Question about writing cif files at the last round of refinement

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Boaz Shaanan

7 Nov 2017 7 Nov '17

4:06 a.m.

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Pavel Afonine

7 Nov 7 Nov

12:39 p.m.

New subject: Question about writing cif files at the last round of refinement

Hi Boaz,

...

Perhaps I'm doing something wrong but it seems as if I follow the instructions correctly. To write cif files (data and model) in the final refinement run I tick the correct boxes in the output box of the gui. I can see in the final.eff that this was accepted. However the data cif file contains only the model derived quantities and not the original Fobs, sigFobs etc. as they are on incoming mtz file. In the next stage, as you propose, mmtbx.prepare_pdb_deposition routine expects those quantities (i.e. Fobs etc.). I'm running the nightly build 2919. Am I doing something wrong? I'd appreciate your advice.

first, you should tick two boxes: "Write final refined model into mmCIF file" and "Write Fobs, Fmodel and R-free-flags into mmCIF file". Then after refinement you should get two CIF files *_refine_*.cif (refined model) and *_refine_*.reflections.cif (reflections). CIF with reflections contains these fields: loop_ _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_sigma_au _refln.pdbx_FWT _refln.pdbx_PHWT _refln.pdbx_DELFWT _refln.pdbx_DELPHWT _refln.pdbx_r_free_flag _refln.status _refln.pdbx_F_calc_with_solvent _refln.pdbx_phase_calc_with_solvent where F_meas_au is a name for Fobs (clearly, a weird way to name Fobs, not sure who invented it!). This is what I get myself using the latest code. Is it different for you? mmtbx.prepare_pdb_deposition seems to broken: I just ran a sample example where I asked to output model and reflection CIFs, and then supplied them to mmtbx.prepare_pdb_deposition and it crashed. Also, it crashes if I give it PDB and MTZ from refinement. Pavel

Boaz Shaanan

1:24 p.m.

New subject: Question about writing cif files at the last round of refinement

Pavel Afonine

1:46 p.m.

New subject: Question about writing cif files at the last round of refinement

Hi Boaz, hm.. this odd. I'm using developers version which is close to latest nightly build. Before I ask for all inputs that reproduce this problem, could you please do this quick and simple test? Step-by-step: 1) Get model and data: phenix.fetch_pdb 1yjp --mtz 2) Start Phenix GUI, then run refinement using 1yjp.mtz and 1yjp.pdb files, do not change any settings except for "Write final refined model into mmCIF file" and "Write Fobs, Fmodel and R-free-flags into mmCIF file" being enabled. This is what I did and I'm getting reflection CIF file with Fobs included. Thanks, Pavel On 11/7/17 13:24, Boaz Shaanan wrote:

...

Hi Pavel,

Thanks for your message. I did tick two boxes (as also evidenced from checking the final.eff. Here is what I get:

loop_ _refln.index_h _refln.index_k _refln.index_l _refln.pdbx_FWT _refln.pdbx_PHWT _refln.pdbx_DELFWT _refln.pdbx_DELPHWT _refln.pdbx_r_free_flag _refln.status _refln.pdbx_F_calc_with_solvent _refln.pdbx_phase_calc_with_solvent

So it seems as if the first two items in your list: _refln.F_meas_au AND _refln.F_meas_sigma_au (which is what I was looking for, that is Fobs and Sigfobs) are missing. What version are you running? I'm running phenix-dev-2919 (I tried 2949, the latest bild as of yesterday, and it failed altogether to start a refinement cycle; I reported it to bugs@...). I'll have a look again on the download site.

