[phenixbb] phenix.model_vs_sequence not working as expected

[Tanner, John J.]

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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