2 HIS A 35 23.672 43.529 31.112 1.00 35.25 C
|
||||
ATOM 263 CE1 HIS A 35 25.494 44.750 30.724 1.00100.00 C
|
||||
ATOM 264 NE2 HIS A 35 24.463 44.573 31.588 1.00 46.69 N
|
||||
ATOM 265 N ALA A 36 23.981 44.104 26.778 1.00 20.84 N
|
||||
ATOM 266 CA ALA A 36 24.334 45.408 26.286 1.00 24.23 C
|
||||
ATOM 267 C ALA A 36 23.305 45.982 25.291 1.00 36.12 C
|
||||
ATOM 268 O ALA A 36 23.444 47.124 24.846 1.00 33.39 O
|
||||
ATOM 269 CB ALA A 36 25.665 45.379 25.545 1.00 19.30 C
|
||||
ATOM 270 N GLY A 37 22.302 45.192 24.903 1.00 24.14 N
|
||||
ATOM 271 CA GLY A 37 21.290 45.659 23.941 1.00 29.84 C
|
||||
ATOM 272 C GLY A 37 21.854 46.026 22.565 1.00 35.89 C
|
||||
ATOM 273 O GLY A 37 21.472 46.990 21.917 1.00 30.09 O
|
||||
ATOM 274 N ARG A 38 22.782 45.260 22.076 1.00 17.99 N
|
||||
ATOM 275 CA ARG A 38 23.322 45.550 20.761 1.00 19.82 C
|
||||
ATOM 276 C ARG A 38 22.220 45.138 19.756 1.00 18.28 C
|
||||
ATOM 277 O ARG A 38 21.405 44.264 20.065 1.00 20.34 O
|
||||
ATOM 278 CB ARG A 38 24.653 44.808 20.523 1.00 19.50 C
|
||||
ATOM 279 CG ARG A 38 25.693 45.271 21.551 1.00 25.48 C
|
||||
ATOM 280 CD ARG A 38 26.965 44.505 21.472 1.00 24.57 C
|
||||
ATOM 281 NE ARG A 38 27.490 44.392 20.140 1.00 20.97 N
|
||||
ATOM 282 CZ ARG A 38 28.580 43.686 19.958 1.00 26.05 C
|
||||
ATOM 283 NH1 ARG A 38 29.167 43.092 20.984 1.00 23.69 N
|
||||
ATOM 284 NH2 ARG A 38 29.095 43.570 18.741 1.00 23.73 N
|
||||
ATOM 285 N LYS A 39 22.188 45.755 18.596 1.00 16.48 N
|
||||
ATOM 286 CA LYS A 39 21.140 45.482 17.629 1.00 17.09 C
|
||||
ATOM 287 C LYS A 39 21.666 44.466 16.675 1.00 16.45 C
|
||||
ATOM 288 O LYS A 39 22.313 44.817 15.683 1.00 18.25 O
|
||||
ATOM 289 CB LYS A 39 20.764 46.788 16.930 1.00 19.95 C
|
||||
ATOM 290 CG LYS A 39 20.222 47.767 17.972 1.00 24.06 C
|
||||
ATOM 291 CD LYS A 39 20.513 49.217 17.614 1.00 32.96 C
|
||||
ATOM 292 CE LYS A 39 19.981 50.191 18.673 1.00 45.86 C
|
||||
ATOM 293 NZ LYS A 39 19.454 51.472 18.095 1.00 53.67 N
|
||||
ATOM 294 N ILE A 40 21.410 43.183 17.021 1.00 13.44 N
|
||||
ATOM 295 CA ILE A 40 21.938 42.065 16.280 1.00 15.20 C
|
||||
ATOM 296 C ILE A 40 20.773 41.250 15.766 1.00 13.22 C
|
||||
ATOM 297 O ILE A 40 19.848 40.929 16.498 1.00 12.59 O
|
||||
ATOM 298 CB ILE A 40 22.888 41.267 17.200 1.00 10.03 C
|
||||
ATOM 299 CG1 ILE A 40 24.136 42.108 17.439 1.00 12.39 C
|
||||
ATOM 300 CG2 ILE A 40 23.375 40.058 16.441 1.00 12.12 C
|
||||
ATOM 301 CD1 ILE A 40 24.876 41.612 18.651 1.00 16.76 C
|
||||
ATOM 302 N PHE A 41 20.831 40.957 14.469 1.00 13.05 N
|
||||
ATOM 303 CA PHE A 41 19.729 40.244 13.782 1.00 13.58 C
|
||||
ATOM 304 C PHE A 41 20.273 39.045 13.004 1.00 17.16 C
|
||||
ATOM 305 O PHE A 41 21.284 39.108 12.333 1.00 15.68 O
|
||||
ATOM 306 CB PHE A 41 18.882 41.229 12.858 1.00 21.85 C
|
||||
ATOM 307 CG PHE A 41 18.442 42.514 13.603 1.00 18.36 C
|
||||
ATOM 308 CD1 PHE A 41 17.305 42.513 14.419 1.00 24.71 C
|
||||
ATOM 309 CD2 PHE A 41 19.182 43.703 13.501 1.00 20.79 C
|
||||
ATOM 310 CE1 PHE A 41 16.918 43.656 15.133 1.00 21.54 C
|
||||
ATOM 311 CE2 PHE A 41 18.813 44.845 14.214 1.00 17.68 C
|
||||
ATOM 312 CZ PHE A 41 17.672 44.826 15.021 1.00 18.87 C
|
||||
ATOM 313 N LEU A 42 19.580 37.919 13.130 1.00 13.76 N
|
||||
ATOM 314 CA LEU A 42 20.040 36.694 12.507 1.00 13.18 C
|
||||
ATOM 315 C LEU A 42 19.086 36.217 11.421 1.00 17.74 C
|
||||
ATOM 316 O LEU A 42 17.873 36.362 11.506 1.00 17.28 O
|
||||
ATOM 317 CB LEU A 42 19.994 35.580 13.591 1.00 15.42 C
|
||||
ATOM 318 CG LEU A 42 21.233 35.539 14.492 1.00 18.78 C
|
||||
ATOM 319 CD1 LEU A 42 21.341 36.862 15.260 1.00 23.71 C
|
||||
ATOM 320 CD2 LEU A 42 21.058 34.350 15.470 1.00 25.37 C
|
||||
ATOM 321 N THR A 43 19.673 35.634 10.383 1.00 16.26 N
|
||||
ATOM 322 CA THR A 43 18.880 35.050 9.288 1.00 15.99 C
|
||||
ATOM 323 C THR A 43 19.275 33.561 9.186 1.00 17.09 C
|
||||
ATOM 324 O THR A 43 20.473 33.256 9.056 1.00 17.62 O
|
||||
ATOM 325 CB THR A 43 19.298 35.726 7.940 1.00 22.81 C
|
||||
ATOM 326 OG1 THR A 43 18.835 37.049 8.024 1.00 25.25 O
|
||||
ATOM 327 CG2 THR A 43 18.677 35.005 6.742 1.00 31.16 C
|
||||
ATOM 328 N ILE A 44 18.298 32.679 9.252 1.00 15.60 N
|
||||
ATOM 329 CA ILE A 44 18.568 31.274 9.131 1.00 20.91 C
|
||||
ATOM 330 C ILE A 44 18.383 30.861 7.696 1.00 15.87 C
|
||||
ATOM 331 O ILE A 44 17.359 31.193 7.095 1.00 18.91 O
|
||||
ATOM 332 CB ILE A 44 17.632 30.429 10.008 1.00 30.28 C
|
||||
ATOM 333 CG1 ILE A 44 17.843 30.827 11.458 1.00 46.11 C
|
||||
ATOM 334 CG2 ILE A 44 17.844 28.902 9.819 1.00 25.10 C
|
||||
ATOM 335 CD1 ILE A 44 16.714 30.328 12.352 1.00 70.44 C
|
||||
ATOM 336 N ASN A 45 19.384 30.184 7.182 1.00 14.10 N
|
||||
ATOM 337 CA ASN A 45 19.327 29.689 5.821 1.00 20.16 C
|
||||
ATOM 338 C ASN A 45 18.803 28.263 5.824 1.00 19.07 C
|
||||
ATOM 339 O ASN A 45 18.874 27.527 6.819 1.00 17.69 O
|
||||
ATOM 340 CB ASN A 45 20.686 29.784 5.149 1.00 20.11 C
|
||||
ATOM 341 CG ASN A 45 21.184 31.231 5.162 1.00 24.66 C
|
||||
ATOM 342 OD1 ASN A 45 20.402 32.125 4.864 1.00 26.94 O
|
||||
ATOM 343 ND2 ASN A 45 22.436 31.444 5.569 1.00 26.52 N
|
||||
ATOM 344 N ALA A 46 18.251 27.870 4.705 1.00 22.61 N
|
||||
ATOM 345 CA ALA A 46 17.669 26.544 4.653 1.00 24.21 C
|
||||
ATOM 346 C ALA A 46 18.690 25.448 4.868 1.00 24.78 C
|
||||
ATOM 347 O ALA A 46 18.367 24.365 5.260 1.00 22.23 O
|
||||
ATOM 348 CB ALA A 46 16.890 26.345 3.375 1.00 22.88 C
|
||||
ATOM 349 N ASP A 47 19.940 25.755 4.671 1.00 21.26 N
|
||||
ATOM 350 CA ASP A 47 20.948 24.771 4.860 1.00 17.60 C
|
||||
ATOM 351 C ASP A 47 21.370 24.710 6.266 1.00 20.70 C
|
||||
ATOM 352 O ASP A 47 22.319 24.028 6.584 1.00 25.05 O
|
||||
ATOM 353 CB ASP A 47 22.175 25.020 3.980 1.00 23.87 C
|
||||
ATOM 354 CG ASP A 47 22.912 26.289 4.380 1.00 32.11 C
|
||||
ATOM 355 OD1 ASP A 47 22.589 27.015 5.289 1.00 28.98 O
|
||||
ATOM 356 OD2 ASP A 47 23.950 26.520 3.643 1.00 37.94 O
|
||||
ATOM 357 N GLY A 48 20.729 25.468 7.113 1.00 19.80 N
|
||||
ATOM 358 CA GLY A 48 21.127 25.428 8.525 1.00 23.59 C
|
||||
ATOM 359 C GLY A 48 22.139 26.456 8.966 1.00 24.53 C
|
||||
ATOM 360 O GLY A 48 22.305 26.655 10.164 1.00 27.05 O
|
||||
ATOM 361 N SER A 49 22.816 27.109 8.050 1.00 19.46 N
|
||||
ATOM 362 CA SER A 49 23.797 28.088 8.500 1.00 16.49 C
|
||||
ATOM 363 C SER A 49 23.061 29.352 8.896 1.00 20.85 C
|
||||
ATOM 364 O SER A 49 21.918 29.501 8.514 1.00 19.20 O
|
||||
ATOM 365 CB SER A 49 24.762 28.375 7.397 1.00 16.59 C
|
||||
ATOM 366 OG SER A 49 24.021 28.847 6.295 1.00 21.47 O
|
||||
ATOM 367 N VAL A 50 23.714 30.240 9.682 1.00 15.49 N
|
||||
ATOM 368 CA VAL A 50 23.094 31.441 10.161 1.00 14.53 C
|
||||
ATOM 369 C VAL A 50 23.925 32.627 9.792 1.00 16.31 C
|
||||
ATOM 370 O VAL A 50 25.113 32.563 9.905 1.00 20.11 O
|
||||
ATOM 371 CB VAL A 50 22.977 31.330 11.699 1.00 15.44 C
|
||||
ATOM 372 CG1 VAL A 50 22.459 32.568 12.367 1.00 17.50 C
|
||||
ATOM 373 CG2 VAL A 50 22.009 30.175 11.994 1.00 19.25 C
|
||||
ATOM 374 N TYR A 51 23.309 33.678 9.343 1.00 16.72 N
|
||||
ATOM 375 CA TYR A 51 24.067 34.887 9.017 1.00 21.29 C
|
||||
ATOM 376 C TYR A 51 23.627 35.971 10.032 1.00 20.19 C
|
||||
ATOM 377 O TYR A 51 22.451 36.117 10.309 1.00 20.05 O
|
||||
ATOM 378 CB TYR A 51 23.801 35.345 7.558 1.00 21.31 C
|
||||
ATOM 379 CG TYR A 51 24.146 36.813 7.269 1.00 22.84 C
|
||||
ATOM 380 CD1 TYR A 51 25.466 37.186 7.021 1.00 29.04 C
|
||||
ATOM 381 CD2 TYR A 51 23.158 37.789 7.193 1.00 27.80 C
|
||||
ATOM 382 CE1 TYR A 51 25.841 38.500 6.745 1.00 29.93 C
|
||||
ATOM 383 CE2 TYR A 51 23.506 39.112 6.911 1.00 28.96 C
|
||||
ATOM 384 CZ TYR A 51 24.837 39.466 6.685 1.00 28.90 C
|
||||
ATOM 385 OH TYR A 51 25.164 40.777 6.417 1.00 75.56 O
|
||||
ATOM 386 N ALA A 52 24.576 36.653 10.690 1.00 14.21 N
|
||||
ATOM 387 CA ALA A 52 24.167 37.639 11.639 1.00 13.99 C
|
||||
ATOM 388 C ALA A 52 24.736 38.973 11.230 1.00 16.81 C
|
||||
ATOM 389 O ALA A 52 25.857 39.062 10.734 1.00 17.86 O
|
||||
ATOM 390 CB ALA A 52 24.691 37.252 13.008 1.00 15.37 C
|
||||
ATOM 391 N GLU A 53 23.966 40.019 11.468 1.00 16.09 N
|
||||
ATOM 392 CA GLU A 53 24.423 41.342 11.157 1.00 16.97 C
|
||||
ATOM 393 C GLU A 53 24.076 42.266 12.282 1.00 15.88 C
|
||||
ATOM 394 O GLU A 53 23.093 42.080 12.971 1.00 18.62 O
|
||||
ATOM 395 CB GLU A 53 23.888 41.872 9.817 1.00 19.03 C
|
||||
ATOM 396 CG GLU A 53 22.411 42.061 9.859 1.00 24.25 C
|
||||
ATOM 397 CD GLU A 53 21.897 42.057 8.458 1.00 35.71 C
|
||||
ATOM 398 OE1 GLU A 53 22.525 42.491 7.526 1.00 27.95 O
|
||||
ATOM 399 OE2 GLU A 53 20.769 41.448 8.336 1.00 36.91 O
|
||||
ATOM 400 N GLU A 54 24.926 43.267 12.481 1.00 15.46 N
|
||||
ATOM 401 CA GLU A 54 24.720 44.221 13.546 1.00 16.14 C
|
||||
ATOM 402 C GLU A 54 24.543 45.641 12.961 1.00 21.40 C
|
||||
ATOM 403 O GLU A 54 25.130 46.003 11.948 1.00 25.19 O
|
||||
ATOM 404 CB GLU A 54 25.935 44.261 14.482 1.00 14.41 C
|
||||
ATOM 405 CG GLU A 54 25.673 45.177 15.692 1.00 18.40 C
|
||||
ATOM 406 CD GLU A 54 26.800 45.153 16.699 1.00 26.54 C
|
||||
ATOM 407 OE1 GLU A 54 27.830 44.520 16.500 1.00 30.33 O
|
||||
ATOM 408 OE2 GLU A 54 26.550 45.857 17.788 1.00 25.55 O
|
||||
ATOM 409 N VAL A 55 23.667 46.370 13.573 1.00 21.13 N
|
||||
ATOM 410 CA VAL A 55 23.440 47.727 13.144 1.00 27.58 C
|
||||
ATOM 411 C VAL A 55 24.110 48.583 14.182 1.00 27.92 C
|
||||
ATOM 412 O VAL A 55 23.780 48.514 15.389 1.00 25.31 O
|
||||
ATOM 413 CB VAL A 55 21.968 48.051 13.114 1.00 29.65 C
|
||||
ATOM 414 CG1 VAL A 55 21.807 49.529 12.757 1.00 38.38 C
|
||||
ATOM 415 CG2 VAL A 55 21.329 47.161 12.055 1.00 23.49 C
|
||||
ATOM 416 N LYS A 56 25.062 49.374 13.733 1.00 28.14 N
|
||||
ATOM 417 CA LYS A 56 25.762 50.207 14.693 1.00 58.37 C
|
||||
ATOM 418 C LYS A 56 26.180 51.499 14.044 1.00 33.42 C
|
||||
ATOM 419 O LYS A 56 26.815 51.453 12.959 1.00 31.02 O
|
||||
ATOM 420 CB LYS A 56 27.010 49.460 15.125 1.00 49.75 C
|
||||
ATOM 421 CG LYS A 56 27.697 49.942 16.393 1.00 39.95 C
|
||||
ATOM 422 CD LYS A 56 28.812 48.968 16.750 1.00100.00 C
|
||||
ATOM 423 CE LYS A 56 29.778 49.430 17.831 1.00100.00 C
|
||||
ATOM 424 NZ LYS A 56 30.915 48.498 18.004 1.00100.00 N
|
||||
ATOM 425 N ASP A 56A 25.831 52.621 14.696 1.00 53.90 N
|
||||
ATOM 426 CA ASP A 56A 26.191 53.931 14.169 1.00 49.50 C