Thanks for pointing out the problem with mmtbx.prepare_pdb_deposition

Boaz /Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel

E-mail: [email protected] Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 / // // /

/ ------------------------------------------------------------------------ *From:* Pavel Afonine [[email protected]] *Sent:* Tuesday, November 07, 2017 10:39 PM *To:* בעז שאנן; [email protected] *Subject:* Re: Question about writing cif files at the last round of refinement

Hi Boaz,

...
Perhaps I'm doing something wrong but it seems as if I follow the instructions correctly. To write cif files (data and model) in the final refinement run I tick the correct boxes in the output box of the gui. I can see in the final.eff that this was accepted. However the data cif file contains only the model derived quantities and not the original Fobs, sigFobs etc. as they are on incoming mtz file. In the next stage, as you propose, mmtbx.prepare_pdb_deposition routine expects those quantities (i.e. Fobs etc.). I'm running the nightly build 2919. Am I doing something wrong? I'd appreciate your advice.

first, you should tick two boxes: "Write final refined model into mmCIF file" and "Write Fobs, Fmodel and R-free-flags into mmCIF file". Then after refinement you should get two CIF files *_refine_*.cif (refined model) and *_refine_*.reflections.cif (reflections).

CIF with reflections contains these fields:

loop_ _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_sigma_au _refln.pdbx_FWT _refln.pdbx_PHWT _refln.pdbx_DELFWT _refln.pdbx_DELPHWT _refln.pdbx_r_free_flag _refln.status _refln.pdbx_F_calc_with_solvent _refln.pdbx_phase_calc_with_solvent

where F_meas_au is a name for Fobs (clearly, a weird way to name Fobs, not sure who invented it!).

This is what I get myself using the latest code. Is it different for you?

mmtbx.prepare_pdb_deposition seems to broken: I just ran a sample example where I asked to output model and reflection CIFs, and then supplied them to mmtbx.prepare_pdb_deposition and it crashed. Also, it crashes if I give it PDB and MTZ from refinement.

Pavel

Paul Adams

2:54 p.m.

New subject: Question about writing cif files at the last round of refinement

Also, for running mmtbx.prepare_pdb_deposition you need to specify the files (you can’t just give the two mmcif files on the command line): mmtbx.prepare_pdb_deposition pdb=file.cif data=data-file.cif seq=file.fa

...

On Nov 7, 2017, at 1:46 PM, Pavel Afonine wrote:

Hi Boaz,

hm.. this odd. I'm using developers version which is close to latest nightly build.

Before I ask for all inputs that reproduce this problem, could you please do this quick and simple test? Step-by-step:

1) Get model and data:

phenix.fetch_pdb 1yjp --mtz

2) Start Phenix GUI, then run refinement using 1yjp.mtz and 1yjp.pdb files, do not change any settings except for "Write final refined model into mmCIF file" and "Write Fobs, Fmodel and R-free-flags into mmCIF file" being enabled.

This is what I did and I'm getting reflection CIF file with Fobs included.

Thanks, Pavel

On 11/7/17 13:24, Boaz Shaanan wrote:

...
Hi Pavel,

Thanks for your message. I did tick two boxes (as also evidenced from checking the final.eff. Here is what I get:

loop_ _refln.index_h _refln.index_k _refln.index_l _refln.pdbx_FWT _refln.pdbx_PHWT _refln.pdbx_DELFWT _refln.pdbx_DELPHWT _refln.pdbx_r_free_flag _refln.status _refln.pdbx_F_calc_with_solvent _refln.pdbx_phase_calc_with_solvent

So it seems as if the first two items in your list: _refln.F_meas_au AND _refln.F_meas_sigma_au (which is what I was looking for, that is Fobs and Sigfobs) are missing. What version are you running? I'm running phenix-dev-2919 (I tried 2949, the latest bild as of yesterday, and it failed altogether to start a refinement cycle; I reported it to bugs@...). I'll have a look again on the download site.

