[phenixbb] phenix.model_vs_sequence not working as expected

[Oleg Sobolev]

Hi John,

Thank you for reporting the issue. I have fixed it. This tool should work
again in Phenix builds starting from 5188.

Best regards,
Oleg Sobolev.

On Wed, Dec 20, 2023 at 9:35 AM Tanner, John J. <TannerJJ at missouri.edu>
wrote:

> I’ve noticed that command line phenix.model_vs_sequence does not work in
> phenix-1.21rc1-5156.
>
>
>
> Here’s the data:
>
>
>
> [tannerjj at dizzy pdbs]$ which phenix.model_vs_sequence
>
> /linux/src/phenix-1.21rc1-5156/build/bin/phenix.model_vs_sequence
>
> [tannerjj at dizzy pdbs]$ phenix.model_vs_sequence 8DKP.pdb
> ../depo/8DKP.fasta
>
> Traceback (most recent call last):
>
>   File
> "/linux/src/phenix-1.21rc1-5156/build/../modules/cctbx_project/mmtbx/command_line/model_vs_sequence.py",
> line 75, in <module>
>
>     run(sys.argv[1:])
>
>   File
> "/linux/src/phenix-1.21rc1-5156/build/../modules/cctbx_project/mmtbx/command_line/model_vs_sequence.py",
> line 48, in run
>
>     pdb_in = iotbx.pdb.inpu(params.input.pdb_file)
>
> AttributeError: 'module' object has no attribute 'inpu'
>
>
>
>
>
> It worked fine in phenix-1.20.1-4487:
>
>
>
> [tannerjj at dizzy pdbs]$ source /linux/src/phenix-1.20.1-4487/phenix_env.csh
>
> [tannerjj at dizzy pdbs]$ which phenix.model_vs_sequence
>
> /linux/src/phenix-1.20.1-4487/build/bin/phenix.model_vs_sequence
>
> [tannerjj at dizzy pdbs]$ phenix.model_vs_sequence 8DKP.pdb
> ../depo/8DKP.fasta
>
> Skipping non-polymer chain 'A'
>
> Skipping non-polymer chain 'B'
>
> Skipping non-polymer chain 'A'
>
> Skipping non-polymer chain 'B'
>
> Chain 'A':
>
>   best matching sequence: 8DKP_1|Chains
>
>   sequence identity: 100.00%
>
>   10 residue(s) missing from PDB chain (3 at start, 1 at end)
>
>   1 gap(s) in chain
>
>
>
>
>
> PDB file      ---QSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHXXXXX
>
>
>                  ||||||||||||||||||||||||||||||||||||||||||||||||||||
>
>
> sequence      SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGS
>
>
>
>
> PDB file      XGSXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
>
>
>                ||
>
>
> sequence      SGS---------------------------------------------------------
>
>
>
>
> PDB file      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMMGEQFVTGETIREA
>
>
>                                                            |||||||||||||||
>
>
> sequence      ---------------------------------------------MMGEQFVTGETIREA
>
>
>
>
> PDB file      LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI
>
>
>               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>
>
> sequence      LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI
>
>
>
>
> PDB file      KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC
>
>
>               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>
>
> sequence      KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC
>
>
>
>
> PDB file      LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD
>
>
>               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>
>
> sequence      LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD
>
>
>
>
> PDB file      GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY
>
>
>               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>
>
> sequence      GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY
>
>
>
>
> PDB file      EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN
>
>
>               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>
>
> sequence      EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN
>
>
>
>
> PDB file      DPKVSIDELIADPVEVV-
>
>               |||||||||||||||||
>
> sequence      DPKVSIDELIADPVEVVR
>
>
>
> Chain 'B':
>
>   best matching sequence: 8DKP_1|Chains
>
>   sequence identity: 100.00%
>
>   8 residue(s) missing from PDB chain (0 at start, 1 at end)
>
>   1 gap(s) in chain
>
>
>
>
>
> PDB file      SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHXXXXX
>
>
>               |||||||||||||||||||||||||||||||||||||||||||||||||||||||
>
>
> sequence      SRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTARKLIEALRGKHSGSGS
>
>
>
>
> PDB file      XXSXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
>
>
>                 |
>
>
> sequence      SGS---------------------------------------------------------
>
>
>
>
> PDB file      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMMGEQFVTGETIREA
>
>
>                                                            |||||||||||||||
>
>
> sequence      ---------------------------------------------MMGEQFVTGETIREA
>
>
>
>
> PDB file      LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI
>
>
>               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>
>
> sequence      LKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGKASAGRGIYEGPGISI
>
>
>
>
> PDB file      KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC
>
>
>               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>
>
> sequence      KLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEEADRLELSLDLLEVLC
>
>
>
>
> PDB file      LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD
>
>
>               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>
>
> sequence      LDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLVKGAYWDAEIKRAQLD
>
>
>
>
> PDB file      GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY
>
>
>               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>
>
> sequence      GLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLAAIYHMAGKDFHVGKY
>
>
>
>
> PDB file      EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN
>
>
>               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>
>
> sequence      EFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRRLLENGANSSFVHRIN
>
>
>
>
> PDB file      DPKVSIDELIADPVEVV-
>
>               |||||||||||||||||
>
> sequence      DPKVSIDELIADPVEVVR
>
>
>
> [tannerjj at dizzy pdbs]$
>
>
>
>
>
>
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