|
||||
ATOM 427 C ASP A 56A 25.702 54.051 12.772 1.00 54.12 C
|
||||
ATOM 428 O ASP A 56A 26.476 54.298 11.863 1.00 49.28 O
|
||||
ATOM 429 CB ASP A 56A 27.710 54.134 14.031 1.00 47.57 C
|
||||
ATOM 430 CG ASP A 56A 28.484 53.954 15.317 1.00100.00 C
|
||||
ATOM 431 OD1 ASP A 56A 28.021 54.228 16.433 1.00 92.41 O
|
||||
ATOM 432 OD2 ASP A 56A 29.701 53.474 15.101 1.00100.00 O
|
||||
ATOM 433 N GLY A 56B 24.457 53.821 12.567 1.00 39.18 N
|
||||
ATOM 434 CA GLY A 56B 24.042 53.992 11.222 1.00 28.07 C
|
||||
ATOM 435 C GLY A 56B 24.539 52.950 10.315 1.00 36.07 C
|
||||
ATOM 436 O GLY A 56B 23.996 52.846 9.210 1.00 57.51 O
|
||||
ATOM 437 N GLU A 56C 25.519 52.134 10.743 1.00 28.59 N
|
||||
ATOM 438 CA GLU A 56C 25.964 51.070 9.818 1.00 40.34 C
|
||||
ATOM 439 C GLU A 56C 25.580 49.623 10.131 1.00 27.57 C
|
||||
ATOM 440 O GLU A 56C 25.320 49.256 11.286 1.00 35.60 O
|
||||
ATOM 441 CB GLU A 56C 27.401 51.139 9.280 1.00 47.14 C
|
||||
ATOM 442 CG GLU A 56C 27.803 52.562 8.881 1.00 68.41 C
|
||||
ATOM 443 CD GLU A 56C 27.611 52.798 7.413 1.00100.00 C
|
||||
ATOM 444 OE1 GLU A 56C 27.850 51.956 6.548 1.00100.00 O
|
||||
ATOM 445 OE2 GLU A 56C 27.166 54.002 7.176 1.00100.00 O
|
||||
ATOM 446 N VAL A 56D 25.610 48.868 9.016 1.00 30.28 N
|
||||
ATOM 447 CA VAL A 56D 25.278 47.464 8.936 1.00 30.80 C
|
||||
ATOM 448 C VAL A 56D 26.504 46.588 8.684 1.00 65.18 C
|
||||
ATOM 449 O VAL A 56D 27.082 46.538 7.616 1.00 31.22 O
|
||||
ATOM 450 CB VAL A 56D 24.104 47.217 7.973 1.00 46.38 C
|
||||
ATOM 451 CG1 VAL A 56D 24.562 47.175 6.517 1.00 64.25 C
|
||||
ATOM 452 CG2 VAL A 56D 23.430 45.913 8.324 1.00 41.05 C
|
||||
ATOM 453 N LYS A 56E 26.927 45.885 9.709 1.00 32.07 N
|
||||
ATOM 454 CA LYS A 56E 28.089 45.034 9.600 1.00 33.83 C
|
||||
ATOM 455 C LYS A 56E 27.784 43.617 10.073 1.00 26.57 C
|
||||
ATOM 456 O LYS A 56E 26.887 43.381 10.856 1.00 23.11 O
|
||||
ATOM 457 CB LYS A 56E 29.150 45.562 10.580 1.00 24.98 C
|
||||
ATOM 458 CG LYS A 56E 29.528 47.024 10.411 1.00 56.26 C
|
||||
ATOM 459 CD LYS A 56E 30.733 47.223 9.465 1.00100.00 C
|
||||
ATOM 460 CE LYS A 56E 30.415 47.974 8.156 1.00100.00 C
|
||||
ATOM 461 NZ LYS A 56E 30.878 47.300 6.922 1.00100.00 N
|
||||
ATOM 462 N PRO A 57 28.618 42.711 9.677 1.00 31.74 N
|
||||
ATOM 463 CA PRO A 57 28.533 41.324 10.100 1.00 30.22 C
|
||||
ATOM 464 C PRO A 57 28.844 41.214 11.584 1.00 24.56 C
|
||||
ATOM 465 O PRO A 57 29.574 42.010 12.109 1.00 22.29 O
|
||||
ATOM 466 CB PRO A 57 29.695 40.627 9.395 1.00 56.22 C
|
||||
ATOM 467 CG PRO A 57 30.582 41.730 8.819 1.00100.00 C
|
||||
ATOM 468 CD PRO A 57 29.703 42.961 8.705 1.00 57.16 C
|
||||
ATOM 469 N PHE A 58 28.273 40.220 12.248 1.00 17.63 N
|
||||
ATOM 470 CA PHE A 58 28.556 39.967 13.639 1.00 18.93 C
|
||||
ATOM 471 C PHE A 58 28.895 38.479 13.733 1.00 25.61 C
|
||||
ATOM 472 O PHE A 58 28.195 37.659 13.133 1.00 26.61 O
|
||||
ATOM 473 CB PHE A 58 27.305 40.192 14.482 1.00 17.79 C
|
||||
ATOM 474 CG PHE A 58 27.530 39.734 15.890 1.00 25.73 C
|
||||
ATOM 475 CD1 PHE A 58 28.200 40.537 16.816 1.00 25.33 C
|
||||
ATOM 476 CD2 PHE A 58 27.080 38.479 16.310 1.00 25.86 C
|
||||
ATOM 477 CE1 PHE A 58 28.407 40.112 18.135 1.00 17.65 C
|
||||
ATOM 478 CE2 PHE A 58 27.279 38.039 17.628 1.00 20.68 C
|
||||
ATOM 479 CZ PHE A 58 27.961 38.851 18.537 1.00 23.05 C
|
||||
ATOM 480 N PRO A 59 29.937 38.104 14.484 1.00 25.63 N
|
||||
ATOM 481 CA PRO A 59 30.784 38.992 15.209 1.00 25.99 C
|
||||
ATOM 482 C PRO A 59 31.647 39.704 14.228 1.00 49.28 C
|
||||
ATOM 483 O PRO A 59 31.863 39.264 13.106 1.00 28.39 O
|
||||
ATOM 484 CB PRO A 59 31.738 38.121 15.985 1.00 25.40 C
|
||||
ATOM 485 CG PRO A 59 31.704 36.771 15.325 1.00 25.66 C
|
||||
ATOM 486 CD PRO A 59 30.415 36.709 14.528 1.00 30.42 C
|
||||
ATOM 487 N SER A 60 32.184 40.798 14.653 1.00 49.75 N
|
||||
ATOM 488 CA SER A 60 33.009 41.550 13.738 1.00100.00 C
|
||||
ATOM 489 C SER A 60 34.406 41.011 13.645 1.00100.00 C
|
||||
ATOM 490 O SER A 60 34.934 40.769 12.543 1.00 95.05 O
|
||||
ATOM 491 CB SER A 60 33.118 42.996 14.188 1.00100.00 C
|
||||
ATOM 492 OG SER A 60 34.194 43.115 15.114 1.00100.00 O
|
||||
ATOM 493 N ASN A 61 34.965 40.865 14.851 1.00100.00 N
|
||||
ATOM 494 CA ASN A 61 36.322 40.475 15.074 1.00100.00 C
|
||||
ATOM 495 C ASN A 61 36.615 40.874 16.519 1.00100.00 C
|
||||
ATOM 496 O ASN A 61 36.488 42.053 16.901 1.00100.00 O
|
||||
ATOM 497 CB ASN A 61 37.166 41.359 14.114 1.00100.00 C
|
||||
ATOM 498 CG ASN A 61 38.647 41.049 13.964 1.00100.00 C
|
||||
ATOM 499 OD1 ASN A 61 39.421 41.895 13.468 1.00100.00 O
|
||||
ATOM 500 ND2 ASN A 61 39.046 39.835 14.348 1.00100.00 N
|
||||
TER 501 ASN A 61
|
||||
HETATM 502 O HOH A 100 16.567 43.265 4.042 1.00 34.53 O
|
||||
HETATM 503 O HOH A 101 20.456 38.947 9.389 1.00 23.99 O
|
||||
HETATM 504 O HOH A 102 12.849 38.495 16.591 1.00 22.30 O
|
||||
HETATM 505 O HOH A 103 13.926 40.856 20.884 1.00 41.05 O
|
||||
HETATM 506 O HOH A 104 18.819 40.954 20.655 1.00 19.73 O
|
||||
HETATM 507 O HOH A 105 22.693 27.151 27.634 1.00 70.09 O
|
||||
HETATM 508 O HOH A 106 21.061 42.196 21.789 1.00 41.39 O
|
||||
HETATM 509 O HOH A 107 18.782 42.676 18.500 1.00 18.57 O
|
||||
HETATM 510 O HOH A 108 16.220 42.191 21.534 1.00 50.13 O
|
||||
HETATM 511 O HOH A 109 17.337 35.292 25.464 1.00 39.26 O
|
||||
HETATM 512 O HOH A 112 10.684 35.559 22.027 1.00 57.92 O
|
||||
HETATM 513 O HOH A 113 20.062 26.858 12.663 1.00 44.33 O
|
||||
HETATM 514 O HOH A 114 21.057 25.359 22.646 1.00 20.07 O
|
||||
HETATM 515 O HOH A 115 10.987 37.712 13.387 1.00 53.83 O
|
||||
HETATM 516 O HOH A 116 21.175 25.792 25.461 1.00 45.82 O
|
||||
HETATM 517 O HOH A 117 26.070 29.114 11.027 1.00 22.17 O
|
||||
HETATM 518 O HOH A 118 11.734 37.820 3.909 1.00 69.47 O
|
||||
HETATM 519 O HOH A 119 11.313 40.892 19.018 1.00 47.45 O
|
||||
HETATM 520 O HOH A 120 9.440 37.991 19.579 1.00 59.14 O
|
||||
HETATM 521 O HOH A 121 12.308 39.937 22.921 1.00 66.69 O
|
||||
HETATM 522 O HOH A 123 31.715 37.994 27.757 1.00 35.80 O
|
||||
HETATM 523 O HOH A 124 33.332 38.551 25.542 1.00 72.97 O
|
||||
HETATM 524 O HOH A 125 28.935 43.074 23.912 1.00 34.25 O
|
||||
HETATM 525 O HOH A 126 29.860 40.122 23.720 1.00 32.71 O
|
||||
HETATM 526 O HOH A 127 15.525 33.748 9.130 1.00 31.50 O
|
||||
HETATM 527 O HOH A 128 31.988 41.342 17.207 1.00 59.78 O
|
||||
HETATM 528 O HOH A 129 29.634 43.327 14.724 1.00 33.16 O
|
||||
HETATM 529 O HOH A 130 22.330 39.552 29.588 1.00 65.61 O
|
||||
HETATM 530 O HOH A 131 27.765 44.818 28.495 1.00 38.62 O
|
||||
HETATM 531 O HOH A 133 24.462 47.460 17.919 1.00 23.88 O
|
||||
HETATM 532 O HOH A 134 24.899 49.304 19.604 1.00 47.82 O
|
||||
HETATM 533 O HOH A 135 26.021 28.115 30.069 1.00 59.83 O
|
||||
HETATM 534 O HOH A 136 18.018 27.146 28.371 1.00 70.16 O
|
||||
HETATM 535 O HOH A 138 16.935 29.765 26.527 1.00 48.67 O
|
||||
HETATM 536 O HOH A 139 18.048 29.690 2.604 1.00 43.98 O
|
||||
HETATM 537 O HOH A 141 31.065 26.910 15.705 1.00 64.63 O
|
||||
HETATM 538 O HOH A 142 30.020 29.019 13.276 1.00 57.01 O
|
||||
HETATM 539 O HOH A 143 29.845 26.873 22.152 1.00 79.81 O
|
||||
HETATM 540 O HOH A 146 13.383 39.438 6.579 1.00 63.02 O
|
||||
HETATM 541 O HOH A 147 20.711 27.622 2.096 1.00 49.53 O
|
||||
HETATM 542 O HOH A 148 14.196 30.133 28.935 1.00 79.60 O
|
||||
HETATM 543 O HOH A 150 28.792 35.220 12.803 1.00 70.46 O
|
||||
HETATM 544 O HOH A 151 27.559 30.392 9.833 1.00 74.79 O
|
||||
HETATM 545 O HOH A 152 28.329 26.679 12.467 1.00 58.31 O
|
||||
HETATM 546 O HOH A 154 27.463 36.350 10.486 1.00 61.38 O
|
||||
HETATM 547 O HOH A 156 18.107 32.722 3.682 1.00 53.96 O
|
||||
HETATM 548 O HOH A 161 25.605 26.383 11.780 1.00 58.16 O
|
||||
HETATM 549 O HOH A 162 16.433 43.785 10.736 1.00 59.32 O
|
||||
HETATM 550 O HOH A 163 10.518 36.164 16.394 1.00 64.24 O
|
||||
HETATM 551 O HOH A 166 19.795 28.946 27.147 1.00 45.05 O
|
||||
HETATM 552 O HOH A 171 13.409 41.652 13.265 1.00 61.60 O
|
||||
HETATM 553 O HOH A 174 27.287 32.431 11.584 1.00 64.21 O
|
||||
HETATM 554 O HOH A 180 23.741 29.905 2.072 1.00 58.63 O
|
||||
HETATM 555 O HOH A 181 32.794 51.457 17.245 1.00 65.72 O
|
||||
HETATM 556 O HOH A 183 9.101 40.801 20.870 1.00 71.78 O
|
||||
HETATM 557 O AHOH A 301 13.464 41.125 8.469 0.50 20.23 O
|
||||
HETATM 558 O BHOH A 301 12.554 42.700 8.853 0.50 26.40 O
|
||||
HETATM 559 O AHOH A 303 22.944 52.797 14.104 0.50 34.59 O
|
||||
HETATM 560 O BHOH A 303 22.676 52.579 15.869 0.50 32.63 O
|
||||
MASTER 259 0 0 3 3 0 0 6 559 1 0 6
|
||||
END
|
||||
8073
data/sample/2P0R.cif
Normal file
8073
data/sample/2P0R.cif
Normal file
File diff suppressed because it is too large
Load Diff
8073
data/sample/2P0R_mod.cif
Normal file
8073
data/sample/2P0R_mod.cif
Normal file
File diff suppressed because it is too large
Load Diff
5456
data/sample/2P0R_wrote.cif
Normal file
5456
data/sample/2P0R_wrote.cif
Normal file
File diff suppressed because it is too large
Load Diff
5439
data/sample/2P0R_wrote.pdb
Normal file
5439
data/sample/2P0R_wrote.pdb
Normal file
File diff suppressed because it is too large
Load Diff
30184
data/sample/3VI4.cif
Normal file
30184
data/sample/3VI4.cif
Normal file
File diff suppressed because it is too large
Load Diff
18510
data/sample/5RGF.cif
Normal file
18510
data/sample/5RGF.cif
Normal file
File diff suppressed because it is too large
Load Diff
20071
data/sample/6TL9.cif
Normal file
20071
data/sample/6TL9.cif
Normal file
File diff suppressed because it is too large
Load Diff
4494
data/sample/6X3P.cif
Normal file
4494
data/sample/6X3P.cif
Normal file
File diff suppressed because it is too large
Load Diff
@@ -37,6 +37,10 @@ Here you have a very simple and straightforward example of how to run fpocket on
|
||||
|
||||
`fpocket -f sample/1UYD.pdb`
|
||||
|
||||
It is also possible to run fpocket on a PDBx/mmcif file type, for example :
|
||||
|
||||
`fpocket -f sample/2P0R.cif`
|
||||
|
||||
It is mandatory to give a PDB input file using the -f flag in command line. If nothing is given, fpocket prints the fpocket usage/help to the screen. fpocket will use standard parameters for the detection of pockets. Fore more information about these parameters see the [advanced fpocket features](#fpocket-advanced).
