Re: [phenixbb] phenixbb Digest, Vol 216, Issue 7 (out of office)

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Send phenixbb mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit http://phenix-online.org/mailman/listinfo/phenixbb or, via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. Re: phenix.model_vs_sequence not working as expected (Oleg Sobolev) 2. real space refinement of the model in cryo-EM map (Dmitry Semchonok) 3. Re: real space refinement of the model in cryo-EM map (Pavel Afonine) ---------------------------------------------------------------------- Message: 1 Date: Fri, 22 Dec 2023 11:21:13 -0800 From: Oleg Sobolev To: "Tanner, John J." Cc: "[email protected]" Subject: Re: [phenixbb] phenix.model_vs_sequence not working as expected Message-ID: Content-Type: text/plain; charset="utf-8" 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. wrote:

I?ve noticed that command line phenix.model_vs_sequence does not work in phenix-1.21rc1-5156.

Here?s the data:

[tannerjj@dizzy pdbs]$ which phenix.model_vs_sequence

/linux/src/phenix-1.21rc1-5156/build/bin/phenix.model_vs_sequence

[tannerjj@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@dizzy pdbs]$ source /linux/src/phenix-1.20.1-4487/phenix_env.csh

[tannerjj@dizzy pdbs]$ which phenix.model_vs_sequence

/linux/src/phenix-1.20.1-4487/build/bin/phenix.model_vs_sequence

[tannerjj@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@dizzy pdbs]$

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