mirror of
https://github.com/Discngine/fpocket.git
synced 2026-06-04 20:04:22 +08:00
Compare commits
88 Commits
testToDele
...
mmcif
| Author | SHA1 | Date | |
|---|---|---|---|
|
6e80f9203c | ||
|
|
e22d38054a | ||
|
|
439da234a3 | ||
|
|
b68d547fd5 | ||
|
|
e57afc2bad | ||
|
|
9617bda214 | ||
|
|
8e81c0c807 | ||
|
7b500b4dd6 | ||
|
209f93aa69 | ||
|
|
c50e921077 | ||
|
|
a2c1745242 | ||
|
|
877014bd60 | ||
|
|
9d11cbb2fb | ||
|
|
296fb4789c | ||
|
|
e89a312df2 | ||
|
|
0d1a74253c | ||
|
|
f4208748ed | ||
|
|
b91c92d5b4 | ||
|
|
e191b547dc | ||
|
|
73ce917ea0 | ||
|
|
10fd5e5cef | ||
|
|
b715bec165 | ||
|
|
2a1702fceb | ||
|
|
28031f4cf8 | ||
|
|
84af7678e1 | ||
|
|
f58b5ffa43 | ||
|
|
1f01eefe25 | ||
|
|
17d63260d5 | ||
|
|
1572782a39 | ||
|
|
888a6eee19 | ||
|
|
76d21c256b | ||
|
|
fad1337ad5 | ||
|
|
fce9c66825 | ||
|
|
cffeb8f14d | ||
|
|
3363536b08 | ||
|
|
267e63050c | ||
|
|
620f3431c6 | ||
|
|
74471a1123 | ||
|
927c988b09 | ||
|
|
0a92618189 | ||
|
|
06e8ee4ab0 | ||
|
|
9a7a1d321c | ||
|
|
f31205a0b8 | ||
|
|
ff35953eb5 | ||
|
|
1565cc0701 | ||
|
|
653472798e | ||
|
|
bbb138378e | ||
|
|
0e15bc672d | ||
|
|
521f6a2701 | ||
|
|
faf35bb9c0 | ||
|
|
98fdedb1c5 | ||
|
|
e635a3e359 | ||
|
|
70917d144b | ||
|
|
5b177bc7bd | ||
|
|
01b2099469 | ||
|
|
ae1f26089c | ||
|
|
fca9e379c5 | ||
|
|
3ef844937b | ||
|
|
6b87b664ab | ||
|
|
81618554df | ||
|
|
78a6e541fb | ||
|
|
4287ca1a27 | ||
|
|
d0e25956ab | ||
|
|
62d1a12438 | ||
|
|
e82a452044 | ||
|
|
de94aada19 | ||
|
|
858073a4e1 | ||
|
|
93772970c9 | ||
|
|
f0e7efa86d | ||
|
|
642bc8f12b | ||
|
|
e5b2d2d9af | ||
|
|
294b1a6e07 | ||
|
|
70de53b855 | ||
|
|
df613de93a | ||
|
|
7f0b864de2 | ||
|
|
370a8aa016 | ||
|
|
a0eaccea0a | ||
|
|
3e96d21c37 | ||
|
|
e4c728043d | ||
|
|
fe4dd1c68f | ||
|
|
846465d8c3 | ||
|
|
a5c7a69125 | ||
|
|
6e0d0330f3 | ||
|
|
0f3bf034ff | ||
|
|
32aaabe217 | ||
|
|
5ae071daf4 | ||
|
|
2bfc2a15a6 | ||
|
|
2b97e041f7 |
2
.gitattributes
vendored
Normal file
2
.gitattributes
vendored
Normal file
@@ -0,0 +1,2 @@
|
||||
*.tcl linguist-detectable=false
|
||||
*.c linguist-detectable=true
|
||||
28
.github/workflows/c-cpp.yml
vendored
Normal file
28
.github/workflows/c-cpp.yml
vendored
Normal file
@@ -0,0 +1,28 @@
|
||||
name: C/C++ CI
|
||||
|
||||
on:
|
||||
push:
|
||||
branches: [ master ]
|
||||
pull_request:
|
||||
branches: [ master ]
|
||||
|
||||
jobs:
|
||||
build-and-test-linux:
|
||||
runs-on: ubuntu-latest
|
||||
steps:
|
||||
- uses: actions/checkout@v2
|
||||
- name: netcdf
|
||||
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
|
||||
run : |
|
||||
eval "$(conda shell.bash hook)"
|
||||
conda activate fpocket_test
|
||||
pytest
|
||||
@@ -2,8 +2,7 @@
|
||||
|
||||
|
||||
[](https://dev.azure.com/3decision/fpocket/_build/latest?definitionId=2&branchName=master)
|
||||
[](https://gitter.im/fpocket/community?utm_source=badge&utm_medium=badge&utm_content=badge)
|
||||
|
||||
[](https://gitter.im/fpocket-official/community?utm_source=badge&utm_medium=badge&utm_content=badge)
|
||||
|
||||
The fpocket suite of programs is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level.