|
||||
|
||||
If fpocket works properly the output on the screen should look like this :
|
||||
@@ -63,7 +67,7 @@ A script for fast visualization using PyMOL is also provided. PyMOL provides nic
|
||||
|
||||
#### Mandatory (1 OR 2):
|
||||
|
||||
1: flag -f : one standard PDB file name.
|
||||
1: flag -f : one standard PDB or PDBx/mmcif file name.
|
||||
2: flag -F : one text file containing a simple list of pdb path
|
||||
|
||||
#### Optional:
|
||||
@@ -462,6 +466,8 @@ The simplest way to run fpocket is either by providing a single pdb file, or by
|
||||
-k char : (Default is none): Use this flag to choose which chains you want to keep before running fpocket. The selected chains can be specified with ',' or ':' delimiters, for example you can use it '-k A,B,E' or '-k A:B:E'. You can keep up to 20 different chains.
|
||||
|
||||
-a char : (Default is none): With this flag you can select a chain you want to be considered as a ligand. Works the same way as the "-r" flag but with a whole chain. Only a single chain can be chosen, for example '-a D'.
|
||||
|
||||
-w char : (Default is 'd') : With this flag you are able to choose what kind of writing file output you want, 'd' -> default (same format outpout as input)| 'b' or "both"-> both pdb and mmcif | 'p' or "pdb"-> pdb | 'm' or "cif" or "mmcif" -> mmcif, for example "-w cif" or "-w p"
|
||||
|
||||
|
||||
### Output files description
|
||||
|
||||
@@ -36,7 +36,7 @@ typedef struct s_atm
|
||||
float x, y, z ; /**< Coords */
|
||||
char name[5], /**< Atom name */
|
||||
type[7], /**< Atom type */
|
||||
chain[2], /**< Chain name */
|
||||
chain[16], /**< Chain name */
|
||||
symbol[3], /**< Chemical symbol of the atom */
|
||||
res_name[8]; /**< Atom residue name */
|
||||
|
||||
|
||||
@@ -117,6 +117,10 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
|
||||
#define M_PAR_CHAIN_AS_LIGAND 'a' /**flag, to define which chains are defined as a ligand*/
|
||||
#define M_PAR_CHAIN_AS_LIGAND_LONG "chain_as_ligand"
|
||||
|
||||
#define M_PAR_WRITE_MODE 'w' /**flag, to define which chains are defined as a ligand*/
|
||||
#define M_PAR_WRITE_MODE_LONG "write_mode"
|
||||
|
||||
|
||||
|
||||
|
||||
#define M_FP_USAGE "\n\
|
||||
@@ -203,6 +207,7 @@ typedef struct s_fparams
|
||||
char chain_delete[M_MAX_CHAINS_DELETE]; /*chosen chain to delete before calculation*/
|
||||
char chain_as_ligand[M_MAX_CHAINS_DELETE];
|
||||
int chain_is_kept;/* To choose if we keep the chains or not*/
|
||||
char write_par[10]; /*write mode : d -> default | b -> both pdb and mmcif | p ->pdb | m -> mmcif*/
|
||||
|
||||
} s_fparams ;
|
||||
|
||||
|
||||
@@ -25,12 +25,17 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
|
||||
#include "fparams.h"
|
||||
#include "fpout.h"
|
||||
#include "topology.h"
|
||||
#include "read_mmcif.h"
|
||||
|
||||
#include "memhandler.h"
|
||||
|
||||
#include "libmolfile_plugin.h"
|
||||
#include "molfile_plugin.h"
|
||||
|
||||
/* ------------------------------PROTOTYPES-----------------------------------*/
|
||||
|
||||
|
||||
void process_pdb(char *pdbname, s_fparams *params) ;
|
||||
|
||||
s_pdb *open_file_format(char *fpath, const char *ligan, const int keep_lig, int model_number, s_fparams *par);
|
||||
void read_file_format(s_pdb *pdb, const char *ligan, const int keep_lig, int model_number, s_fparams *par);
|
||||
#endif
|
||||
|
||||
28
headers/read_mmcif.h
Normal file
28
headers/read_mmcif.h
Normal file
@@ -0,0 +1,28 @@
|
||||
#ifndef DH_READ_MMCIF
|
||||
#define DH_READ_MMCIF
|
||||
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
|
||||
#include "atom.h"
|
||||
#include "pertable.h"
|
||||
#include "utils.h"
|
||||
#include "memhandler.h"
|
||||
#include "math.h"
|
||||
#include "fparams.h"
|
||||
#include "rpdb.h"
|
||||
|
||||
|
||||
/*
|
||||
* Plugin header files; get plugin source from www.ks.uiuc.edu/Research/vmd"
|
||||
*/
|
||||
#include "libmolfile_plugin.h"
|
||||
#include "molfile_plugin.h"
|
||||
|
||||
s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_number, s_fparams *par);
|
||||
|
||||
void print_molfile_atom_t(molfile_atom_t *at_in, molfile_timestep_t ts_in, int inatoms);
|
||||
void write_files(molfile_atom_t *at_in, molfile_timestep_t ts_in, int inatoms, int optflags, char *filetype);
|
||||
void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_number, s_fparams *params);
|
||||
#endif
|
||||
@@ -141,5 +141,6 @@ s_atom_ptr_list *init_atom_ptr_list(void);
|
||||
|
||||
|
||||
short get_mm_type_from_element(char *symbol);
|
||||
int chains_to_delete(char *chains_selected, char *current_line_chain, int is_chain_kept);
|
||||
int chains_to_delete(char *chains_selected, char current_line_chain, int is_chain_kept);
|
||||
int is_ligand(char *chains_selected, char current_line_chain);
|
||||
#endif
|
||||
|
||||
@@ -148,6 +148,7 @@ int is_in_lst_vert_p(s_vvertice **lst_vert, int nb_vert, s_vvertice *vert);
|
||||
|
||||
void write_pqr_vert(FILE *f, s_vvertice *v, int i) ;
|
||||
void write_pdb_vert(FILE *f, s_vvertice *v, int i) ;
|
||||
void write_mmcif_vert(FILE *f, s_vvertice *v, int i);
|
||||
float get_verts_volume_ptr(s_vvertice **verts, int nvert, int niter,float correct);
|
||||
float get_convex_hull_volume(s_vvertice **verts, int nvert);
|
||||
|
||||
|
||||
@@ -30,6 +30,8 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
|
||||
void write_visualization(char *pdb_name,char *pdb_out_name);
|
||||
void write_vmd(char *pdb_name,char *pdb_out_name);
|
||||
void write_pymol(char *pdb_name,char *pdb_out_name);
|
||||
void write_vmd_mmcif(char *pdb_name,char *pdb_out_name);
|
||||
void write_pymol_mmcif(char *pdb_name, char *pdb_out_name);
|
||||
|
||||
#endif
|
||||
|
||||
|
||||
@@ -25,4 +25,9 @@ void write_pqr_atom_line(FILE *f, const char *rec_name, int id, const char *atom
|
||||
char alt_loc, const char *res_name, const char *chain,
|
||||
int res_id, const char insert, float x, float y, float z, float charge,
|
||||
float radius);
|
||||
|
||||
void write_mmcif_atom_line(FILE *f, const char rec_name[], int id, const char atom_name[],
|
||||
char alt_loc, const char res_name[], const char chain[],
|
||||
int res_id, const char insert, float x, float y, float z, float occ,
|
||||
float bfactor, int abpa, const char *symbol, int charge,float abpa_prob) ;
|
||||
#endif
|
||||
|
||||
@@ -41,4 +41,7 @@ void write_each_pocket_for_DB(const char out_path[], c_lst_pockets *pockets,s_pd
|
||||
void write_pocket_pqr_DB(const char out[], s_pocket *pocket);
|
||||
void write_pocket_pdb_DB(const char out[], s_pocket *pocket,s_pdb *pdb);
|
||||
|
||||
void write_mmcif_atoms(FILE *f, s_atm *atoms, int natoms);
|
||||
void write_pockets_single_mmcif(const char out[], s_pdb *pdb, c_lst_pockets *pockets);
|
||||
void write_pocket_mmcif(const char out[], s_pocket *pocket);
|
||||
#endif
|
||||
|
||||
20
makefile
20
makefile
@@ -22,7 +22,8 @@ TPOCKET = tpocket
|
||||
DPOCKET = dpocket
|
||||
MDPOCKET = mdpocket
|
||||
CHECK = pcheck
|
||||
PROGFPOCKET = $(PATH_BIN)$(FPOCKET) $(PATH_BIN)$(TPOCKET) $(PATH_BIN)$(DPOCKET) $(PATH_BIN)$(MDPOCKET)
|
||||
PROGFPOCKET = $(PATH_BIN)$(FPOCKET) $(PATH_BIN)$(TPOCKET) $(PATH_BIN)$(DPOCKET)
|
||||
PROGALL = $(PATH_BIN)$(FPOCKET) $(PATH_BIN)$(TPOCKET) $(PATH_BIN)$(DPOCKET) $(PATH_BIN)$(MDPOCKET)
|
||||
PROGMDPOCKET = $(PATH_BIN)$(MDPOCKET)
|
||||
|
||||
ifeq ($(CXX),g++)
|
||||
@@ -40,7 +41,7 @@ endif
|
||||
CGSL = -DMD_NOT_USE_GSL -I$(PATH_GSL)include
|
||||
COS = -DM_OS_LINUX
|
||||
CDEBUG = -DMNO_MEM_DEBUG
|
||||
CWARN = -Wall -Wextra -Wwrite-strings -Wstrict-prototypes
|
||||
CWARN = -W -Wextra -Wwrite-strings -Wstrict-prototypes
|
||||
|
||||
CFLAGS = $(CWARN) $(COS) $(CDEBUG) -O2 -g -pg -std=c99 -I$(PLUGINDIR)/include -I$(PLUGINDIR)/$(ARCH)/molfile
|
||||
QCFLAGS = -O -g -pg -ansi
|
||||
@@ -82,7 +83,7 @@ CHOBJ = $(PATH_OBJ)check.o $(PATH_OBJ)psorting.o $(PATH_OBJ)pscoring.o \
|
||||
$(PATH_OBJ)descriptors.o $(PATH_OBJ)aa.o \
|
||||
$(PATH_OBJ)fpocket.o $(PATH_OBJ)write_visu.o $(PATH_OBJ)fpout.o \
|
||||
$(PATH_OBJ)atom.o $(PATH_OBJ)writepocket.o $(PATH_OBJ)voronoi_lst.o \
|
||||
$(PATH_OBJ)neighbor.o $(PATH_OBJ)asa.o $(PATH_OBJ)clusterlib.o $(PATH_OBJ)energy.o \
|
||||
$(PATH_OBJ)neighbor.o $(PATH_OBJ)asa.o $(PATH_OBJ)clusterlib.o $(PATH_OBJ)energy.o $(PATH_OBJ)read_mmcif.o \
|
||||
|
||||
|
||||
FPOBJ = $(PATH_OBJ)fpmain.o $(PATH_OBJ)psorting.o $(PATH_OBJ)pscoring.o \
|
||||
@@ -93,7 +94,7 @@ FPOBJ = $(PATH_OBJ)fpmain.o $(PATH_OBJ)psorting.o $(PATH_OBJ)pscoring.o \
|
||||
$(PATH_OBJ)descriptors.o $(PATH_OBJ)aa.o \
|
||||
$(PATH_OBJ)fpocket.o $(PATH_OBJ)write_visu.o $(PATH_OBJ)fpout.o \
|
||||
$(PATH_OBJ)atom.o $(PATH_OBJ)writepocket.o $(PATH_OBJ)voronoi_lst.o $(PATH_OBJ)asa.o \
|
||||
$(PATH_OBJ)clusterlib.o $(PATH_OBJ)energy.o $(PATH_OBJ)topology.o \
|
||||
$(PATH_OBJ)clusterlib.o $(PATH_OBJ)energy.o $(PATH_OBJ)topology.o $(PATH_OBJ)read_mmcif.o \
|
||||
$(QOBJS)
|
||||
|
||||
TPOBJ = $(PATH_OBJ)tpmain.o $(PATH_OBJ)psorting.o $(PATH_OBJ)pscoring.o \
|
||||
@@ -105,7 +106,7 @@ TPOBJ = $(PATH_OBJ)tpmain.o $(PATH_OBJ)psorting.o $(PATH_OBJ)pscoring.o \
|
||||
$(PATH_OBJ)aa.o $(PATH_OBJ)fpocket.o $(PATH_OBJ)write_visu.o \
|
||||
$(PATH_OBJ)fpout.o $(PATH_OBJ)atom.o $(PATH_OBJ)writepocket.o \
|
||||
$(PATH_OBJ)voronoi_lst.o $(PATH_OBJ)neighbor.o $(PATH_OBJ)asa.o\
|
||||
$(PATH_OBJ)clusterlib.o $(PATH_OBJ)energy.o $(PATH_OBJ)topology.o\
|
||||
$(PATH_OBJ)clusterlib.o $(PATH_OBJ)energy.o $(PATH_OBJ)topology.o $(PATH_OBJ)read_mmcif.o\
|
||||
$(PATH_QHULL)/qvoronoi/qvoronoi.o $(PATH_QHULL)/qconvex/qconvex.o
|
||||
|
||||
DPOBJ = $(PATH_OBJ)dpmain.o $(PATH_OBJ)psorting.o $(PATH_OBJ)pscoring.o \
|
||||
@@ -116,7 +117,7 @@ DPOBJ = $(PATH_OBJ)dpmain.o $(PATH_OBJ)psorting.o $(PATH_OBJ)pscoring.o \
|
||||
$(PATH_OBJ)writepdb.o $(PATH_OBJ)memhandler.o $(PATH_OBJ)pocket.o \
|
||||
$(PATH_OBJ)refine.o $(PATH_OBJ)fparams.o \
|
||||
$(PATH_OBJ)fpocket.o $(PATH_OBJ)fpout.o $(PATH_OBJ)writepocket.o \
|
||||
$(PATH_OBJ)write_visu.o $(PATH_OBJ)asa.o\
|
||||
$(PATH_OBJ)write_visu.o $(PATH_OBJ)asa.o $(PATH_OBJ)read_mmcif.o\
|
||||
$(PATH_OBJ)voronoi_lst.o $(PATH_OBJ)clusterlib.o $(QOBJS) $(PATH_OBJ)energy.o \
|
||||
$(PATH_OBJ)topology.o
|
||||
|
||||
@@ -128,7 +129,7 @@ MDPOBJ = $(PATH_OBJ)mdpmain.o $(PATH_OBJ)mdpocket.o $(PATH_OBJ)mdpbase.o $(PATH_
|
||||
$(PATH_OBJ)writepdb.o $(PATH_OBJ)memhandler.o $(PATH_OBJ)pocket.o \
|
||||
$(PATH_OBJ)refine.o $(PATH_OBJ)fparams.o \
|
||||
$(PATH_OBJ)fpocket.o $(PATH_OBJ)fpout.o \
|
||||
$(PATH_OBJ)writepocket.o $(PATH_OBJ)write_visu.o $(PATH_OBJ)asa.o \
|
||||
$(PATH_OBJ)writepocket.o $(PATH_OBJ)write_visu.o $(PATH_OBJ)asa.o $(PATH_OBJ)read_mmcif.o\
|
||||
$(PATH_OBJ)voronoi_lst.o $(PATH_OBJ)clusterlib.o $(QOBJS) $(PATH_OBJ)energy.o $(PATH_OBJ)topology.o
|
||||
|
||||
#------------------------------------------------------------
|
||||
@@ -148,10 +149,7 @@ $(PATH_OBJ)%.o: $(PATH_SRC)%.cpp
|
||||
# RULES FOR EXECUTABLES
|
||||
#-----------------------------------------------------------
|
||||
|
||||
all:
|
||||
make qhull
|
||||
make fpocket
|
||||
make mdpocket
|
||||
all: qhull $(PROGALL)
|
||||
fpocket: qhull $(PROGFPOCKET) # $(PATH_BIN)$(CHECK)
|
||||
mdpocket: qhull $(PROGMDPOCKET)
|
||||
|
||||
|
||||
Binary file not shown.
