[phenixbb] Question about writing cif files at the last round of refinement

[Paul Adams]

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 <PAfonine at lbl.gov> 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 at ...).
>> 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: bshaanan at bgu.ac.il
>> Phone: 972-8-647-2220  Skype: boaz.shaanan                  
>> Fax:   972-8-647-2992 or 972-8-646-1710    
>>  
>>  
>>                  
>> 
>> From: Pavel Afonine [pafonine at lbl.gov]
>> Sent: Tuesday, November 07, 2017 10:39 PM
>> To: בעז שאנן; phenixbb at phenix-online.org
>> 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
>> 
> 
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-- 
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
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