Thanks for pointing out the problem with mmtbx.prepare_pdb_deposition

Boaz

Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel

E-mail: [email protected] Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

From: Pavel Afonine [[email protected]] Sent: Tuesday, November 07, 2017 10:39 PM To: בעז שאנן; [email protected] Subject: Re: Question about writing cif files at the last round of refinement

Hi Boaz,

...
Perhaps I'm doing something wrong but it seems as if I follow the instructions correctly. To write cif files (data and model) in the final refinement run I tick the correct boxes in the output box of the gui. I can see in the final.eff that this was accepted. However the data cif file contains only the model derived quantities and not the original Fobs, sigFobs etc. as they are on incoming mtz file. In the next stage, as you propose, mmtbx.prepare_pdb_deposition routine expects those quantities (i.e. Fobs etc.). I'm running the nightly build 2919. Am I doing something wrong? I'd appreciate your advice.

first, you should tick two boxes: "Write final refined model into mmCIF file" and "Write Fobs, Fmodel and R-free-flags into mmCIF file". Then after refinement you should get two CIF files *_refine_*.cif (refined model) and *_refine_*.reflections.cif (reflections).

CIF with reflections contains these fields:

loop_ _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_sigma_au _refln.pdbx_FWT _refln.pdbx_PHWT _refln.pdbx_DELFWT _refln.pdbx_DELPHWT _refln.pdbx_r_free_flag _refln.status _refln.pdbx_F_calc_with_solvent _refln.pdbx_phase_calc_with_solvent

where F_meas_au is a name for Fobs (clearly, a weird way to name Fobs, not sure who invented it!).

This is what I get myself using the latest code. Is it different for you?

mmtbx.prepare_pdb_deposition seems to broken: I just ran a sample example where I asked to output model and reflection CIFs, and then supplied them to mmtbx.prepare_pdb_deposition and it crashed. Also, it crashes if I give it PDB and MTZ from refinement.

Pavel

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

-- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ [email protected] ][ 1-510-495-2506 ] --

Paul Adams

2:24 p.m.

New subject: Question about writing cif files at the last round of refinement

mmtbx.prepare_pdb_deposition works for me in dev-2940 for files written from phenix.refine. You need to supply the sequence of the sample in a fasta file for it to write output. However, it shouldn’t crash. It won’t work with a PDB file, and an MTZ file is just used to pull symmetry and other info - the reflections aren’t combined with the model information in the output cif.

...

On Nov 7, 2017, at 12:39 PM, Pavel Afonine wrote:

Hi Boaz,

...
Perhaps I'm doing something wrong but it seems as if I follow the instructions correctly. To write cif files (data and model) in the final refinement run I tick the correct boxes in the output box of the gui. I can see in the final.eff that this was accepted. However the data cif file contains only the model derived quantities and not the original Fobs, sigFobs etc. as they are on incoming mtz file. In the next stage, as you propose, mmtbx.prepare_pdb_deposition routine expects those quantities (i.e. Fobs etc.). I'm running the nightly build 2919. Am I doing something wrong? I'd appreciate your advice.

first, you should tick two boxes: "Write final refined model into mmCIF file" and "Write Fobs, Fmodel and R-free-flags into mmCIF file". Then after refinement you should get two CIF files *_refine_*.cif (refined model) and *_refine_*.reflections.cif (reflections).

CIF with reflections contains these fields:

loop_ _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_sigma_au _refln.pdbx_FWT _refln.pdbx_PHWT _refln.pdbx_DELFWT _refln.pdbx_DELPHWT _refln.pdbx_r_free_flag _refln.status _refln.pdbx_F_calc_with_solvent _refln.pdbx_phase_calc_with_solvent

where F_meas_au is a name for Fobs (clearly, a weird way to name Fobs, not sure who invented it!).

This is what I get myself using the latest code. Is it different for you?

mmtbx.prepare_pdb_deposition seems to broken: I just ran a sample example where I asked to output model and reflection CIFs, and then supplied them to mmtbx.prepare_pdb_deposition and it crashed. Also, it crashes if I give it PDB and MTZ from refinement.

Pavel

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

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Boaz Shaanan
Paul Adams
Pavel Afonine