|
||||
|
||||
@@ -153,6 +152,11 @@ You can run fpocket using the following command line as an example:
|
||||
fpocket -f 1uyd.pdb
|
||||
```
|
||||
|
||||
fpocket now also eats cif as input, so this would work as well. Make sure to use proper file extensions
|
||||
```bash
|
||||
fpocket -f 1uyd.cif
|
||||
```
|
||||
|
||||
This will detect all pockets on the input pdb file, named 1uyd.pdb
|
||||
If you want to get all command line args for fpocket, simply type `fpocket``
|
||||
|
||||
|
||||
@@ -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
|
||||
|
||||
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
6218
data/sample/2P0R_mod.pdb
Normal file
6218
data/sample/2P0R_mod.pdb
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:
|
||||
@@ -413,7 +417,7 @@ The simplest way to run fpocket is either by providing a single pdb file, or by
|
||||
|
||||
#### Optional:
|
||||
|
||||
-m float: (default 3.4Å) This flag enables the user to modify the minimum radius an alpha sphere might have in a binding pocket. An alpha sphere is a contact sphere, that touches 4 atoms in 3D space without having any internal atoms. Here 3Å allow filtering of too small (protein internal) alpha spheres. I you want to analyze internal interstices, lower this parameter. In the contrary, if you want to analyze more solvent exposed cavities, you can raise this parameter in order to filter out too buried cavities.
|
||||
-m float: (default 3.4Å) This flag enables the user to modify the minimum radius an alpha sphere might have in a binding pocket. An alpha sphere is a contact sphere, that touches 4 atoms in 3D space without having any internal atoms. Here 3Å allow filtering of too small (protein internal) alpha spheres. If you want to analyze internal interstices, lower this parameter. In the contrary, if you want to analyze more solvent exposed cavities, you can raise this parameter in order to filter out too buried cavities.
|
||||
|
||||
-M float: (default 6.2Å) Here you can modify the maximum radius of alpha spheres in a pocket. An alpha sphere is a contact sphere, that touches 4 atoms in 3D space without having any internal atoms. Here 7Å allow to filter out too large contact spheres, that are lying on the protein surface. If you want to analyze very flat and solvent exposed surface depressions, raise this parameter. For analysis of buried parts of the protein you can lower this parameter. Higher radii might be more interesting for identification of protein protein binding sites or polysaccharide binding sites. Smaller radii enable detection of buried cavities for small organic molecules (drugs, for instance).
|
||||
|
||||
@@ -445,19 +449,25 @@ The simplest way to run fpocket is either by providing a single pdb file, or by
|
||||
|
||||
-v int: (default 2500) By default, pockets volume are calculated using a monte-carlo algorithm. Basically, the algorithm picks a random point in the space and check if it is included in any alpha sphere, and stores this status. This is repeated N times, and we estimate the volume of the pocket using ratio between the number of hit and the number of iteration, scaled by the size of the box. This parameter defines the number of iteration to perform. Of course, the higher the value is, the greater the accuracy will be, but the performance will be slowed down.
