I am attempting to use Whiscy using my own predicted pdb file and a sample alignment fasta file but I get the following error. How are my inputs incorrectly formatted?
Full error message below:
===========================================================================
command: whiscy_setup proteinOfInterest.pdb A --alignment proteinOfInterest.fasta --alignment_format FASTA
exit status: 0
log:
2024-07-04 17:50:26,782 cli_setup:192 INFO - PDB structure with chain A saved to proteinOfInterest_A.pdb
2024-07-04 17:50:26,942 cli_setup:199 INFO - Atom accessibility calculated to proteinOfInterest_A.rsa
2024-07-04 17:50:26,944 cli_setup:203 INFO - Surface and buried residues calculated
2024-07-04 17:50:27,078 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2024-07-04 17:50:27,098 cli_setup:310 INFO - Protdist calculated
2024-07-04 17:50:27,146 cli_setup:317 INFO - Conversion table file generated
2024-07-04 17:50:27,146 cli_setup:319 INFO - Whiscy setup finished
command: whiscy proteinOfInterest_A.sur proteinOfInterest_A.conv proteinOfInterest_A.phylseq proteinOfInterest_A.out -o proteinOfInterest_A.cons
exit status: 0
log:
2024-07-04 17:50:26,782 cli_setup:192 INFO - PDB structure with chain A saved to proteinOfInterest_A.pdb
2024-07-04 17:50:26,942 cli_setup:199 INFO - Atom accessibility calculated to proteinOfInterest_A.rsa
2024-07-04 17:50:26,944 cli_setup:203 INFO - Surface and buried residues calculated
2024-07-04 17:50:27,078 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2024-07-04 17:50:27,098 cli_setup:310 INFO - Protdist calculated
2024-07-04 17:50:27,146 cli_setup:317 INFO - Conversion table file generated
2024-07-04 17:50:27,146 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [INFO] Calculating scores…
whiscy [ERROR] Surface residue out of range
command: whiscy proteinOfInterest_A.lac proteinOfInterest_A.conv proteinOfInterest_A.phylseq proteinOfInterest_A.out -o proteinOfInterest_A.lcons
exit status: 0
log:
2024-07-04 17:50:26,782 cli_setup:192 INFO - PDB structure with chain A saved to proteinOfInterest_A.pdb
2024-07-04 17:50:26,942 cli_setup:199 INFO - Atom accessibility calculated to proteinOfInterest_A.rsa
2024-07-04 17:50:26,944 cli_setup:203 INFO - Surface and buried residues calculated
2024-07-04 17:50:27,078 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2024-07-04 17:50:27,098 cli_setup:310 INFO - Protdist calculated
2024-07-04 17:50:27,146 cli_setup:317 INFO - Conversion table file generated
2024-07-04 17:50:27,146 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [INFO] Calculating scores…
whiscy [ERROR] Surface residue out of range
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [INFO] Calculating scores…
whiscy [ERROR] Surface residue out of range
command: whiscy_consadjust proteinOfInterest_A.cons -o proteinOfInterest_A.acons
exit status: 0
log:
2024-07-04 17:50:26,782 cli_setup:192 INFO - PDB structure with chain A saved to proteinOfInterest_A.pdb
2024-07-04 17:50:26,942 cli_setup:199 INFO - Atom accessibility calculated to proteinOfInterest_A.rsa
2024-07-04 17:50:26,944 cli_setup:203 INFO - Surface and buried residues calculated
2024-07-04 17:50:27,078 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2024-07-04 17:50:27,098 cli_setup:310 INFO - Protdist calculated
2024-07-04 17:50:27,146 cli_setup:317 INFO - Conversion table file generated
2024-07-04 17:50:27,146 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [INFO] Calculating scores…
whiscy [ERROR] Surface residue out of range
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [INFO] Calculating scores…
whiscy [ERROR] Surface residue out of range
consadjust [ERROR] Conservation file proteinOfInterest_A.cons does not exist
command: whiscy_resdist proteinOfInterest_A.pdb proteinOfInterest_A.conv proteinOfInterest_A.rd
exit status: 0
log:
2024-07-04 17:50:26,782 cli_setup:192 INFO - PDB structure with chain A saved to proteinOfInterest_A.pdb
2024-07-04 17:50:26,942 cli_setup:199 INFO - Atom accessibility calculated to proteinOfInterest_A.rsa
