Re: [phenixbb] regarding number of unique reflections

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. 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

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*From: *[email protected] < [email protected]> on behalf of Viney Singh < [email protected]> *Date: *Wednesday, January 12, 2022 at 6:52 AM *To: *[email protected] *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