|
||||
|
||||
-b (none): (NOT USED BY DEFAULT) This option allows the user to chose a discrete algorithm to calculate the volume of each pocket instead of the Monte Carlo method. This algorithm puts each pocket into a grid of dimention (1/N*X ; 1/N*Y ; 1/N*Z), N being the value given using this option, and X, Y and Z being the box dimensions, determined using coordinates of vertices. Then, a triple iteration on each dimensions is used to estimate the volume, checking if each points given by the iteration is in one of the pocket’s vertices. This parameter defines the grid discretization. If this parameter is used, this algorithm will be used instead of the Monte Carlo algorithm.
|
||||
-b (none): (NOT USED BY DEFAULT) This option allows the user to choose a discrete algorithm to calculate the volume of each pocket instead of the Monte Carlo method. This algorithm puts each pocket into a grid of dimension (1/N*X ; 1/N*Y ; 1/N*Z), N being the value given using this option, and X, Y and Z being the box dimensions, determined using coordinates of vertices. Then, a triple iteration on each dimensions is used to estimate the volume, checking if each points given by the iteration is in one of the pocket’s vertices. This parameter defines the grid discretization. If this parameter is used, this algorithm will be used instead of the Monte Carlo algorithm.
|
||||
Warning: Although this algorithm could be more accurate, a high value might dramatically slow down the program, as this algorithm has a maximum complexity of N*N*N*nb_vertices, and a minimum of N*N*N !!!
|
||||
|
||||
|
||||
-d (none): Option allowing you to output pockets and properties in a condensed format. This will put to the stdout pocket properties in a tab separated string and write pocket files in a subfolder
|
||||
|
||||
-r string: (None) This parameter allows you to run fpocket in a restricted mode. Let's suppose you have a very shallow or large pocket with a ligand inside and the automatic pocket prediction always splits up you pocket or you have only a part of the pocket found. Specifying your ligand residue with -r allows you to detect and characterize you ligand binding site explicitely. For instance for `1UYD.pdb` you can specify `-r 1224:PU8:A` (residue number of the ligand: residue name of the ligand: chain of the ligand)
|
||||
-r string: (None) This parameter allows you to run fpocket in a restricted mode. Let's suppose you have a very shallow or large pocket with a ligand inside and the automatic pocket prediction always splits up you pocket or you have only a part of the pocket found. Specifying your ligand residue with -r allows you to detect and characterize you ligand binding site explicitly. For instance for `1UYD.pdb` you can specify `-r 1224:PU8:A` (residue number of the ligand: residue name of the ligand: chain of the ligand)
|
||||
|
||||
-y string: (filename) EXPERIMENTAL: here you can specify a topology filename in the Amber prmtop format. This can then be used by fpocket & mdpocket to calculate energy grids for your pockets. NB: you have to specify the -x flag to run energy calculations
|
||||
|
||||
-x None: (None) EXPERIMENTAL: specify this flag if you want to run energy calculations on calculated pockets. That's not fully functional and only one or two probes are currently generated and output density grids written. Use with caution
|
||||
|
||||
-c char : (Default is none): Use this flag to chose which chains you want to delete before running fpocket. The selected chains can be specified with ',' or ':' delimiters, for example you can use it '-c B,D' or '-c B:D'. You can delete up to 20 different chains.
|
||||
-c char : (Default is none): Use this flag to choose which chains you want to delete before running fpocket. The selected chains can be specified with ',' or ':' delimiters, for example you can use it '-c B,D' or '-c B:D'. You can delete up to 20 different chains.
