[phenixbb] phenixbb Digest, Vol 216, Issue 7 (out of office)
Elisabeth Laurent
elisabeth.laurent at boku.ac.at
Wed Dec 27 08:44:45 PST 2023
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Elisabeth Laurent
>>> <phenixbb-request at phenix-online.org> 27.12.23 17:32 >>>
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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 <osobolev at lbl.gov>
To: "Tanner, John J." <TannerJJ at missouri.edu>
Cc: "phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
Subject: Re: [phenixbb] phenix.model_vs_sequence not working as
expected
Message-ID:
<CADd3otGkgta4heL2mHYB1sfkm_AxEw77Psd7RdS+pGQhjED7dA at mail.gmail.com>
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. <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]$
>
>
>
>
>
>
> _______________________________________________
> phenixbb mailing list
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Message: 2
Date: Wed, 27 Dec 2023 11:11:35 +0000
From: Dmitry Semchonok <semchonok at gmail.com>
To: "Phenix email list " <phenixbb at phenix-online.org>
Subject: [phenixbb] real space refinement of the model in cryo-EM map
Message-ID:
<DB8PR09MB3994667095B98211D32AC427F39FA at DB8PR09MB3994.eurprd09.prod.outlook.com>
Content-Type: text/plain; charset="utf-8"
Dear colleagues,
Does anyone know how to improve the Ramachandran plot Z score (Rama-Z)?
Ours seems to be too good (low) ?
Is there any cure in Phenix for that?
Maybe changing certain parameters/restraints can aid?
Thank you.
Kind regards,
Dmitry
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Message: 3
Date: Wed, 27 Dec 2023 08:32:40 -0800
From: Pavel Afonine <pafonine at lbl.gov>
To: Dmitry Semchonok <semchonok at gmail.com>, Phenix email list
<phenixbb at phenix-online.org>
Subject: Re: [phenixbb] real space refinement of the model in cryo-EM
map
Message-ID: <eff39cd7-bb61-4210-9c18-98db85b3e0e6 at lbl.gov>
Content-Type: text/plain; charset="utf-8"; Format="flowed"
Hi Dmitry,
would you mind sharing the Rama-Z number you get as well as the
Ramachandran plot (General) that you can quickly get using this command:
phenix.ramalyze plot=True show_labels=False markerfacecolor=yellow
markeredgecolor=red model.pdb
That'll give a better starting point to offer suggestions.
Thanks!
Pavel
On 12/27/23 03:11, Dmitry Semchonok wrote:
> Dear colleagues,
> Does anyone know how to improve the Ramachandran plot Z score (Rama-Z)?
>
> Ours seems to be too good (low) ?
>
> Is there any cure in Phenix for that?
> Maybe changing certain parameters/restraints can aid?
>
> Thank you.
>
> Kind regards,
> Dmitry
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe:phenixbb-leave at phenix-online.org
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