Re: [phenixbb] Phenix.Refine fix WXC has no effect

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 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Mon, Aug 10, 2020 at 1:10 PM White, Mark 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

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