|
||||
|
||||
-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 */
|
||||
|
||||
|
||||
@@ -24,6 +24,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
|
||||
#include "atom.h"
|
||||
#include "aa.h"
|
||||
#include "utils.h"
|
||||
//#include "asa.h"
|
||||
|
||||
|
||||
/* --------------------------------STRUCTURES---------------------------------*/
|
||||
@@ -88,6 +89,10 @@ typedef struct s_desc
|
||||
|
||||
/* ------------------------------PROTOTYPES---------------------------------- */
|
||||
|
||||
//explicit definition from asa.h
|
||||
void set_ASA(s_desc *desc,s_pdb *pdb, s_vvertice **tvert,int nvert);
|
||||
|
||||
|
||||
s_desc* allocate_s_desc(void) ;
|
||||
void reset_desc(s_desc *desc) ;
|
||||
|
||||
|
||||
@@ -111,6 +111,17 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
|
||||
#define M_PAR_DROP_CHAINS 'c' /**flag, to define which chain are dropped before the pocket detection*/
|
||||
#define M_PAR_DROP_CHAINS_LONG "drop_chains"
|
||||
|
||||
#define M_PAR_KEEP_CHAINS 'k' /**flag, to define which chains are kept before the pocket detection*/
|
||||
#define M_PAR_KEEP_CHAINS_LONG "keep_chains"
|
||||
|
||||
#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\
|
||||
***** USAGE (fpocket) *****\n\
|
||||
@@ -194,7 +205,9 @@ typedef struct s_fparams
|
||||
min_as_density, /**<Minimum alpha sphere density for a pocket to be retained*/
|
||||
asph_max_size ; /**< Maximum size of alpha spheres to keep */
|
||||
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 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.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
@@ -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
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
File diff suppressed because it is too large
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.
|
||||
|
||||
@@ -1,12 +0,0 @@
|
||||
# Tcl package index file, version 1.1
|
||||
# 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 $dir must contain the
|
||||
# full path name of this file's directory.
|
||||
|
||||
package ifneeded clustalw 1.0 "set env(CLUSTALWPLUGINDIR) {$dir}; set env(CLUSTALWDIR) {$dir}; [list source [file join $dir clustalw.tcl]]"
|
||||
|
||||
Binary file not shown.
@@ -1,95 +0,0 @@
|
||||
############################################################################
|
||||
#cr
|
||||
#cr (C) Copyright 1995-2003 The Board of Trustees of the
|
||||
#cr University of Illinois
|
||||
#cr All Rights Reserved
|
||||
#cr
|
||||
############################################################################
|
||||
|
||||
package provide cluster 1.1
|
||||
|
||||
namespace eval ::Cluster {
|
||||
|
||||
# Directory to write temp files.
|
||||
global env
|
||||
variable tempDir $env(TMPDIR)
|
||||
|
||||
# The prefix for temp files.
|
||||
variable filePrefix "cluster"
|
||||
|
||||
# This method sets the temp file options used by the cluster 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 creates a UPGMA tree given a similarity matrix.
|
||||
# args: matrix - The similarity matrix.
|
||||
# return: The UPGMA tree in JE format.
|
||||
proc createUPGMATree {matrix} {
|
||||
|
||||
# Import global variables.
|
||||
variable tempDir
|
||||
variable filePrefix
|
||||
|
||||
# Delete any old files.
|
||||
foreach file [glob -nocomplain $tempDir/$filePrefix.*] {
|
||||
file delete -force $file
|
||||
}
|
||||
|
||||
# Write out the matrix.
|
||||
set fp [open "$tempDir/$filePrefix.matrix" w]
|
||||
foreach row $matrix {
|
||||
puts $fp [join $row " "]
|
||||
}
|
||||
close $fp
|
||||
|
||||
# Run the cluster command.
|
||||
set out [run "$tempDir" "$filePrefix.matrix"]
|
||||
|
||||
return $out
|
||||
}
|
||||
|
||||
|
||||
proc run {wd args} {
|
||||
|
||||
variable clusterdir
|
||||
global env
|
||||
|
||||
set clusterdir $env(CLUSTERPLUGINDIR)
|
||||
|
||||
switch [vmdinfo arch] {
|
||||
WIN32 {
|
||||
set cmd "exec {$clusterdir/cluster.exe}"
|
||||
append wd "/"
|
||||
}
|
||||
default {
|
||||
set cmd "exec {$clusterdir/cluster}"
|
||||
}
|
||||
}
|
||||
|
||||
set pwd [pwd]
|
||||
|
||||
cd "$wd"
|
||||
|
||||
foreach arg $args {
|
||||
append cmd " $arg"
|
||||
}
|
||||
|
||||
puts "Cluster Info) Running cluster with command $cmd"
|
||||
|
||||
set rc [catch {eval $cmd} out]
|
||||
|
||||
cd $pwd
|
||||
|
||||
return $out
|
||||
}
|
||||
}
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user