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@@ -1,355 +0,0 @@
|
||||
#ifndef LIBMOLFILE_PLUGIN_H
|
||||
#define LIBMOLFILE_PLUGIN_H
|
||||
#include "vmdplugin.h"
|
||||
|
||||
#ifdef __cplusplus
|
||||
extern "C" {
|
||||
#endif
|
||||
|
||||
extern int molfile_biomoccaplugin_init(void);
|
||||
extern int molfile_biomoccaplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_biomoccaplugin_fini(void);
|
||||
extern int molfile_cpmdplugin_init(void);
|
||||
extern int molfile_cpmdplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_cpmdplugin_fini(void);
|
||||
extern int molfile_psfplugin_init(void);
|
||||
extern int molfile_psfplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_psfplugin_fini(void);
|
||||
extern int molfile_pdbplugin_init(void);
|
||||
extern int molfile_pdbplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_pdbplugin_fini(void);
|
||||
extern int molfile_dcdplugin_init(void);
|
||||
extern int molfile_dcdplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_dcdplugin_fini(void);
|
||||
extern int molfile_babelplugin_init(void);
|
||||
extern int molfile_babelplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_babelplugin_fini(void);
|
||||
extern int molfile_gromacsplugin_init(void);
|
||||
extern int molfile_gromacsplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_gromacsplugin_fini(void);
|
||||
extern int molfile_parmplugin_init(void);
|
||||
extern int molfile_parmplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_parmplugin_fini(void);
|
||||
extern int molfile_crdplugin_init(void);
|
||||
extern int molfile_crdplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_crdplugin_fini(void);
|
||||
extern int molfile_namdbinplugin_init(void);
|
||||
extern int molfile_namdbinplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_namdbinplugin_fini(void);
|
||||
extern int molfile_binposplugin_init(void);
|
||||
extern int molfile_binposplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_binposplugin_fini(void);
|
||||
extern int molfile_graspplugin_init(void);
|
||||
extern int molfile_graspplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_graspplugin_fini(void);
|
||||
extern int molfile_msmsplugin_init(void);
|
||||
extern int molfile_msmsplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_msmsplugin_fini(void);
|
||||
extern int molfile_stlplugin_init(void);
|
||||
extern int molfile_stlplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_stlplugin_fini(void);
|
||||
extern int molfile_cubeplugin_init(void);
|
||||
extern int molfile_cubeplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_cubeplugin_fini(void);
|
||||
extern int molfile_edmplugin_init(void);
|
||||
extern int molfile_edmplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_edmplugin_fini(void);
|
||||
extern int molfile_ccp4plugin_init(void);
|
||||
extern int molfile_ccp4plugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_ccp4plugin_fini(void);
|
||||
extern int molfile_dsn6plugin_init(void);
|
||||
extern int molfile_dsn6plugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_dsn6plugin_fini(void);
|
||||
extern int molfile_brixplugin_init(void);
|
||||
extern int molfile_brixplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_brixplugin_fini(void);
|
||||
extern int molfile_pltplugin_init(void);
|
||||
extern int molfile_pltplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_pltplugin_fini(void);
|
||||
extern int molfile_raster3dplugin_init(void);
|
||||
extern int molfile_raster3dplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_raster3dplugin_fini(void);
|
||||
extern int molfile_parm7plugin_init(void);
|
||||
extern int molfile_parm7plugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_parm7plugin_fini(void);
|
||||
extern int molfile_rst7plugin_init(void);
|
||||
extern int molfile_rst7plugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_rst7plugin_fini(void);
|
||||
extern int molfile_tinkerplugin_init(void);
|
||||
extern int molfile_tinkerplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_tinkerplugin_fini(void);
|
||||
extern int molfile_uhbdplugin_init(void);
|
||||
extern int molfile_uhbdplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_uhbdplugin_fini(void);
|
||||
extern int molfile_vaspchgcarplugin_init(void);
|
||||
extern int molfile_vaspchgcarplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_vaspchgcarplugin_fini(void);
|
||||
extern int molfile_vaspposcarplugin_init(void);
|
||||
extern int molfile_vaspposcarplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_vaspposcarplugin_fini(void);
|
||||
extern int molfile_vaspoutcarplugin_init(void);
|
||||
extern int molfile_vaspoutcarplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_vaspoutcarplugin_fini(void);
|
||||
extern int molfile_vaspxdatcarplugin_init(void);
|
||||
extern int molfile_vaspxdatcarplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_vaspxdatcarplugin_fini(void);
|
||||
extern int molfile_vaspxmlplugin_init(void);
|
||||
extern int molfile_vaspxmlplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_vaspxmlplugin_fini(void);
|
||||
extern int molfile_dlpolyplugin_init(void);
|
||||
extern int molfile_dlpolyplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_dlpolyplugin_fini(void);
|
||||
extern int molfile_lammpsplugin_init(void);
|
||||
extern int molfile_lammpsplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_lammpsplugin_fini(void);
|
||||
extern int molfile_vtfplugin_init(void);
|
||||
extern int molfile_vtfplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_vtfplugin_fini(void);
|
||||
extern int molfile_xyzplugin_init(void);
|
||||
extern int molfile_xyzplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_xyzplugin_fini(void);
|
||||
extern int molfile_corplugin_init(void);
|
||||
extern int molfile_corplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_corplugin_fini(void);
|
||||
extern int molfile_moldenplugin_init(void);
|
||||
extern int molfile_moldenplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_moldenplugin_fini(void);
|
||||
extern int molfile_phiplugin_init(void);
|
||||
extern int molfile_phiplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_phiplugin_fini(void);
|
||||
extern int molfile_pbeqplugin_init(void);
|
||||
extern int molfile_pbeqplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_pbeqplugin_fini(void);
|
||||
extern int molfile_grdplugin_init(void);
|
||||
extern int molfile_grdplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_grdplugin_fini(void);
|
||||
extern int molfile_situsplugin_init(void);
|
||||
extern int molfile_situsplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_situsplugin_fini(void);
|
||||
extern int molfile_dxplugin_init(void);
|
||||
extern int molfile_dxplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_dxplugin_fini(void);
|
||||
extern int molfile_spiderplugin_init(void);
|
||||
extern int molfile_spiderplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_spiderplugin_fini(void);
|
||||
extern int molfile_mapplugin_init(void);
|
||||
extern int molfile_mapplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_mapplugin_fini(void);
|
||||
extern int molfile_avsplugin_init(void);
|
||||
extern int molfile_avsplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_avsplugin_fini(void);
|
||||
extern int molfile_fs4plugin_init(void);
|
||||
extern int molfile_fs4plugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_fs4plugin_fini(void);
|
||||
extern int molfile_pqrplugin_init(void);
|
||||
extern int molfile_pqrplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_pqrplugin_fini(void);
|
||||
extern int molfile_mol2plugin_init(void);
|
||||
extern int molfile_mol2plugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_mol2plugin_fini(void);
|
||||
extern int molfile_gridplugin_init(void);
|
||||
extern int molfile_gridplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_gridplugin_fini(void);
|
||||
extern int molfile_carplugin_init(void);
|
||||
extern int molfile_carplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_carplugin_fini(void);
|
||||
extern int molfile_mdfplugin_init(void);
|
||||
extern int molfile_mdfplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_mdfplugin_fini(void);
|
||||
extern int molfile_gamessplugin_init(void);
|
||||
extern int molfile_gamessplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_gamessplugin_fini(void);
|
||||
extern int molfile_xsfplugin_init(void);
|
||||
extern int molfile_xsfplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_xsfplugin_fini(void);
|
||||
extern int molfile_bgfplugin_init(void);
|
||||
extern int molfile_bgfplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_bgfplugin_fini(void);
|
||||
extern int molfile_xbgfplugin_init(void);
|
||||
extern int molfile_xbgfplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_xbgfplugin_fini(void);
|
||||
extern int molfile_webpdbplugin_init(void);
|
||||
extern int molfile_webpdbplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_webpdbplugin_fini(void);
|
||||
extern int molfile_netcdfplugin_init(void);
|
||||
extern int molfile_netcdfplugin_register(void *, vmdplugin_register_cb);
|
||||
extern int molfile_netcdfplugin_fini(void);
