WHISCY active residues prediction error

HADDOCK
1

Hello,
I am trying to use whiscy to predict active residues for my proteins. I made an alignment. I tried several of them with homologous protein of the same type (more similar to each other) - 7 proteins in total and also an alignment with the proteins of the different types - 58 sequences. I submit my alignment in fasta format and the pdb with my protein structure which is a frame of an md simulation (I use this file before for my trial with HADDOCK, it was working but I added a chain ID “A” using sed to use it for WHISCY).
The sequence of the protein of interest is the first in my alignment file, although there is no any specific numbering given.
I saw in the previous related topics that people use HSSP alignments, however, I did not understand where the database is available. I would be appreciated if someone could guide me there.

Nevertheless, I get the following error message with my own alignments:

===========================================================================

command: /opt/software/whiscy/whiscy_setup.py CHI1A_22527_WHISCY.pdb A --alignment CHI1A_22527_WHISCY_A.phylseq --alignment_format FASTA
exit status: 0
log:
whiscy_setup [INFO] PDB structure with chain A saved to CHI1A_22527_WHISCY_A.pdb
whiscy_setup [INFO] Atom accessibility calculated to CHI1A_22527_WHISCY_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 CHI1A_22527_WHISCY_A
exit status: 0
log:
whiscy_setup [INFO] PDB structure with chain A saved to CHI1A_22527_WHISCY_A.pdb
whiscy_setup [INFO] Atom accessibility calculated to CHI1A_22527_WHISCY_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 CHI1A_22527_WHISCY_A.cons does not exist
residue_distance [INFO] Reading conversion table
residue_distance [INFO] Reading PDB structure from CHI1A_22527_WHISCY_A.pdb
residue_distance [INFO] Residue distances written to CHI1A_22527_WHISCY_A.rd
parasmooth [INFO] Reading input files
parasmooth [ERROR] [Errno 2] No such file or directory: ‘CHI1A_22527_WHISCY_A.acons’
command: /opt/software/whiscy/bin/whiscy2bfactor.py CHI1A_22527_WHISCY_A.pdb CHI1A_22527_WHISCY_A_bfactor.pdb CHI1A_22527_WHISCY_A.pscons
exit status: 1
log:
whiscy_setup [INFO] PDB structure with chain A saved to CHI1A_22527_WHISCY_A.pdb
whiscy_setup [INFO] Atom accessibility calculated to CHI1A_22527_WHISCY_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 CHI1A_22527_WHISCY_A.cons does not exist
residue_distance [INFO] Reading conversion table
residue_distance [INFO] Reading PDB structure from CHI1A_22527_WHISCY_A.pdb
residue_distance [INFO] Residue distances written to CHI1A_22527_WHISCY_A.rd
parasmooth [INFO] Reading input files
parasmooth [ERROR] [Errno 2] No such file or directory: ‘CHI1A_22527_WHISCY_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: ‘CHI1A_22527_WHISCY_A.pscons’

Would be really grateful if you can help me.

2

Hello, I am having the same problem, I am using a PDB file from AlphaFolds. Have you already fixed this problem?

3

Hello!
No, unfortunately, I have no idea how to fix this problem and how I continue my protein-protein docking.
In my case, the pdb files are frames from md simulations if it is helpful.
KK.

4

Hello @Katarina @Aron_1226, thanks for raising this issue.

In the message above I see that the first error that comes up is

whiscy [ERROR] Can not read sequence number

If it’s possible, please send us the input data that you are using at < bonvinlab.support@uu.nl > then I can dig deeper into the code and see why this error is happening.

5

For anyone else coming to this topic, there was an issue in the web interface in which the provided alignment was not being used.

This has now been fixed. :mechanic:t5: