[phenixbb] regarding number of unique reflections

[Randy John Read]

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.
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> 
> --
> 
> John J. Tanner 
> 
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> 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
> 
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> 
> Dear all,
> 
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> 
> First of all sorry for the novice question.
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> 
> 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.
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> 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. 
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> 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.
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> I would really appreciate if someone can guide me to resolve this discrepancy. 
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> 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
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