|
||||
|
||||
#define MOLFILE_INIT_ALL \
|
||||
molfile_biomoccaplugin_init(); \
|
||||
molfile_cpmdplugin_init(); \
|
||||
molfile_psfplugin_init(); \
|
||||
molfile_pdbplugin_init(); \
|
||||
molfile_dcdplugin_init(); \
|
||||
molfile_babelplugin_init(); \
|
||||
molfile_gromacsplugin_init(); \
|
||||
molfile_parmplugin_init(); \
|
||||
molfile_crdplugin_init(); \
|
||||
molfile_namdbinplugin_init(); \
|
||||
molfile_binposplugin_init(); \
|
||||
molfile_graspplugin_init(); \
|
||||
molfile_msmsplugin_init(); \
|
||||
molfile_stlplugin_init(); \
|
||||
molfile_cubeplugin_init(); \
|
||||
molfile_edmplugin_init(); \
|
||||
molfile_ccp4plugin_init(); \
|
||||
molfile_dsn6plugin_init(); \
|
||||
molfile_brixplugin_init(); \
|
||||
molfile_pltplugin_init(); \
|
||||
molfile_raster3dplugin_init(); \
|
||||
molfile_parm7plugin_init(); \
|
||||
molfile_rst7plugin_init(); \
|
||||
molfile_tinkerplugin_init(); \
|
||||
molfile_uhbdplugin_init(); \
|
||||
molfile_vaspchgcarplugin_init(); \
|
||||
molfile_vaspposcarplugin_init(); \
|
||||
molfile_vaspoutcarplugin_init(); \
|
||||
molfile_vaspxdatcarplugin_init(); \
|
||||
molfile_vaspxmlplugin_init(); \
|
||||
molfile_dlpolyplugin_init(); \
|
||||
molfile_lammpsplugin_init(); \
|
||||
molfile_vtfplugin_init(); \
|
||||
molfile_xyzplugin_init(); \
|
||||
molfile_corplugin_init(); \
|
||||
molfile_moldenplugin_init(); \
|
||||
molfile_phiplugin_init(); \
|
||||
molfile_pbeqplugin_init(); \
|
||||
molfile_grdplugin_init(); \
|
||||
molfile_situsplugin_init(); \
|
||||
molfile_dxplugin_init(); \
|
||||
molfile_spiderplugin_init(); \
|
||||
molfile_mapplugin_init(); \
|
||||
molfile_avsplugin_init(); \
|
||||
molfile_fs4plugin_init(); \
|
||||
molfile_pqrplugin_init(); \
|
||||
molfile_mol2plugin_init(); \
|
||||
molfile_gridplugin_init(); \
|
||||
molfile_carplugin_init(); \
|
||||
molfile_mdfplugin_init(); \
|
||||
molfile_gamessplugin_init(); \
|
||||
molfile_xsfplugin_init(); \
|
||||
molfile_bgfplugin_init(); \
|
||||
molfile_xbgfplugin_init(); \
|
||||
molfile_webpdbplugin_init(); \
|
||||
molfile_netcdfplugin_init(); \
|
||||
|
||||
#define MOLFILE_REGISTER_ALL(v, cb) \
|
||||
molfile_biomoccaplugin_register(v, cb); \
|
||||
molfile_cpmdplugin_register(v, cb); \
|
||||
molfile_psfplugin_register(v, cb); \
|
||||
molfile_pdbplugin_register(v, cb); \
|
||||
molfile_dcdplugin_register(v, cb); \
|
||||
molfile_babelplugin_register(v, cb); \
|
||||
molfile_gromacsplugin_register(v, cb); \
|
||||
molfile_parmplugin_register(v, cb); \
|
||||
molfile_crdplugin_register(v, cb); \
|
||||
molfile_namdbinplugin_register(v, cb); \
|
||||
molfile_binposplugin_register(v, cb); \
|
||||
molfile_graspplugin_register(v, cb); \
|
||||
molfile_msmsplugin_register(v, cb); \
|
||||
molfile_stlplugin_register(v, cb); \
|
||||
molfile_cubeplugin_register(v, cb); \
|
||||
molfile_edmplugin_register(v, cb); \
|
||||
molfile_ccp4plugin_register(v, cb); \
|
||||
molfile_dsn6plugin_register(v, cb); \
|
||||
molfile_brixplugin_register(v, cb); \
|
||||
molfile_pltplugin_register(v, cb); \
|
||||
molfile_raster3dplugin_register(v, cb); \
|
||||
molfile_parm7plugin_register(v, cb); \
|
||||
molfile_rst7plugin_register(v, cb); \
|
||||
molfile_tinkerplugin_register(v, cb); \
|
||||
molfile_uhbdplugin_register(v, cb); \
|
||||
molfile_vaspchgcarplugin_register(v, cb); \
|
||||
molfile_vaspposcarplugin_register(v, cb); \
|
||||
molfile_vaspoutcarplugin_register(v, cb); \
|
||||
molfile_vaspxdatcarplugin_register(v, cb); \
|
||||
molfile_vaspxmlplugin_register(v, cb); \
|
||||
molfile_dlpolyplugin_register(v, cb); \
|
||||
molfile_lammpsplugin_register(v, cb); \
|
||||
molfile_vtfplugin_register(v, cb); \
|
||||
molfile_xyzplugin_register(v, cb); \
|
||||
molfile_corplugin_register(v, cb); \
|
||||
molfile_moldenplugin_register(v, cb); \
|
||||
molfile_phiplugin_register(v, cb); \
|
||||
molfile_pbeqplugin_register(v, cb); \
|
||||
molfile_grdplugin_register(v, cb); \
|
||||
molfile_situsplugin_register(v, cb); \
|
||||
molfile_dxplugin_register(v, cb); \
|
||||
molfile_spiderplugin_register(v, cb); \
|
||||
molfile_mapplugin_register(v, cb); \
|
||||
molfile_avsplugin_register(v, cb); \
|
||||
molfile_fs4plugin_register(v, cb); \
|
||||
molfile_pqrplugin_register(v, cb); \
|
||||
molfile_mol2plugin_register(v, cb); \
|
||||
molfile_gridplugin_register(v, cb); \
|
||||
molfile_carplugin_register(v, cb); \
|
||||
molfile_mdfplugin_register(v, cb); \
|
||||
molfile_gamessplugin_register(v, cb); \
|
||||
molfile_xsfplugin_register(v, cb); \
|
||||
molfile_bgfplugin_register(v, cb); \
|
||||
molfile_xbgfplugin_register(v, cb); \
|
||||
molfile_webpdbplugin_register(v, cb); \
|
||||
molfile_netcdfplugin_register(v, cb); \
|
||||
|
||||
#define MOLFILE_FINI_ALL \
|
||||
molfile_biomoccaplugin_fini(); \
|
||||
molfile_cpmdplugin_fini(); \
|
||||
molfile_psfplugin_fini(); \
|
||||
molfile_pdbplugin_fini(); \
|
||||
molfile_dcdplugin_fini(); \
|
||||
molfile_babelplugin_fini(); \
|
||||
molfile_gromacsplugin_fini(); \
|
||||
molfile_parmplugin_fini(); \
|
||||
molfile_crdplugin_fini(); \
|
||||
molfile_namdbinplugin_fini(); \
|
||||
molfile_binposplugin_fini(); \
|
||||
molfile_graspplugin_fini(); \
|
||||
molfile_msmsplugin_fini(); \
|
||||
molfile_stlplugin_fini(); \
|
||||
molfile_cubeplugin_fini(); \
|
||||
molfile_edmplugin_fini(); \
|
||||
molfile_ccp4plugin_fini(); \
|
||||
molfile_dsn6plugin_fini(); \
|
||||
molfile_brixplugin_fini(); \
|
||||
molfile_pltplugin_fini(); \
|
||||
molfile_raster3dplugin_fini(); \
|
||||
molfile_parm7plugin_fini(); \
|
||||
molfile_rst7plugin_fini(); \
|
||||
molfile_tinkerplugin_fini(); \
|
||||
molfile_uhbdplugin_fini(); \
|
||||
molfile_vaspchgcarplugin_fini(); \
|
||||
molfile_vaspposcarplugin_fini(); \
|
||||
molfile_vaspoutcarplugin_fini(); \
|
||||
molfile_vaspxdatcarplugin_fini(); \
|
||||
molfile_vaspxmlplugin_fini(); \
|
||||
molfile_dlpolyplugin_fini(); \
|
||||
molfile_lammpsplugin_fini(); \
|
||||
molfile_vtfplugin_fini(); \
|
||||
molfile_xyzplugin_fini(); \
|
||||
molfile_corplugin_fini(); \
|
||||
molfile_moldenplugin_fini(); \
|
||||
molfile_phiplugin_fini(); \
|
||||
molfile_pbeqplugin_fini(); \
|
||||
molfile_grdplugin_fini(); \
|
||||
molfile_situsplugin_fini(); \
|
||||
molfile_dxplugin_fini(); \
|
||||
molfile_spiderplugin_fini(); \
|
||||
molfile_mapplugin_fini(); \
|
||||
molfile_avsplugin_fini(); \
|
||||
molfile_fs4plugin_fini(); \
|
||||
molfile_pqrplugin_fini(); \
|
||||
molfile_mol2plugin_fini(); \
|
||||
molfile_gridplugin_fini(); \
|
||||
molfile_carplugin_fini(); \
|
||||
molfile_mdfplugin_fini(); \
|
||||
molfile_gamessplugin_fini(); \
|
||||
molfile_xsfplugin_fini(); \
|
||||
molfile_bgfplugin_fini(); \
|
||||
molfile_xbgfplugin_fini(); \
|
||||
molfile_webpdbplugin_fini(); \
|
||||
molfile_netcdfplugin_fini(); \
|
||||
|
||||
#ifdef __cplusplus
|
||||
}
|
||||
#endif
|
||||
#endif
|
||||
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Load Diff
@@ -1,12 +0,0 @@
|
||||
# Tcl package index file, version 1.2
|
||||
# This file is generated by the "pkg_mkIndex" command
|
||||
# and sourced either when an application starts up or
|
||||
# by a "package unknown" script. It invokes the
|
||||
# "package ifneeded" command to set up package-related
|
||||
# information so that packages will be loaded automatically
|
||||
# in response to "package require" commands. When this
|
||||
# script is sourced, the variable $dir must contain the
|
||||
# full path name of this file's directory.
|
||||
|
||||
package ifneeded psfcheck 0 [list load [file join $dir psfcheck.so]]
|
||||
package ifneeded autopsf 1.2 "source [list [file join $dir autopsf.tcl]] ; set env(AUTOPSFDIR) [list $dir]"
|
||||
Binary file not shown.
@@ -1,259 +0,0 @@
|
||||
package require exectool
|
||||
package provide cionize 1.0
|
||||
|
||||
namespace eval ::cionize:: {
|
||||
namespace export cionize
|
||||
|
||||
# variables for package settings
|
||||
variable jobname ;# prefix for output files
|
||||
variable tmpname ;# prefix for temporary files
|
||||
variable r_ion_solute
|
||||
variable r_ion_ion
|
||||
variable bordersize
|
||||
variable gridspacing
|
||||
variable gridfile
|
||||
variable xyzdim
|
||||
variable gridout ;# Grid output before ion placement
|
||||
variable gridafter ;# Grid output after ion placement
|
||||
variable ions ;# list of ions to be placed
|
||||
variable nprocs
|
||||
variable runtype ;# Calculation method to be used
|
||||
variable molid ;# Molecule ID to run on
|
||||
}
|
||||
|
||||
proc ::cionize::init_defaults {} {
|
||||
# Initialize all of the namespace variables. Should be called before each run
|
||||
variable jobname
|
||||
variable tmpname
|
||||
variable r_ion_solute
|
||||
variable r_ion_ion
|
||||
variable bordersize
|
||||
variable gridspacing
|
||||
variable gridfile
|
||||
variable gridafter
|
||||
variable xyzdim
|
||||
variable gridout
|
||||
variable ions
|
||||
variable nprocs
|
||||
variable runtype
|
||||
variable molid
|
||||
|
||||
set jobname "cionize"
|
||||
set tmpname "cionize-temp"
|
||||
set r_ion_solute ""
|
||||
set r_ion_ion ""
|
||||
set bordersize ""
|
||||
set gridspacing ""
|
||||
set gridfile ""
|
||||
set xyzdim ""
|
||||
set gridout ""
|
||||
set gridafter ""
|
||||
set ions ""
|
||||
set nprocs 1
|
||||
set runtype "single"
|
||||
set molid ""
|
||||
}
|
||||
|
||||
proc ::cionize::show_usage {} {
|
||||
# Give usage instructions
|
||||
puts "cionize: Calculate a coulombic potential and place ions"
|
||||
puts "Usage: cionize -mol <molnumber> <option1> <option2>..."
|
||||
puts "Options:"
|
||||
puts " Switches:"
|
||||
puts " -mg (Use multilevel summation approximation)"
|
||||
puts " -dp (Use double precision calculation)"
|
||||
puts " Single argument options:"
|
||||
puts " -mol <molecule> (REQUIRED: Run on molid <molecule>)"
|
||||
puts " -prefix <prefix> (Use <prefix> as the prefix for output files"
|
||||
puts " -ris <radius> (Enforce a minimum ion-solute distance of <radius>)"
|
||||
puts " -rii <radius> (Enforce a minimum ion-ion distance of <radius>)"
|
||||
puts " -border <length> (Pad the system by <length> in each direction)"
|
||||
puts " -gridspacing <spacing> (Density of potential grid)"
|
||||
puts " -ingrid <file> (Read grid from <file> instead of calculating it)"
|
||||
puts " -xyzdim <xmin ymin zmin xmax ymax zmax> (Use specified grid boundary)"
|
||||
puts " -go <file> (Output grid to <file> after potential calculation)"
|
||||
puts " -ga <file> (Output grid to <file> after ion placement)"
|
||||
puts " -np <number> (Use <number> processors)"
|
||||
puts " Ion placement options:"
|
||||
puts " -ions <ionstring> (Place ions contained in <ionstring>"
|
||||
puts " <ionstring> should be a set of bracket enclosed ions, with each ion"
|
||||
puts " containing the information {name number charge} for the ion to be"
|
||||
puts " placed. <ionstring> should be contained in quotes; e.g.,"
|
||||
puts " \"\{SOD 4 1\} \{CLA 4 -1\}\" places 4 sodium and for chloride ions."
|
||||
}
|
||||
|
||||
proc ::cionize::cionize { args } {
|
||||
# perform a cionize run
|
||||
|
||||
puts "Starting cionize..."
|
||||
|
||||
init_defaults
|
||||
|
||||
set numargs [llength $args]
|
||||
if {$numargs == 0} {show_usage; return}
|
||||
|
||||
# Parse command line arguments
|
||||
if {[parse_args $args] != 0} {show_usage; return}
|
||||
|
||||
# Construct cionize input file
|
||||
set infile [write_input_file]
|
||||
|
||||
# Run cionize
|
||||
run_cionize $infile
|
||||
|
||||
# clean up
|
||||
cleanup_cionize_run
|
||||
|
||||
puts "cionize completed! See VMD Console for details"
|
||||
|
||||
}
|
||||
|
||||
proc ::cionize::parse_args {argblock} {
|
||||
# Parse all command line arguments to cionize and set the correct
|
||||
# namespace variables. Return 0 on success, other value on failure
|
||||
variable jobname
|
||||
variable tmpname
|
||||
variable r_ion_solute
|
||||
variable r_ion_ion
|
||||
variable bordersize
|
||||
variable gridspacing
|
||||
variable gridfile
|
||||
variable gridafter
|
||||
variable xyzdim
|
||||
variable gridout
|
||||
variable ions
|
||||
variable nprocs
|
||||
variable runtype
|
||||
variable molid
|
||||
|
||||
#puts "Argblock: $argblock"
|
||||
#puts "Args: [lindex $argblock 0]"
|
||||
set args $argblock
|
||||
|
||||
set argnum 0
|
||||
set arglist $args
|
||||
|
||||
# Parse switches
|
||||
foreach i $args {
|
||||
if {$i == "-mg"} {
|
||||
if {$runtype == "double"} {
|
||||
puts "WARNING: Can only choose one of -dp or -mg. Using multilevel summation."
|
||||
}
|
||||
set runtype "multigrid"
|
||||
set arglist [lreplace $arglist $argnum $argnum]
|
||||
continue
|
||||
}
|
||||
|
||||
if {$i == "-dp"} {
|
||||
if {$runtype == "multigrid"} {
|
||||
puts "WARNING: Can only choose one of -dp or -mg. Using double precision."
|
||||
}
|
||||
set runtype "double"
|
||||
set arglist [lreplace $arglist $argnum $argnum]
|
||||
continue
|
||||
}
|
||||
|
||||
incr argnum
|
||||
}
|
||||
|
||||
# Parse single option variables
|
||||
set otherarglist {}
|
||||
# puts "Arglist: $arglist"
|
||||
foreach {i j} $arglist {
|
||||
# puts "Parsing $i | $j"
|
||||
if {$i == "-mol"} { set molid $j ; continue}
|
||||
if {$i == "-prefix"} {
|
||||
set jobname "$j"
|
||||
set tmpname "$j-temp"
|
||||
continue
|
||||
}
|
||||
if {$i == "-ris"} {set r_ion_solute $j; continue}
|
||||
if {$i == "-rii"} {set r_ion_ion $j; continue}
|
||||
if {$i == "-border"} {set bordersize $j; continue}
|
||||
if {$i == "-ingrid"} {set gridfile $j; continue}
|
||||
if {$i == "-go"} {set gridout $j; continue}
|
||||
if {$i == "-ga"} {set gridafter $j; continue}
|
||||
if {$i == "-np"} {set nprocs $j; continue}
|
||||
if {$i == "-ions"} {set ions $j; continue}
|
||||
if {$i == "-gridspacing"} {set gridspacing $j; continue}
|
||||
lappend otherarglist $i $j
|
||||
}
|
||||
|
||||
if {[llength $otherarglist] > 0} {
|
||||
puts "WARNING: Unrecognized command line arguments $otherarglist will be ignored"
|
||||
}
|
||||
|
||||
return 0
|
||||
|
||||
}
|
||||
|
||||
proc ::cionize::write_input_file {} {
|
||||
# Write an input file for cionize based on the defined namespace variables
|
||||
|
||||
variable jobname
|
||||
variable tmpname
|
||||
variable r_ion_solute
|
||||
variable r_ion_ion
|
||||
variable bordersize
|
||||
variable gridspacing
|
||||
variable gridfile
|
||||
variable gridafter
|
||||
variable xyzdim
|
||||
variable gridout
|
||||
variable ions
|
||||
variable nprocs
|
||||
variable runtype
|
||||
variable molid
|
||||
|
||||
set inpfile [open "$jobname.in" "w"]
|
||||
|
||||
if {$r_ion_solute != ""} {puts $inpfile "R_ION_SOLUTE $r_ion_solute"}
|
||||
if {$r_ion_ion != ""} {puts $inpfile "R_ION_ION $r_ion_ion"}
|
||||
if {$bordersize != ""} {puts $inpfile "BORDERSIZE $bordersize"}
|
||||
if {$gridspacing != ""} {puts $inpfile "GRIDSPACING $gridspacing"}
|
||||
if {$xyzdim != ""} {puts $inpfile "XYZDIM $xyzdim"}
|
||||
if {$gridfile != ""} {puts $inpfile "GRIDFILE $gridfile"}
|
||||
|
||||
puts $inpfile "BEGIN"
|
||||
|
||||
if {$gridout != ""} {puts $inpfile "SAVEGRID $gridout"}
|
||||
set ionnum 1
|
||||
foreach ion $ions {
|
||||
set name [lindex $ion 0]
|
||||
set n [lindex $ion 1]
|
||||
set charge [lindex $ion 2]
|
||||
set oname "$jobname-ions_$ionnum-$name.pdb"
|
||||
puts $inpfile "PLACEION $name $n $charge"
|
||||
puts $inpfile "SAVEION $oname"
|
||||
}
|
||||
if {$gridafter != ""} {puts $inpfile "SAVEGRID $gridafter"}
|
||||
|
||||
close $inpfile
|
||||
return "$jobname.in"
|
||||
}
|
||||
|
||||
proc ::cionize::run_cionize { inputfile } {
|
||||
# Run cionize on the chosen input file
|
||||
global env
|
||||
variable molid
|
||||
variable tmpname
|
||||
variable runtype
|
||||
variable nprocs
|
||||
|
||||
# First write the structure to be ionized
|
||||
set sel [atomselect $molid all]
|
||||
$sel writepqr $tmpname.pqr
|
||||
$sel delete
|
||||
|
||||
# Find and run cionize
|
||||
eval ::ExecTool::exec "$env(CIONIZEBINDIR)/cionize" -i $inputfile -m $runtype -p $nprocs $tmpname.pqr >&@ stdout
|
||||
|
||||
}
|
||||
|
||||
proc ::cionize::cleanup_cionize_run {} {
|
||||
variable tmpname
|
||||
|
||||
file delete [glob "$tmpname*"]
|
||||
}
|
||||
|
||||
|
||||
@@ -1,11 +0,0 @@
|
||||
# Tcl package index file, version 1.0
|
||||
# This file is generated by the "pkg_mkIndex" command
|
||||
# and sourced either when an application starts up or
|
||||
# by a "package unknown" script. It invokes the
|
||||
# "package ifneeded" command to set up package-related
|
||||
# information so that packages will be loaded automatically
|
||||
# in response to "package require" commands. When this
|
||||
# script is sourced, the variable $dir must contain the
|
||||
# full path name of this file's directory.
|
||||
|
||||
package ifneeded cionize 1.0 "source [list [file join $dir cionize.tcl]] ; set env(CIONIZEDIR) [list $dir] ; set env(CIONIZEBINDIR) [list [file join $dir ../../bin/cionize1.0]]"
|
||||
Binary file not shown.
