Hello, I am attempting to predict the active residues involved in a DNA binding protein and generate a TBL restraints file for HADDOCK. Will WHISCY work for this? Even if it is not suitable, I get an error when attempting to use the WHISCY Server and the runs always fail. If anyone has any alternative recommendations for creating a TGL restraints file for DNA binding, I’d be appreciative.
The error code can be seen below:
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command: /opt/software/whiscy/whiscy_setup.py Dimer1.pdb A --alignment Dimer1_A.phylseq --alignment_format FASTA
exit status: 0
log:
whiscy_setup [INFO] PDB structure with chain A saved to Dimer1_A.pdb
whiscy_setup [INFO] Atom accessibility calculated to Dimer1_A.rsa
whiscy_setup [INFO] Surface and buried residues calculated
whiscy_setup [INFO] Protdist calculated
whiscy_setup [INFO] Conversion table file generated
whiscy_setup [INFO] Whiscy setup finished
command: /opt/software/whiscy/whiscy_protocol.sh Dimer1_A
exit status: 0
log:
whiscy_setup [INFO] PDB structure with chain A saved to Dimer1_A.pdb
whiscy_setup [INFO] Atom accessibility calculated to Dimer1_A.rsa
whiscy_setup [INFO] Surface and buried residues calculated
whiscy_setup [INFO] Protdist calculated
whiscy_setup [INFO] Conversion table file generated
whiscy_setup [INFO] Whiscy setup finished
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [ERROR] Can not read sequence number
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [ERROR] Can not read sequence number
consadjust [ERROR] Conservation file Dimer1_A.cons does not exist
residue_distance [INFO] Reading conversion table
residue_distance [INFO] Reading PDB structure from Dimer1_A.pdb
residue_distance [INFO] Residue distances written to Dimer1_A.rd
parasmooth [INFO] Reading input files
parasmooth [ERROR] [Errno 2] No such file or directory: ‘Dimer1_A.acons’
command: /opt/software/whiscy/bin/whiscy2bfactor.py Dimer1_A.pdb Dimer1_A_bfactor.pdb Dimer1_A.pscons
exit status: 1
log:
whiscy_setup [INFO] PDB structure with chain A saved to Dimer1_A.pdb
whiscy_setup [INFO] Atom accessibility calculated to Dimer1_A.rsa
whiscy_setup [INFO] Surface and buried residues calculated
whiscy_setup [INFO] Protdist calculated
whiscy_setup [INFO] Conversion table file generated
whiscy_setup [INFO] Whiscy setup finished
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [ERROR] Can not read sequence number
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [ERROR] Can not read sequence number
consadjust [ERROR] Conservation file Dimer1_A.cons does not exist
residue_distance [INFO] Reading conversion table
residue_distance [INFO] Reading PDB structure from Dimer1_A.pdb
residue_distance [INFO] Residue distances written to Dimer1_A.rd
parasmooth [INFO] Reading input files
parasmooth [ERROR] [Errno 2] No such file or directory: ‘Dimer1_A.acons’
Traceback (most recent call last):
File “/opt/software/whiscy/bin/whiscy2bfactor.py”, line 47, in
scores = parse_whiscy_scores(whiscy_scores_file_name)
File “/opt/software/whiscy/bin/whiscy2bfactor.py”, line 21, in parse_whiscy_scores
with open(file_name) as input:
FileNotFoundError: [Errno 2] No such file or directory: ‘Dimer1_A.pscons’