add .env, can remove paths later

.env

@@ -10,7 +10,7 @@
 # expected that you use the same saving conventions as the RCSB PDB, which means:
 #   `1a2b` --> /path/to/pdb_mirror/a2/1a2b.cif.gz
 # To set up a mirror, you can use tha atomworks commandline: `atomworks pdb sync /path/to/mirror`
-PDB_MIRROR_PATH=
+PDB_MIRROR_PATH=/projects/ml/frozen_pdb_copies/2024_12_01_pdb
 
 # The `CCD_MIRROR_PATH` is a path to a local mirror of the CCD database.
 # It's expected that you use the same saving conventions as the RCSB CCD, which means:
@@ -19,7 +19,7 @@ PDB_MIRROR_PATH=
 # If no mirror is provided, the internal biotite CCD will be used as a fallback. To provide a 
 # custom CCD for a ligand, you can place it in the in the CCD mirror path following the CCDs pattern.
 # Example: /path/to/ccd_mirror/M/MYLIGAND1/MYLIGAND1.cif
-CCD_MIRROR_PATH=
+CCD_MIRROR_PATH=/projects/ml/frozen_pdb_copies/2024_12_11_ccd
 
 # --- Local MSA directories ---
 LOCAL_MSA_DIRS=
@@ -29,14 +29,14 @@ LOCAL_MSA_DIRS=
 # The HBPLUS_PATH is a path to the hbplus tool, which is used for hydrogen bond calculation
 # during training and during metrics computation.
 # Example: /path/to/hbplus
-HBPLUS_PATH=
+HBPLUS_PATH=/projects/ml/hbplus
 
 # The `X3DNA_PATH` is a path to the x3dna tool, which is used for DNA structure analysis.
 # Example: /path/to/x3dna-v2.4
-X3DNA_PATH=
+X3DNA_PATH=/projects/ml/prot_dna/x3dna-v2.4
 
 # For secondary structure prediction (not currently used)
-DSSP_PATH=
+DSSP_PATH=/projects/ml/dssp/install/bin/mkdssp
 
 # The `HHFILTER_PATH` is a path to the hhfilter tool from the HH-suite, which is used for
 # filtering MSAs to reduce redundancy.