@@ -1,288 +0,0 @@
|
||||
############################################################################
|
||||
#cr
|
||||
#cr (C) Copyright 1995-2003 The Board of Trustees of the
|
||||
#cr University of Illinois
|
||||
#cr All Rights Reserved
|
||||
#cr
|
||||
############################################################################
|
||||
|
||||
|
||||
# Package for using clustalw on sequences obtained from the seqdata package.
|
||||
|
||||
package provide clustalw 1.0
|
||||
package require seqdata 1.0
|
||||
package require phylotree 1.0
|
||||
|
||||
namespace eval ::ClustalW:: {
|
||||
|
||||
# Export the package namespace.
|
||||
namespace export ClustalW
|
||||
|
||||
# Directory to write temp files.
|
||||
global env
|
||||
variable tempDir ""
|
||||
if {[info exists env(TMPDIR)]} {
|
||||
set tempDir $env(TMPDIR)
|
||||
}
|
||||
|
||||
# The prefix for temp files.
|
||||
variable filePrefix "clustalw"
|
||||
|
||||
# The current CPU architecture.
|
||||
variable architecture ""
|
||||
|
||||
# This method sets the temp file options used by thr stamp package.
|
||||
# args: newTempDir - The new temp directory to use.
|
||||
# newFilePrefix - The prefix to use for temp files.
|
||||
proc setTempFileOptions {newTempDir newFilePrefix} {
|
||||
|
||||
# Import global variables.
|
||||
variable tempDir
|
||||
variable filePrefix
|
||||
|
||||
# Set the temp directory and file prefix.
|
||||
set tempDir $newTempDir
|
||||
set filePrefix $newFilePrefix
|
||||
}
|
||||
|
||||
# This method sets the temp file options used by thr stamp package.
|
||||
# args: newTempDir - The new temp directory to use.
|
||||
# newFilePrefix - The prefix to use for temp files.
|
||||
proc setArchitecture {newArchitecture} {
|
||||
|
||||
# Import global variables.
|
||||
variable architecture
|
||||
|
||||
# Set the temp directory and file prefix.
|
||||
set architecture $newArchitecture
|
||||
}
|
||||
|
||||
# Aligns the passed in sequences.
|
||||
# arg: sequences - The list of sequence ids that should be aligned.
|
||||
# return: The list of aligned sequences ids.
|
||||
proc alignSequences {sequenceIDs} {
|
||||
|
||||
# Import global variables.
|
||||
variable tempDir
|
||||
variable filePrefix
|
||||
|
||||
# Figure out the input and output file names.
|
||||
set originalFilename "$tempDir/$filePrefix.original.fasta"
|
||||
set alignedFilename "$tempDir/$filePrefix.aligned.fasta"
|
||||
|
||||
# Get the sequence ids.
|
||||
set sequenceIndices {}
|
||||
array set sequenceMap {}
|
||||
foreach sequenceID $sequenceIDs {
|
||||
lappend sequenceIndices $sequenceID
|
||||
set sequenceMap($sequenceID) [::SeqData::getName $sequenceID]
|
||||
}
|
||||
|
||||
# Save the sequences as a fasta file.
|
||||
SeqData::Fasta::saveSequences $sequenceIDs $originalFilename $sequenceIndices {} 0 0
|
||||
|
||||
# Run clustalw.
|
||||
set output [run -align -infile=$originalFilename -output=fasta -outfile=$alignedFilename -outorder=input]
|
||||
|
||||
# Load the new sequences.
|
||||
set newSequenceIDs [SeqData::Fasta::loadSequences $alignedFilename [array get sequenceMap]]
|
||||
|
||||
# Copy the attributes
|
||||
set originalSequenceIDs $sequenceIDs
|
||||
for {set i 0} {$i < [llength $originalSequenceIDs] && $i < [llength $newSequenceIDs]} {incr i} {
|
||||
::SeqData::copyAttributes [lindex $originalSequenceIDs $i] [lindex $newSequenceIDs $i]
|
||||
}
|
||||
|
||||
# Return the sequences.
|
||||
return $newSequenceIDs
|
||||
}
|
||||
|
||||
# Aligns the passed in sequences.
|
||||
# arg: sequences - The list of sequence ids that should be aligned.
|
||||
# return: The list of aligned sequences ids.
|
||||
proc alignSequencesToProfile { profile sequences } {
|
||||
|
||||
# Import global variables.
|
||||
variable tempDir
|
||||
variable filePrefix
|
||||
|
||||
# Figure out the input and output file names.
|
||||
set profileFilename "$tempDir/$filePrefix.profile.fasta"
|
||||
set sequencesFilename "$tempDir/$filePrefix.sequences.fasta"
|
||||
set alignedFilename "$tempDir/$filePrefix.aligned.fasta"
|
||||
|
||||
# Get the sequence ids.
|
||||
set profileIndices {}
|
||||
set sequenceIndices {}
|
||||
array set sequenceMap {}
|
||||
foreach sequenceID $profile {
|
||||
lappend profileIndices $sequenceID
|
||||
set sequenceMap($sequenceID) [::SeqData::getName $sequenceID]
|
||||
}
|
||||
foreach sequenceID $sequences {
|
||||
lappend sequenceIndices $sequenceID
|
||||
set sequenceMap($sequenceID) [::SeqData::getName $sequenceID]
|
||||
}
|
||||
|
||||
# Save the sequences as a fasta file.
|
||||
::SeqData::Fasta::saveSequences $profile $profileFilename $profileIndices {} 0 1
|
||||
::SeqData::Fasta::saveSequences $sequences $sequencesFilename $sequenceIndices {} 0 0
|
||||
|
||||
# Run clustalw.
|
||||
set output [run -align -profile1=$profileFilename -profile2=$sequencesFilename -sequences -output=fasta -outfile=$alignedFilename -outorder=input]
|
||||
|
||||
# Load the new sequences.
|
||||
set newSequenceIDs [SeqData::Fasta::loadSequences $alignedFilename [array get sequenceMap]]
|
||||
|
||||
# Copy the attributes
|
||||
set originalSequenceIDs [concat $profile $sequences]
|
||||
for {set i 0} {$i < [llength $originalSequenceIDs] && $i < [llength $newSequenceIDs]} {incr i} {
|
||||
::SeqData::copyAttributes [lindex $originalSequenceIDs $i] [lindex $newSequenceIDs $i]
|
||||
}
|
||||
|
||||
# Return the sequences.
|
||||
return $newSequenceIDs
|
||||
}
|
||||
|
||||
proc alignProfiles { profile1 profile2 } {
|
||||
|
||||
# Import global variables.
|
||||
variable tempDir
|
||||
variable filePrefix
|
||||
|
||||
# Figure out the input and output file names.
|
||||
set profile1Filename "$tempDir/$filePrefix.profile1.fasta"
|
||||
set profile2Filename "$tempDir/$filePrefix.profile2.fasta"
|
||||
set alignedFilename "$tempDir/$filePrefix.aligned.fasta"
|
||||
|
||||
# Get the sequence ids.
|
||||
set profile1Indices {}
|
||||
set profile2Indices {}
|
||||
array set sequenceMap {}
|
||||
foreach sequenceID $profile1 {
|
||||
lappend profile1Indices $sequenceID
|
||||
set sequenceMap($sequenceID) [::SeqData::getName $sequenceID]
|
||||
}
|
||||
foreach sequenceID $profile2 {
|
||||
lappend profile2Indices $sequenceID
|
||||
set sequenceMap($sequenceID) [::SeqData::getName $sequenceID]
|
||||
}
|
||||
|
||||
# Save the sequences as a fasta file.
|
||||
::SeqData::Fasta::saveSequences $profile1 $profile1Filename $profile1Indices {} 0 1
|
||||
::SeqData::Fasta::saveSequences $profile2 $profile2Filename $profile2Indices {} 0 1
|
||||
|
||||
# Run clustalw.
|
||||
set output [run -align -profile1=$profile1Filename -profile2=$profile2Filename -profile -output=fasta -outfile=$alignedFilename -outorder=input]
|
||||
|
||||
# Load the new sequences.
|
||||
set newSequenceIDs [SeqData::Fasta::loadSequences $alignedFilename [array get sequenceMap]]
|
||||
|
||||
# Copy the attributes
|
||||
set originalSequenceIDs [concat $profile1 $profile2]
|
||||
for {set i 0} {$i < [llength $originalSequenceIDs] && $i < [llength $newSequenceIDs]} {incr i} {
|
||||
::SeqData::copyAttributes [lindex $originalSequenceIDs $i] [lindex $newSequenceIDs $i]
|
||||
}
|
||||
|
||||
# Return the sequences.
|
||||
return $newSequenceIDs
|
||||
}
|
||||
|
||||
# Creates a phylogenetic tree of the given sequences.
|
||||
# arg: sequences - The list of sequence ids from whcih the tree should be created.
|
||||
# return: A string containing the tree in Newick format.
|
||||
proc calculatePhylogeneticTree {sequenceIDs {sequenceNames {}}} {
|
||||
|
||||
# Import global variables.
|
||||
variable tempDir
|
||||
variable filePrefix
|
||||
|
||||
# Figure out the input and output file names.
|
||||
set sequencesFilename "$tempDir/$filePrefix.sequences.fasta"
|
||||
set treeFilename "$tempDir/$filePrefix.sequences.ph"
|
||||
|
||||
# Save the sequences as a fasta file with the index in the list as the sequence name.
|
||||
writeSequenceAlignment $sequenceIDs $sequencesFilename $sequenceNames
|
||||
|
||||
# Run clustalw.
|
||||
set output [run -tree -infile=$sequencesFilename -outputtree=phylip]
|
||||
|
||||
# Load the tree.
|
||||
return [::PhyloTree::Newick::loadTreeFile $treeFilename "CLUSTALW Sequence Tree"]
|
||||
}
|
||||
|
||||
proc writeSequenceAlignment {sequenceIDs sequencesFilename indices} {
|
||||
|
||||
# Import global variables.
|
||||
variable tempDir
|
||||
variable filePrefix
|
||||
|
||||
# Extract the segments we will be using in the calculation.
|
||||
set extractedRegions [::SeqData::VMD::extractFirstRegionFromStructures $sequenceIDs]
|
||||
set newSequenceIDs [lindex $extractedRegions 1]
|
||||
set prefixes [lindex $extractedRegions 2]
|
||||
|
||||
# Replace any removed prefix with gaps to preserve the alignment.
|
||||
for {set i 0} {$i < [llength $newSequenceIDs]} {incr i} {
|
||||
set newSequenceID [lindex $newSequenceIDs $i]
|
||||
set prefix [lindex $prefixes $i]
|
||||
if {$prefix != {}} {
|
||||
::SeqData::setSeq $newSequenceID [concat [::SeqData::getGaps [llength $prefix]] [::SeqData::getSeq $newSequenceID]]
|
||||
}
|
||||
}
|
||||
|
||||
# Make sure all of the sequences are aligned.
|
||||
set alignmentLength -1
|
||||
for {set i 0} {$i < [llength $newSequenceIDs]} {incr i} {
|
||||
set newSequenceID [lindex $newSequenceIDs $i]
|
||||
if {$alignmentLength == -1} {
|
||||
set alignmentLength [::SeqData::getSeqLength $newSequenceID]
|
||||
} elseif {[::SeqData::getSeqLength $newSequenceID] != $alignmentLength} {
|
||||
error "The operation could not be performed because the sequences were not aligned."
|
||||
}
|
||||
}
|
||||
|
||||
::SeqData::Fasta::saveSequences $newSequenceIDs $sequencesFilename $indices {} 0
|
||||
|
||||
::SeqData::deleteSequences $newSequenceIDs
|
||||
}
|
||||
|
||||
# Runs the clustal executable. This method should only be called from inside the ClustalW package.
|
||||
# arg: args - The list of arguments that should be passed to the program.
|
||||
proc run { args } {
|
||||
|
||||
# Import global variables.
|
||||
global env
|
||||
variable architecture
|
||||
|
||||
# Get the location of the executable
|
||||
set clustalwdir $env(CLUSTALWPLUGINDIR)
|
||||
|
||||
# Build the name of the executable.
|
||||
switch $architecture {
|
||||
WIN32 {
|
||||
set cmd "exec {$clustalwdir/clustalw.exe}"
|
||||
}
|
||||
default {
|
||||
set cmd "exec {$clustalwdir/clustalw}"
|
||||
}
|
||||
}
|
||||
|
||||
# Append the arguments.
|
||||
foreach arg $args {
|
||||
append cmd " $arg"
|
||||
}
|
||||
|
||||
puts "ClustalW Info) Running CLUSTALW with command $cmd"
|
||||
|
||||
set rc [catch {eval $cmd} out]
|
||||
|
||||
# If there was an error during execution, throw it.
|
||||
if {$rc != 0} {
|
||||
error $out
|
||||
}
|
||||
|
||||
return $out
|
||||
}
|
||||
}
|
||||
|
||||
@@ -1,697 +0,0 @@
|
||||
|
||||
This is the on-line help file for CLUSTAL W ( version 1.83).
|
||||
|
||||
It should be named or defined as: clustalw_help
|
||||
except with MSDOS in which case it should be named CLUSTALW.HLP
|
||||
|
||||
For full details of usage and algorithms, please read the CLUSTALW.DOC file.
|
||||
|
||||
|
||||
Toby Gibson EMBL, Heidelberg, Germany.
|
||||
Des Higgins UCC, Cork, Ireland.
|
||||
Julie Thompson IGBMC, Strasbourg, France.
|
||||
|
||||
|
||||
|
||||
>>NEW <<
|
||||
|
||||
Fasta output
|
||||
===========
|
||||
|
||||
Write/Read sequence with range specified. The command line syntax
|
||||
for range specification is flexible. You can use one of the following
|
||||
syntax.
|
||||
|
||||
-range=n:m
|
||||
-range=n-m
|
||||
-range="n m"
|
||||
|
||||
where m is the starting and m is the length of the sequence.
|
||||
|
||||
Range and range numbers.
|
||||
=======================
|
||||
|
||||
Include range numbers in the ouput.
|
||||
|
||||
-seqno_range=on/off
|
||||
|
||||
The sequence range will be appended as to the names of the sequence.
|
||||
|
||||
|
||||
PIM: Percentage Identity Matrix
|
||||
===============================
|
||||
|
||||
|
||||
|
||||
>>HELP 1 << General help for CLUSTAL W (1.81)
|
||||
|
||||
Clustal W is a general purpose multiple alignment program for DNA or proteins.
|
||||
|
||||
SEQUENCE INPUT: all sequences must be in 1 file, one after another.
|
||||
7 formats are automatically recognised: NBRF-PIR, EMBL-SWISSPROT,
|
||||
Pearson (Fasta), Clustal (*.aln), GCG-MSF (Pileup), GCG9-RSF and GDE flat file.
|
||||
All non-alphabetic characters (spaces, digits, punctuation marks) are ignored
|
||||
except "-" which is used to indicate a GAP ("." in MSF-RSF).
|
||||
|
||||
To do a MULTIPLE ALIGNMENT on a set of sequences, use item 1 from this menu to
|
||||
INPUT them; go to menu item 2 to do the multiple alignment.
|
||||
|
||||
PROFILE ALIGNMENTS (menu item 3) are used to align 2 alignments. Use this to
|
||||
add a new sequence to an old alignment, or to use secondary structure to guide
|
||||
the alignment process. GAPS in the old alignments are indicated using the "-"
|
||||
character. PROFILES can be input in ANY of the allowed formats; just
|
||||
use "-" (or "." for MSF-RSF) for each gap position.
|
||||
|
||||
PHYLOGENETIC TREES (menu item 4) can be calculated from old alignments (read in
|
||||
with "-" characters to indicate gaps) OR after a multiple alignment while the
|
||||
alignment is still in memory.
|
||||
|
||||
|
||||
The program tries to automatically recognise the different file formats used
|
||||
and to guess whether the sequences are amino acid or nucleotide. This is not
|
||||
always foolproof.
|
||||
|
||||
FASTA and NBRF-PIR formats are recognised by having a ">" as the first
|
||||
character in the file.
|
||||
|
||||
EMBL-Swiss Prot formats are recognised by the letters
|
||||
ID at the start of the file (the token for the entry name field).
|
||||
|
||||
CLUSTAL format is recognised by the word CLUSTAL at the beginning of the file.
|
||||
|
||||
GCG-MSF format is recognised by one of the following:
|
||||
- the word PileUp at the start of the file.
|
||||
- the word !!AA_MULTIPLE_ALIGNMENT or !!NA_MULTIPLE_ALIGNMENT
|
||||
at the start of the file.
|
||||
- the word MSF on the first line of the line, and the characters ..
|
||||
at the end of this line.
|
||||
|
||||
GCG-RSF format is recognised by the word !!RICH_SEQUENCE at the beginning of
|
||||
the file.
|
||||
|
||||
|
||||
If 85% or more of the characters in the sequence are from A,C,G,T,U or N, the
|
||||
sequence will be assumed to be nucleotide. This works in 97.3% of cases
|
||||
but watch out!
|
||||
|
||||
>>HELP 2 << Help for multiple alignments
|
||||
|
||||
If you have already loaded sequences, use menu item 1 to do the complete
|
||||
multiple alignment. You will be prompted for 2 output files: 1 for the
|
||||
alignment itself; another to store a dendrogram that describes the similarity
|
||||
of the sequences to each other.
|
||||
|
||||
Multiple alignments are carried out in 3 stages (automatically done from menu
|
||||
item 1 ...Do complete multiple alignments now):
|
||||
|
||||
1) all sequences are compared to each other (pairwise alignments);
|
||||
|
||||
2) a dendrogram (like a phylogenetic tree) is constructed, describing the
|
||||
approximate groupings of the sequences by similarity (stored in a file).
