# WHISCY active residues prediction error **URL:** \ **Category:** HADDOCK\ **Created:** [November 27, 2023, 3:26pm UTC](https://ask.bioexcel.eu/t/whiscy-active-residues-prediction-error/4704 "2023-11-27T15:26:41Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![Katarina](https://avatars.discourse-cdn.com/v4/letter/k/eb8c5e/32.png) [@Katarina](https://ask.bioexcel.eu/u/Katarina)\ **Post date:** [November 27, 2023, 3:26pm UTC](https://ask.bioexcel.eu/t/whiscy-active-residues-prediction-error/4704/1 "2023-11-27T15:26:41Z")
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. ---
**Author:** ![Aron\_1226](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/aron_1226/32/918_2.png) [@Aron\_1226](https://ask.bioexcel.eu/u/Aron_1226)\ **Post date:** [January 17, 2024, 12:03pm UTC](https://ask.bioexcel.eu/t/whiscy-active-residues-prediction-error/4704/2 "2024-01-17T12:03:13Z")
Hello, I am having the same problem, I am using a PDB file from AlphaFolds. Have you already fixed this problem? ---
**Author:** ![Katarina](https://avatars.discourse-cdn.com/v4/letter/k/eb8c5e/32.png) [@Katarina](https://ask.bioexcel.eu/u/Katarina)\ **Post date:** [January 17, 2024, 2:03pm UTC](https://ask.bioexcel.eu/t/whiscy-active-residues-prediction-error/4704/3 "2024-01-17T14:03:04Z")
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. ---
**Author:** ![honoratorv](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/honoratorv/32/672_2.png) [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)\ **Post date:** [January 19, 2024, 11:49am UTC](https://ask.bioexcel.eu/t/whiscy-active-residues-prediction-error/4704/4 "2024-01-19T11:49:28Z")
Hello @Katarina @Aron_1226, thanks for raising this issue. In the message above I see that the first error that comes up is ```auto 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. ---
**Author:** ![honoratorv](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/honoratorv/32/672_2.png) [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)\ **Post date:** [January 22, 2024, 12:30pm UTC](https://ask.bioexcel.eu/t/whiscy-active-residues-prediction-error/4704/5 "2024-01-22T12:30:49Z")
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. 🧑🏾‍🔧