[phenixbb] How to change the FOBS/SIGMA_FOBS value in phenix.refine

Engin Özkan eozkan at uchicago.edu
Mon Jan 8 07:55:17 PST 2018

Dear Randy and Pavel,

There is one complication that arises from the report of the 
MIN(FOBS/SIGMA_FOBS) value in pdb files from phenix.refine. Nearly every 
PDB entry using phenix.refine reports a F/sig(F) cutoff value of 1.3x, 
while Buster and Refmac-generated pdbs have 0 or -/None for that value 
(just checked again with this week's released PDBs). This is clearly not 
intended. Again, the value the Protein Data Bank is reporting is a 
cutoff, based on the minimum value phenix.refine appears to report. 
Since I use French-Wilson for I to F conversions, I have had to correct 
this cutoff value by communicating with PDB with every deposition, but 
it appears that most users rarely go through the trouble.

The issue seems to arise from a lack of a cutoff value in the 
phenix.refine generated .pdb files; Refmac has a DATA CUTOFF (SIGMA(F)) 
(set to NONE by default), which is picked up during structure 
deposition. So, either PDB has to be told that phenix.refine min value 
is just a minumum value and not a cutoff, or phenix.refine might add 
another REMARK card for DATA CUTOFF (SIGMA(F)) under the DATA USED IN 

Hope this helps,

On 1/8/18 2:38 AM, Randy Read wrote:
> Dear Jianxu,
> What you're seeing here is the effect of the French and Wilson algorithm to turn intensities into amplitudes.  As the SIGI gets larger and larger, the French and Wilson algorithm provides an F that becomes closer and closer to the mean amplitude in the Wilson distribution for amplitudes, and the SIGF becomes closer and closer to the rms deviation from the mean amplitude in the Wilson distribution.  As a result the minimum F/SIGF that you can possibly find is about 1.913 for acentric reflections and 1.324 for centric reflections (http://journals.iucr.org/d/issues/2016/03/00/dz5382/index.html#FD29).  The 1.35 that you see would be for a centric reflection that is close to having no information in the original intensity measurement.
> Best wishes,
> Randy Read
>> On 8 Jan 2018, at 03:20, Pavel Afonine <PAfonine at lbl.gov> wrote:
>> Hi Jianxu,
>>> Is there place to set the I/SIGMA_I or FOBS/SIGMA_FOBS values in phenix.refine? I found the default FOBS/SIGMA_FOBS threshold in phenix.refine is 1.35, which means any reflection lower than 1.35 will be excluded in the refinement process. This will generally result in a lower completeness range especially for the relatively weak datasets. When I uses the xray_data.remove_outliers=False, I got the error message "Sorry: Unknown command line parameter definition: remove_outliers = False", and my PHENIX version is phenix-1.12-2829, thanks.
>> phenix.refine does not remove reflections by I/SIGI or F/SIGF criteria. What you see is the file is the result of taking all Fobs, all sigmas, defining one by another, taking min of that and reporting in PDb file header.. So, 1.35 is the actual min(FOBS/SIGFOBS) for data in your file. If you want to aply such a cutoff, then use:
>> xray_data.sigma_fobs_rejection_criterion=VALUE
>> or
>> xray_data.sigma_iobs_rejection_criterion=VALUE
>> Pavel
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> ------
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research      Tel: + 44 1223 336500
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> Hills Road                                    E-mail: rjr27 at cam.ac.uk
> Cambridge CB2 0XY, U.K.                       www-structmed.cimr.cam.ac.uk
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Engin Özkan, Ph.D.
Assistant Professor
Dept of Biochemistry and Molecular Biology
University of Chicago

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