[phenixbb] phenix.model_vs_sequence not working as expected
Tanner, John J.
TannerJJ at missouri.edu
Wed Dec 20 09:24:14 PST 2023
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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