[phenixbb] Phenix.Refine fix WXC has no effect

[Dorothee Liebschner]

Hi Mark,

While waiting for Pavel to return, you could do the following:
Check if the rmsd goes up because all bond rmsds increase or because there
are a few outrageous outliers. The validation tab after refinement lists
the worst offenders for geometry restraints.

Best wishes,

Dorothee

On Mon, Aug 10, 2020 at 3:12 PM Nigel Moriarty <nwmoriarty at lbl.gov> wrote:

> Mark
>
> Pavel is best to answer this but he will return on Thursday. Someone else
> may offer guidance until then.
>
> Cheers
>
> Nigel
>
> ---
> Nigel W. Moriarty
> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov
>
>
> On Mon, Aug 10, 2020 at 1:10 PM White, Mark <mawhite at utmb.edu> wrote:
>
>> Hello,
>>
>> I am refining a 3.5 Å structure using the latest stable version of
>> Phenix.Refine. After switching to the latest version the Bond RMSDs
>> exploded to ~ 0.035 Å, when using optimize wxc.  Turning off Optimize and
>> using the "Fix WXC" parameters in the GUI with increasingly smaller values
>> had almost no effect on the final bond rmsds, which seems to explode from
>> reasonable values in the "3_xyz" step of refinement.  Am I missing
>> something?
>>
>> Best regards,
>> Mark
>>
>> Mark Andrew White, Ph.D.
>> Associate Professor of Biochemistry & Molecular Biology,
>> Manager, SCSB Macromolecular X-ray Laboratory
>> UTMB, Galveston, TX
>> http://xray.utmb.edu
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