|
||||
|
||||
3) the final multiple alignment is carried out, using the dendrogram as a guide.
|
||||
|
||||
|
||||
PAIRWISE ALIGNMENT parameters control the speed-sensitivity of the initial
|
||||
alignments.
|
||||
|
||||
MULTIPLE ALIGNMENT parameters control the gaps in the final multiple alignments.
|
||||
|
||||
|
||||
RESET GAPS (menu item 7) will remove any new gaps introduced into the sequences
|
||||
during multiple alignment if you wish to change the parameters and try again.
|
||||
This only takes effect just before you do a second multiple alignment. You
|
||||
can make phylogenetic trees after alignment whether or not this is ON.
|
||||
If you turn this OFF, the new gaps are kept even if you do a second multiple
|
||||
alignment. This allows you to iterate the alignment gradually. Sometimes, the
|
||||
alignment is improved by a second or third pass.
|
||||
|
||||
SCREEN DISPLAY (menu item 8) can be used to send the output alignments to the
|
||||
screen as well as to the output file.
|
||||
|
||||
You can skip the first stages (pairwise alignments; dendrogram) by using an
|
||||
old dendrogram file (menu item 3); or you can just produce the dendrogram
|
||||
with no final multiple alignment (menu item 2).
|
||||
|
||||
|
||||
OUTPUT FORMAT: Menu item 9 (format options) allows you to choose from 6
|
||||
different alignment formats (CLUSTAL, GCG, NBRF-PIR, PHYLIP, GDE, NEXUS, and FASTA).
|
||||
|
||||
|
||||
>>HELP 3 << Help for pairwise alignment parameters
|
||||
A distance is calculated between every pair of sequences and these are used to
|
||||
construct the dendrogram which guides the final multiple alignment. The scores
|
||||
are calculated from separate pairwise alignments. These can be calculated using
|
||||
2 methods: dynamic programming (slow but accurate) or by the method of Wilbur
|
||||
and Lipman (extremely fast but approximate).
|
||||
|
||||
You can choose between the 2 alignment methods using menu option 8. The
|
||||
slow-accurate method is fine for short sequences but will be VERY SLOW for
|
||||
many (e.g. >100) long (e.g. >1000 residue) sequences.
|
||||
|
||||
SLOW-ACCURATE alignment parameters:
|
||||
These parameters do not have any affect on the speed of the alignments.
|
||||
They are used to give initial alignments which are then rescored to give percent
|
||||
identity scores. These % scores are the ones which are displayed on the
|
||||
screen. The scores are converted to distances for the trees.
|
||||
|
||||
1) Gap Open Penalty: the penalty for opening a gap in the alignment.
|
||||
2) Gap extension penalty: the penalty for extending a gap by 1 residue.
|
||||
3) Protein weight matrix: the scoring table which describes the similarity
|
||||
of each amino acid to each other.
|
||||
4) DNA weight matrix: the scores assigned to matches and mismatches
|
||||
(including IUB ambiguity codes).
|
||||
|
||||
|
||||
FAST-APPROXIMATE alignment parameters:
|
||||
|
||||
These similarity scores are calculated from fast, approximate, global align-
|
||||
ments, which are controlled by 4 parameters. 2 techniques are used to make
|
||||
these alignments very fast: 1) only exactly matching fragments (k-tuples) are
|
||||
considered; 2) only the 'best' diagonals (the ones with most k-tuple matches)
|
||||
are used.
|
||||
|
||||
K-TUPLE SIZE: This is the size of exactly matching fragment that is used.
|
||||
INCREASE for speed (max= 2 for proteins; 4 for DNA), DECREASE for sensitivity.
|
||||
For longer sequences (e.g. >1000 residues) you may need to increase the default.
|
||||
|
||||
GAP PENALTY: This is a penalty for each gap in the fast alignments. It has
|
||||
little affect on the speed or sensitivity except for extreme values.
|
||||
|
||||
TOP DIAGONALS: The number of k-tuple matches on each diagonal (in an imaginary
|
||||
dot-matrix plot) is calculated. Only the best ones (with most matches) are
|
||||
used in the alignment. This parameter specifies how many. Decrease for speed;
|
||||
increase for sensitivity.
|
||||
|
||||
WINDOW SIZE: This is the number of diagonals around each of the 'best'
|
||||
diagonals that will be used. Decrease for speed; increase for sensitivity.
|
||||
|
||||
|
||||
>>HELP 4 << Help for multiple alignment parameters
|
||||
|
||||
These parameters control the final multiple alignment. This is the core of the
|
||||
program and the details are complicated. To fully understand the use of the
|
||||
parameters and the scoring system, you will have to refer to the documentation.
|
||||
|
||||
Each step in the final multiple alignment consists of aligning two alignments
|
||||
or sequences. This is done progressively, following the branching order in
|
||||
the GUIDE TREE. The basic parameters to control this are two gap penalties and
|
||||
the scores for various identical-non-indentical residues.
|
||||
|
||||
1) and 2) The GAP PENALTIES are set by menu items 1 and 2. These control the
|
||||
cost of opening up every new gap and the cost of every item in a gap.
|
||||
Increasing the gap opening penalty will make gaps less frequent. Increasing
|
||||
the gap extension penalty will make gaps shorter. Terminal gaps are not
|
||||
penalised.
|
||||
|
||||
3) The DELAY DIVERGENT SEQUENCES switch delays the alignment of the most
|
||||
distantly related sequences until after the most closely related sequences have
|
||||
been aligned. The setting shows the percent identity level required to delay
|
||||
the addition of a sequence; sequences that are less identical than this level
|
||||
to any other sequences will be aligned later.
|
||||
|
||||
|
||||
|
||||
4) The TRANSITION WEIGHT gives transitions (A <--> G or C <--> T
|
||||
i.e. purine-purine or pyrimidine-pyrimidine substitutions) a weight between 0
|
||||
and 1; a weight of zero means that the transitions are scored as mismatches,
|
||||
while a weight of 1 gives the transitions the match score. For distantly related
|
||||
DNA sequences, the weight should be near to zero; for closely related sequences
|
||||
it can be useful to assign a higher score.
|
||||
|
||||
|
||||
5) PROTEIN WEIGHT MATRIX leads to a new menu where you are offered a choice of
|
||||
weight matrices. The default for proteins in version 1.8 is the PAM series
|
||||
derived by Gonnet and colleagues. Note, a series is used! The actual matrix
|
||||
that is used depends on how similar the sequences to be aligned at this
|
||||
alignment step are. Different matrices work differently at each evolutionary
|
||||
distance.
|
||||
|
||||
6) DNA WEIGHT MATRIX leads to a new menu where a single matrix (not a series)
|
||||
can be selected. The default is the matrix used by BESTFIT for comparison of
|
||||
nucleic acid sequences.
|
||||
|
||||
Further help is offered in the weight matrix menu.
|
||||
|
||||
|
||||
7) In the weight matrices, you can use negative as well as positive values if
|
||||
you wish, although the matrix will be automatically adjusted to all positive
|
||||
scores, unless the NEGATIVE MATRIX option is selected.
|
||||
|
||||
8) PROTEIN GAP PARAMETERS displays a menu allowing you to set some Gap Penalty
|
||||
options which are only used in protein alignments.
|
||||
|
||||
|
||||
>>HELP A << Help for protein gap parameters.
|
||||
1) RESIDUE SPECIFIC PENALTIES are amino acid specific gap penalties that reduce
|
||||
or increase the gap opening penalties at each position in the alignment or
|
||||
sequence. See the documentation for details. As an example, positions that
|
||||
are rich in glycine are more likely to have an adjacent gap than positions that
|
||||
are rich in valine.
|
||||
|
||||
2) 3) HYDROPHILIC GAP PENALTIES are used to increase the chances of a gap within
|
||||
a run (5 or more residues) of hydrophilic amino acids; these are likely to
|
||||
be loop or random coil regions where gaps are more common. The residues that
|
||||
are "considered" to be hydrophilic are set by menu item 3.
|
||||
|
||||
4) GAP SEPARATION DISTANCE tries to decrease the chances of gaps being too
|
||||
close to each other. Gaps that are less than this distance apart are penalised
|
||||
more than other gaps. This does not prevent close gaps; it makes them less
|
||||
frequent, promoting a block-like appearance of the alignment.
|
||||
|
||||
5) END GAP SEPARATION treats end gaps just like internal gaps for the purposes
|
||||
of avoiding gaps that are too close (set by GAP SEPARATION DISTANCE above).
|
||||
If you turn this off, end gaps will be ignored for this purpose. This is
|
||||
useful when you wish to align fragments where the end gaps are not biologically
|
||||
meaningful.
|
||||
>>HELP 5 << Help for output format options.
|
||||
|
||||
Six output formats are offered. You can choose any (or all 6 if you wish).
|
||||
|
||||
CLUSTAL format output is a self explanatory alignment format. It shows the
|
||||
sequences aligned in blocks. It can be read in again at a later date to
|
||||
(for example) calculate a phylogenetic tree or add a new sequence with a
|
||||
profile alignment.
|
||||
|
||||
GCG output can be used by any of the GCG programs that can work on multiple
|
||||
alignments (e.g. PRETTY, PROFILEMAKE, PLOTALIGN). It is the same as the GCG
|
||||
.msf format files (multiple sequence file); new in version 7 of GCG.
|
||||
|
||||
PHYLIP format output can be used for input to the PHYLIP package of Joe
|
||||
Felsenstein. This is an extremely widely used package for doing every
|
||||
imaginable form of phylogenetic analysis (MUCH more than the the modest intro-
|
||||
duction offered by this program).
|
||||
|
||||
NBRF-PIR: this is the same as the standard PIR format with ONE ADDITION. Gap
|
||||
characters "-" are used to indicate the positions of gaps in the multiple
|
||||
alignment. These files can be re-used as input in any part of clustal that
|
||||
allows sequences (or alignments or profiles) to be read in.
|
||||
|
||||
GDE: this is the flat file format used by the GDE package of Steven Smith.
|
||||
|
||||
NEXUS: the format used by several phylogeny programs, including PAUP and
|
||||
MacClade.
|
||||
|
||||
GDE OUTPUT CASE: sequences in GDE format may be written in either upper or
|
||||
lower case.
|
||||
|
||||
CLUSTALW SEQUENCE NUMBERS: residue numbers may be added to the end of the
|
||||
alignment lines in clustalw format.
|
||||
|
||||
OUTPUT ORDER is used to control the order of the sequences in the output
|
||||
alignments. By default, the order corresponds to the order in which the
|
||||
sequences were aligned (from the guide tree-dendrogram), thus automatically
|
||||
grouping closely related sequences. This switch can be used to set the order
|
||||
to the same as the input file.
|
||||
|
||||
PARAMETER OUTPUT: This option allows you to save all your parameter settings
|
||||
in a parameter file. This file can be used subsequently to rerun Clustal W
|
||||
using the same parameters.
|
||||
|
||||
>>HELP 6 << Help for profile and structure alignments
|
||||
|
||||
By PROFILE ALIGNMENT, we mean alignment using existing alignments. Profile
|
||||
alignments allow you to store alignments of your favourite sequences and add
|
||||
new sequences to them in small bunches at a time. A profile is simply an
|
||||
alignment of one or more sequences (e.g. an alignment output file from CLUSTAL
|
||||
W). Each input can be a single sequence. One or both sets of input sequences
|
||||
may include secondary structure assignments or gap penalty masks to guide the
|
||||
alignment.
|
||||
|
||||
The profiles can be in any of the allowed input formats with "-" characters
|
||||
used to specify gaps (except for MSF-RSF where "." is used).
|
||||
|
||||
You have to specify the 2 profiles by choosing menu items 1 and 2 and giving
|
||||
2 file names. Then Menu item 3 will align the 2 profiles to each other.
|
||||
Secondary structure masks in either profile can be used to guide the alignment.
|
||||
|
||||
Menu item 4 will take the sequences in the second profile and align them to
|
||||
the first profile, 1 at a time. This is useful to add some new sequences to
|
||||
an existing alignment, or to align a set of sequences to a known structure.
|
||||
In this case, the second profile would not be pre-aligned.
|
||||
|
||||
|
||||
The alignment parameters can be set using menu items 5, 6 and 7. These are
|
||||
EXACTLY the same parameters as used by the general, automatic multiple
|
||||
alignment procedure. The general multiple alignment procedure is simply a
|
||||
series of profile alignments. Carrying out a series of profile alignments on
|
||||
larger and larger groups of sequences, allows you to manually build up a
|
||||
complete alignment, if necessary editing intermediate alignments.
|
||||
|
||||
SECONDARY STRUCTURE OPTIONS. Menu Option 0 allows you to set 2D structure
|
||||
parameters. If a solved structure is available, it can be used to guide the
|
||||
alignment by raising gap penalties within secondary structure elements, so
|
||||
that gaps will preferentially be inserted into unstructured surface loops.
|
||||
Alternatively, a user-specified gap penalty mask can be supplied directly.
|
||||
|
||||
A gap penalty mask is a series of numbers between 1 and 9, one per position in
|
||||
the alignment. Each number specifies how much the gap opening penalty is to be
|
||||
raised at that position (raised by multiplying the basic gap opening penalty
|
||||
by the number) i.e. a mask figure of 1 at a position means no change
|
||||
in gap opening penalty; a figure of 4 means that the gap opening penalty is
|
||||
four times greater at that position, making gaps 4 times harder to open.
|
||||
|
||||
The format for gap penalty masks and secondary structure masks is explained
|
||||
in the help under option 0 (secondary structure options).
|
||||
>>HELP B << Help for secondary structure - gap penalty masks
|
||||
|
||||
The use of secondary structure-based penalties has been shown to improve the
|
||||
accuracy of multiple alignment. Therefore CLUSTAL W now allows gap penalty
|
||||
masks to be supplied with the input sequences. The masks work by raising gap
|
||||
penalties in specified regions (typically secondary structure elements) so that
|
||||
gaps are preferentially opened in the less well conserved regions (typically
|
||||
surface loops).
|
||||
|
||||
Options 1 and 2 control whether the input secondary structure information or
|
||||
gap penalty masks will be used.
|
||||
|
||||
Option 3 controls whether the secondary structure and gap penalty masks should
|
||||
be included in the output alignment.
|
||||
|
||||
Options 4 and 5 provide the value for raising the gap penalty at core Alpha
|
||||
Helical (A) and Beta Strand (B) residues. In CLUSTAL format, capital residues
|
||||
denote the A and B core structure notation. The basic gap penalties are
|
||||
multiplied by the amount specified.
|
||||
|
||||
Option 6 provides the value for the gap penalty in Loops. By default this
|
||||
penalty is not raised. In CLUSTAL format, loops are specified by "." in the
|
||||
secondary structure notation.
|
||||
|
||||
Option 7 provides the value for setting the gap penalty at the ends of
|
||||
secondary structures. Ends of secondary structures are observed to grow
|
||||
and-or shrink in related structures. Therefore by default these are given
|
||||
intermediate values, lower than the core penalties. All secondary structure
|
||||
read in as lower case in CLUSTAL format gets the reduced terminal penalty.
|
||||
|
||||
Options 8 and 9 specify the range of structure termini for the intermediate
|
||||
penalties. In the alignment output, these are indicated as lower case.
|
||||
For Alpha Helices, by default, the range spans the end helical turn. For
|
||||
Beta Strands, the default range spans the end residue and the adjacent loop
|
||||
residue, since sequence conservation often extends beyond the actual H-bonded
|
||||
Beta Strand.
|
||||
|
||||
CLUSTAL W can read the masks from SWISS-PROT, CLUSTAL or GDE format input
|
||||
files. For many 3-D protein structures, secondary structure information is
|
||||
recorded in the feature tables of SWISS-PROT database entries. You should
|
||||
always check that the assignments are correct - some are quite inaccurate.
|
||||
CLUSTAL W looks for SWISS-PROT HELIX and STRAND assignments e.g.
|
||||
|
||||
FT HELIX 100 115
|
||||
FT STRAND 118 119
|
||||
|
||||
The structure and penalty masks can also be read from CLUSTAL alignment format
|
||||
as comment lines beginning "!SS_" or "!GM_" e.g.
