[phenixbb] regarding number of unique reflections

[Viney Singh]

Thanks a lot, Dr .Tanner. I will try the suggestion. Currently, I tried
running xds_ASCII.HKL on pointless followed by truncate. Seems like mtz is
now all good. But I am wondering if this is the right way to go about it?



On Wed, Jan 12, 2022 at 8:33 PM 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 <tannerjj at missouri.edu>
> https://cafnrfaculty.missouri.edu/tannerlab/
>
> Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
>
> Office: Schlundt Annex 203A
>
>
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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,
>
>
>
> 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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