[phenixbb] regarding number of unique reflections

[Gerard Bricogne]

Dear Randy,

     I absolutely and very strongly agree with you on this point. There
needs to be a return to considering where the genuinely experimental data
are. Short of archiving the raw diffraction images with all the instrumental
metadata that would enable their reprocessing with improved or more expertly
used software, the closest approximation to what the experiment delivered
lies in the unmerged intensities. This is why it seemed so important to do
the extra work on the mmCIF dictionary (and, on the purely wwPDB side, on
the deposition software) enabling their deposition into the PDB, along with
the refined model itself. From this perspective, the stripping operation
recommended by John is extremely counter-productive, even if expedient, and
I join you in strongly advising not to use it.

     John, Viney: perhaps not all processing programs are yet producing the
appropriate mmCIF files for the orderly deposition of unmerged data , but
autoPROC does - see:

                  https://www.globalphasing.com/autoproc/


     With best wishes,

          Gerard.

--
On Thu, Jan 13, 2022 at 10:21:23AM +0000, Randy John Read wrote:
> No, I disagree strongly with that suggestion about pruning the data! The conversion of intensities to amplitudes loses information that cannot be recovered, so the intensities should *always* be included in the deposition. Depositing unmerged intensities (now possible, as Gerard says) is even better and, if you do that, I won’t complain about only depositing amplitudes in the merged data. Removing Bijvoet pairs when you’re sure there is no anomalous signal is fine (but if anyone disagrees and you’ve deposited unmerged intensities, they can get them back).
> 
> Best wishes,
> 
> Randy Read
> 
> > On 12 Jan 2022, at 15:03, Tanner, John J. <TannerJJ at missouri.edu> wrote:
> > 
> > This is a common problem. I use ccp4i CAD to remove all the columns from the .mtz file except for F, SIGF, and FreeR_flag, and then use this new .mtz file in refinement before depositing. For the next structure, remember to do this in the early stages.
> > 
> >  
> > 
> > --
> > 
> > John J. Tanner 
> > 
> > Professor of Biochemistry and Chemistry
> > 
> > Associate Chair of Biochemistry
> > 
> > Department of Biochemistry
> > 
> > University of Missouri
> > 117 Schweitzer Hall
> > 
> > 503 S College Avenue
> > Columbia, MO 65211
> > Phone: 573-884-1280
> > 
> > Email: tannerjj at missouri.edu
> > https://cafnrfaculty.missouri.edu/tannerlab/
> > 
> > Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
> > 
> > Office: Schlundt Annex 203A
> > 
> >  
> > 
> >  
> > 
> >  
> > 
> >  
> > 
> > From: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> on behalf of Viney Singh <vineysingh22 at gmail.com>
> > Date: Wednesday, January 12, 2022 at 6:52 AM
> > To: phenixbb at phenix-online.org <phenixbb at phenix-online.org>
> > Subject: [phenixbb] regarding number of unique reflections
> > 
> > WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email.
> > 
> > Dear all,
> > 
> >  
> > 
> > First of all sorry for the novice question.
> > 
> >  
> > 
> > I processed one of my datasets using xds. Since I was not expecting an anomalous signal, I kept Friedel's Law = True. 
> > 
> > The number of unique reflections I got: 17,000
> > 
> > I used xds_ASCII.HKL after correct.LP and converted it to mtz using Phenix with 10% reflections for Rfree calculations.
> > 
> >  
> > 
> > Now, when I am trying to refine the structure in Phenix, the structure is being refined against 32,300 reflections with 3230 reflections for Rfree calculation. Looks like refinement is treating Friedel's pair as two different reflections. 
> > 
> >  
> > 
> > When I am trying to upload PDB on rcsb, on the refinement tab, the number of reflections used for refinement and Rfree calculations are shown as 32,300 and 3220 respectively, while in the validation report, no. of reflections used for Rfree calculation are shown as 1700.
> > 
> >  
> > 
> > I would really appreciate if someone can guide me to resolve this discrepancy. 
> > 
> >  
> > 
> > Thanks in advance.
> > 
> >  
> > 
> > Viney
> > 
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> -----
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research     Tel: +44 1223 336500
> The Keith Peters Building                               Fax: +44 1223 336827
> Hills Road                                                       E-mail: rjr27 at cam.ac.uk
> Cambridge CB2 0XY, U.K.                              www-structmed.cimr.cam.ac.uk
> 
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