|
||||
|
||||
!SS_HBA_HUMA ..aaaAAAAAAAAAAaaa.aaaAAAAAAAAAAaaaaaaAaaa.........aaaAAAAAA
|
||||
!GM_HBA_HUMA 112224444444444222122244444444442222224222111111111222444444
|
||||
HBA_HUMA VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
|
||||
|
||||
Note that the mask itself is a set of numbers between 1 and 9 each of which is
|
||||
assigned to the residue(s) in the same column below.
|
||||
|
||||
In GDE flat file format, the masks are specified as text and the names must
|
||||
begin with "SS_ or "GM_.
|
||||
|
||||
Either a structure or penalty mask or both may be used. If both are included in
|
||||
an alignment, the user will be asked which is to be used.
|
||||
|
||||
>>HELP C << Help for secondary structure - gap penalty mask output options
|
||||
|
||||
The options in this menu let you choose whether or not to include the masks
|
||||
in the CLUSTAL W output alignments. Showing both is useful for understanding
|
||||
how the masks work. The secondary structure information is itself very useful
|
||||
in judging the alignment quality and in seeing how residue conservation
|
||||
patterns vary with secondary structure.
|
||||
|
||||
|
||||
>>HELP 7 << Help for phylogenetic trees
|
||||
|
||||
1) Before calculating a tree, you must have an ALIGNMENT in memory. This can be
|
||||
input in any format or you should have just carried out a full multiple
|
||||
alignment and the alignment is still in memory.
|
||||
|
||||
|
||||
*************** Remember YOU MUST ALIGN THE SEQUENCES FIRST!!!! ***************
|
||||
|
||||
|
||||
The method used is the NJ (Neighbour Joining) method of Saitou and Nei. First
|
||||
you calculate distances (percent divergence) between all pairs of sequence from
|
||||
a multiple alignment; second you apply the NJ method to the distance matrix.
|
||||
|
||||
2) EXCLUDE POSITIONS WITH GAPS? With this option, any alignment positions where
|
||||
ANY of the sequences have a gap will be ignored. This means that 'like' will be
|
||||
compared to 'like' in all distances, which is highly desirable. It also
|
||||
automatically throws away the most ambiguous parts of the alignment, which are
|
||||
concentrated around gaps (usually). The disadvantage is that you may throw away
|
||||
much of the data if there are many gaps (which is why it is difficult for us to
|
||||
make it the default).
|
||||
|
||||
|
||||
|
||||
3) CORRECT FOR MULTIPLE SUBSTITUTIONS? For small divergence (say <10%) this
|
||||
option makes no difference. For greater divergence, it corrects for the fact
|
||||
that observed distances underestimate actual evolutionary distances. This is
|
||||
because, as sequences diverge, more than one substitution will happen at many
|
||||
sites. However, you only see one difference when you look at the present day
|
||||
sequences. Therefore, this option has the effect of stretching branch lengths
|
||||
in trees (especially long branches). The corrections used here (for DNA or
|
||||
proteins) are both due to Motoo Kimura. See the documentation for details.
|
||||
|
||||
Where possible, this option should be used. However, for VERY divergent
|
||||
sequences, the distances cannot be reliably corrected. You will be warned if
|
||||
this happens. Even if none of the distances in a data set exceed the reliable
|
||||
threshold, if you bootstrap the data, some of the bootstrap distances may
|
||||
randomly exceed the safe limit.
|
||||
|
||||
4) To calculate a tree, use option 4 (DRAW TREE NOW). This gives an UNROOTED
|
||||
tree and all branch lengths. The root of the tree can only be inferred by
|
||||
using an outgroup (a sequence that you are certain branches at the outside
|
||||
of the tree .... certain on biological grounds) OR if you assume a degree
|
||||
of constancy in the 'molecular clock', you can place the root in the 'middle'
|
||||
of the tree (roughly equidistant from all tips).
|
||||
|
||||
5) TOGGLE PHYLIP BOOTSTRAP POSITIONS
|
||||
By default, the bootstrap values are correctly placed on the tree branches of
|
||||
the phylip format output tree. The toggle allows them to be placed on the
|
||||
nodes, which is incorrect, but some display packages (e.g. TreeTool, TreeView
|
||||
and Phylowin) only support node labelling but not branch labelling. Care
|
||||
should be taken to note which branches and labels go together.
|
||||
|
||||
6) OUTPUT FORMATS: four different formats are allowed. None of these displays
|
||||
the tree visually. Useful display programs accepting PHYLIP format include
|
||||
NJplot (from Manolo Gouy and supplied with Clustal W), TreeView (Mac-PC), and
|
||||
PHYLIP itself - OR get the PHYLIP package and use the tree drawing facilities
|
||||
there. (Get the PHYLIP package anyway if you are interested in trees). The
|
||||
NEXUS format can be read into PAUP or MacClade.
|
||||
|
||||
>>HELP 8 << Help for choosing a weight matrix
|
||||
|
||||
For protein alignments, you use a weight matrix to determine the similarity of
|
||||
non-identical amino acids. For example, Tyr aligned with Phe is usually judged
|
||||
to be 'better' than Tyr aligned with Pro.
|
||||
|
||||
There are three 'in-built' series of weight matrices offered. Each consists of
|
||||
several matrices which work differently at different evolutionary distances. To
|
||||
see the exact details, read the documentation. Crudely, we store several
|
||||
matrices in memory, spanning the full range of amino acid distance (from almost
|
||||
identical sequences to highly divergent ones). For very similar sequences, it
|
||||
is best to use a strict weight matrix which only gives a high score to
|
||||
identities and the most favoured conservative substitutions. For more divergent
|
||||
sequences, it is appropriate to use "softer" matrices which give a high score
|
||||
to many other frequent substitutions.
|
||||
|
||||
1) BLOSUM (Henikoff). These matrices appear to be the best available for
|
||||
carrying out database similarity (homology searches). The matrices used are:
|
||||
Blosum 80, 62, 45 and 30. (BLOSUM was the default in earlier Clustal W
|
||||
versions)
|
||||
|
||||
2) PAM (Dayhoff). These have been extremely widely used since the late '70s.
|
||||
We use the PAM 20, 60, 120 and 350 matrices.
|
||||
|
||||
3) GONNET. These matrices were derived using almost the same procedure as the
|
||||
Dayhoff one (above) but are much more up to date and are based on a far larger
|
||||
data set. They appear to be more sensitive than the Dayhoff series. We use the
|
||||
GONNET 80, 120, 160, 250 and 350 matrices. This series is the default for
|
||||
Clustal W version 1.8.
|
||||
|
||||
We also supply an identity matrix which gives a score of 1.0 to two identical
|
||||
amino acids and a score of zero otherwise. This matrix is not very useful.
|
||||
Alternatively, you can read in your own (just one matrix, not a series).
|
||||
|
||||
A new matrix can be read from a file on disk, if the filename consists only
|
||||
of lower case characters. The values in the new weight matrix must be integers
|
||||
and the scores should be similarities. You can use negative as well as positive
|
||||
values if you wish, although the matrix will be automatically adjusted to all
|
||||
positive scores.
|
||||
|
||||
|
||||
|
||||
For DNA, a single matrix (not a series) is used. Two hard-coded matrices are
|
||||
available:
|
||||
|
||||
|
||||
1) IUB. This is the default scoring matrix used by BESTFIT for the comparison
|
||||
of nucleic acid sequences. X's and N's are treated as matches to any IUB
|
||||
ambiguity symbol. All matches score 1.9; all mismatches for IUB symbols score 0.
|
||||
|
||||
|
||||
2) CLUSTALW(1.6). The previous system used by Clustal W, in which matches score
|
||||
1.0 and mismatches score 0. All matches for IUB symbols also score 0.
|
||||
|
||||
INPUT FORMAT The format used for a new matrix is the same as the BLAST program.
|
||||
Any lines beginning with a # character are assumed to be comments. The first
|
||||
non-comment line should contain a list of amino acids in any order, using the
|
||||
1 letter code, followed by a * character. This should be followed by a square
|
||||
matrix of integer scores, with one row and one column for each amino acid. The
|
||||
last row and column of the matrix (corresponding to the * character) contain
|
||||
the minimum score over the whole matrix.
|
||||
|
||||
>>HELP 9 << Help for command line parameters
|
||||
DATA (sequences)
|
||||
|
||||
-INFILE=file.ext :input sequences.
|
||||
-PROFILE1=file.ext and -PROFILE2=file.ext :profiles (old alignment).
|
||||
|
||||
|
||||
VERBS (do things)
|
||||
|
||||
-OPTIONS :list the command line parameters
|
||||
-HELP or -CHECK :outline the command line params.
|
||||
-ALIGN :do full multiple alignment
|
||||
-TREE :calculate NJ tree.
|
||||
-BOOTSTRAP(=n) :bootstrap a NJ tree (n= number of bootstraps; def. = 1000).
|
||||
-CONVERT :output the input sequences in a different file format.
|
||||
|
||||
|
||||
PARAMETERS (set things)
|
||||
|
||||
***General settings:****
|
||||
-INTERACTIVE :read command line, then enter normal interactive menus
|
||||
-QUICKTREE :use FAST algorithm for the alignment guide tree
|
||||
-TYPE= :PROTEIN or DNA sequences
|
||||
-NEGATIVE :protein alignment with negative values in matrix
|
||||
-OUTFILE= :sequence alignment file name
|
||||
-OUTPUT= :GCG, GDE, PHYLIP, PIR or NEXUS
|
||||
-OUTORDER= :INPUT or ALIGNED
|
||||
-CASE :LOWER or UPPER (for GDE output only)
|
||||
-SEQNOS= :OFF or ON (for Clustal output only)
|
||||
-SEQNO_RANGE=:OFF or ON (NEW: for all output formats)
|
||||
-RANGE=m,n :sequence range to write starting m to m+n.
|
||||
|
||||
***Fast Pairwise Alignments:***
|
||||
-KTUPLE=n :word size
|
||||
-TOPDIAGS=n :number of best diags.
|
||||
-WINDOW=n :window around best diags.
|
||||
-PAIRGAP=n :gap penalty
|
||||
-SCORE :PERCENT or ABSOLUTE
|
||||
|
||||
|
||||
***Slow Pairwise Alignments:***
|
||||
-PWMATRIX= :Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename
|
||||
-PWDNAMATRIX= :DNA weight matrix=IUB, CLUSTALW or filename
|
||||
-PWGAPOPEN=f :gap opening penalty
|
||||
-PWGAPEXT=f :gap opening penalty
|
||||
|
||||
|
||||
***Multiple Alignments:***
|
||||
-NEWTREE= :file for new guide tree
|
||||
-USETREE= :file for old guide tree
|
||||
-MATRIX= :Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename
|
||||
-DNAMATRIX= :DNA weight matrix=IUB, CLUSTALW or filename
|
||||
-GAPOPEN=f :gap opening penalty
|
||||
-GAPEXT=f :gap extension penalty
|
||||
-ENDGAPS :no end gap separation pen.
|
||||
-GAPDIST=n :gap separation pen. range
|
||||
-NOPGAP :residue-specific gaps off
|
||||
-NOHGAP :hydrophilic gaps off
|
||||
-HGAPRESIDUES= :list hydrophilic res.
|
||||
-MAXDIV=n :% ident. for delay
|
||||
-TYPE= :PROTEIN or DNA
|
||||
-TRANSWEIGHT=f :transitions weighting
|
||||
|
||||
|
||||
***Profile Alignments:***
|
||||
-PROFILE :Merge two alignments by profile alignment
|
||||
-NEWTREE1= :file for new guide tree for profile1
|
||||
-NEWTREE2= :file for new guide tree for profile2
|
||||
-USETREE1= :file for old guide tree for profile1
|
||||
-USETREE2= :file for old guide tree for profile2
|
||||
|
||||
|
||||
***Sequence to Profile Alignments:***
|
||||
-SEQUENCES :Sequentially add profile2 sequences to profile1 alignment
|
||||
-NEWTREE= :file for new guide tree
|
||||
-USETREE= :file for old guide tree
|
||||
|
||||
|
||||
***Structure Alignments:***
|
||||
-NOSECSTR1 :do not use secondary structure-gap penalty mask for profile 1
|
||||
-NOSECSTR2 :do not use secondary structure-gap penalty mask for profile 2
|
||||
-SECSTROUT=STRUCTURE or MASK or BOTH or NONE :output in alignment file
|
||||
-HELIXGAP=n :gap penalty for helix core residues
|
||||
-STRANDGAP=n :gap penalty for strand core residues
|
||||
-LOOPGAP=n :gap penalty for loop regions
|
||||
-TERMINALGAP=n :gap penalty for structure termini
|
||||
-HELIXENDIN=n :number of residues inside helix to be treated as terminal
|
||||
-HELIXENDOUT=n :number of residues outside helix to be treated as terminal
|
||||
-STRANDENDIN=n :number of residues inside strand to be treated as terminal
|
||||
-STRANDENDOUT=n:number of residues outside strand to be treated as terminal
|
||||
|
||||
|
||||
***Trees:***
|
||||
-OUTPUTTREE=nj OR phylip OR dist OR nexus
|
||||
-SEED=n :seed number for bootstraps.
|
||||
-KIMURA :use Kimura's correction.
|
||||
-TOSSGAPS :ignore positions with gaps.
|
||||
-BOOTLABELS=node OR branch :position of bootstrap values in tree display
|
||||
|
||||
>>HELP 0 << Help for tree output format options
|
||||
|
||||
Four output formats are offered: 1) Clustal, 2) Phylip, 3) Just the distances
|
||||
4) Nexus
|
||||
|
||||
None of these formats displays the results graphically. Many packages can
|
||||
display trees in the the PHYLIP format 2) below. It can also be imported into
|
||||
the PHYLIP programs RETREE, DRAWTREE and DRAWGRAM for graphical display.
|
||||
NEXUS format trees can be read by PAUP and MacClade.
|
||||
|
||||
1) Clustal format output.
|
||||
This format is verbose and lists all of the distances between the sequences and
|
||||
the number of alignment positions used for each. The tree is described at the
|
||||
end of the file. It lists the sequences that are joined at each alignment step
|
||||
and the branch lengths. After two sequences are joined, it is referred to later
|
||||
as a NODE. The number of a NODE is the number of the lowest sequence in that
|
||||
NODE.
|
||||
|
||||
2) Phylip format output.
|
||||
This format is the New Hampshire format, used by many phylogenetic analysis
|
||||
packages. It consists of a series of nested parentheses, describing the
|
||||
branching order, with the sequence names and branch lengths. It can be used by
|
||||
the RETREE, DRAWGRAM and DRAWTREE programs of the PHYLIP package to see the
|
||||
trees graphically. This is the same format used during multiple alignment for
|
||||
the guide trees.
|
||||
|
||||
Use this format with NJplot (Manolo Gouy), supplied with Clustal W. Some other
|
||||
packages that can read and display New Hampshire format are TreeView (Mac/PC),
|
||||
TreeTool (UNIX), and Phylowin.
|
||||
|
||||
3) The distances only.
|
||||
This format just outputs a matrix of all the pairwise distances in a format
|
||||
that can be used by the Phylip package. It used to be useful when one could not
|
||||
produce distances from protein sequences in the Phylip package but is now
|
||||
redundant (Protdist of Phylip 3.5 now does this).
|
||||
|
||||
4) NEXUS FORMAT TREE. This format is used by several popular phylogeny programs,
|
||||
including PAUP and MacClade. The format is described fully in:
|
||||
Maddison, D. R., D. L. Swofford and W. P. Maddison. 1997.
|
||||
NEXUS: an extensible file format for systematic information.
|
||||
Systematic Biology 46:590-621.
|
||||
|
||||
5) TOGGLE PHYLIP BOOTSTRAP POSITIONS
|
||||
By default, the bootstrap values are placed on the nodes of the phylip format
|
||||
output tree. This is inaccurate as the bootstrap values should be associated
|
||||
with the tree branches and not the nodes. However, this format can be read and
|
||||
displayed by TreeTool, TreeView and Phylowin. An option is available to
|
||||
correctly place the bootstrap values on the branches with which they are
|
||||
associated.
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user