2024-07-04 17:50:26,944 cli_setup:203 INFO - Surface and buried residues calculated
2024-07-04 17:50:27,078 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2024-07-04 17:50:27,098 cli_setup:310 INFO - Protdist calculated
2024-07-04 17:50:27,146 cli_setup:317 INFO - Conversion table file generated
2024-07-04 17:50:27,146 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [INFO] Calculating scores…
whiscy [ERROR] Surface residue out of range
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [INFO] Calculating scores…
whiscy [ERROR] Surface residue out of range
consadjust [ERROR] Conservation file proteinOfInterest_A.cons does not exist
residue_distance [INFO] Reading conversion table
residue_distance [INFO] Reading PDB structure from proteinOfInterest_A.pdb
residue_distance [INFO] Residue distances written to proteinOfInterest_A.rd
command: whiscy_parasmooth proteinOfInterest_A.acons proteinOfInterest_A.lcons proteinOfInterest_A.rd -o proteinOfInterest_A.pscons
exit status: 0
log:
2024-07-04 17:50:26,782 cli_setup:192 INFO - PDB structure with chain A saved to proteinOfInterest_A.pdb
2024-07-04 17:50:26,942 cli_setup:199 INFO - Atom accessibility calculated to proteinOfInterest_A.rsa
2024-07-04 17:50:26,944 cli_setup:203 INFO - Surface and buried residues calculated
2024-07-04 17:50:27,078 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2024-07-04 17:50:27,098 cli_setup:310 INFO - Protdist calculated
2024-07-04 17:50:27,146 cli_setup:317 INFO - Conversion table file generated
2024-07-04 17:50:27,146 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [INFO] Calculating scores…
whiscy [ERROR] Surface residue out of range
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [INFO] Calculating scores…
whiscy [ERROR] Surface residue out of range
consadjust [ERROR] Conservation file proteinOfInterest_A.cons does not exist
residue_distance [INFO] Reading conversion table
residue_distance [INFO] Reading PDB structure from proteinOfInterest_A.pdb
residue_distance [INFO] Residue distances written to proteinOfInterest_A.rd
parasmooth [INFO] Reading input files
parasmooth [ERROR] [Errno 2] No such file or directory: ‘proteinOfInterest_A.acons’
command: whiscy_bfactor proteinOfInterest_A.pdb proteinOfInterest_A_bfactor.pdb proteinOfInterest_A.pscons
exit status: 1
log:
2024-07-04 17:50:26,782 cli_setup:192 INFO - PDB structure with chain A saved to proteinOfInterest_A.pdb
2024-07-04 17:50:26,942 cli_setup:199 INFO - Atom accessibility calculated to proteinOfInterest_A.rsa
2024-07-04 17:50:26,944 cli_setup:203 INFO - Surface and buried residues calculated
2024-07-04 17:50:27,078 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2024-07-04 17:50:27,098 cli_setup:310 INFO - Protdist calculated
2024-07-04 17:50:27,146 cli_setup:317 INFO - Conversion table file generated
2024-07-04 17:50:27,146 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [INFO] Calculating scores…
whiscy [ERROR] Surface residue out of range
whiscy [INFO] Parsing surface list…
whiscy [INFO] Loading conversion table…
whiscy [INFO] Converting…
whiscy [INFO] Initializing score calculation…
whiscy [INFO] Calculating scores…
whiscy [ERROR] Surface residue out of range
consadjust [ERROR] Conservation file proteinOfInterest_A.cons does not exist
residue_distance [INFO] Reading conversion table
residue_distance [INFO] Reading PDB structure from proteinOfInterest_A.pdb
residue_distance [INFO] Residue distances written to proteinOfInterest_A.rd
parasmooth [INFO] Reading input files
parasmooth [ERROR] [Errno 2] No such file or directory: ‘proteinOfInterest_A.acons’
Traceback (most recent call last):
File “/usr/local/bin/whiscy_bfactor”, line 6, in
sys.exit(main())
^^^^^^
File “/opt/software/whiscy/src/whiscy/cli_bfactor.py”, line 68, in main
scores = parse_whiscy_scores(whiscy_scores_file_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/opt/software/whiscy/src/whiscy/cli_bfactor.py”, line 31, in parse_whiscy_scores
with open(file_name) as input:
^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: ‘proteinOfInterest_A.pscons’