Re: [phenixbb] On refine automatically correct N/Q/H errors

For a very detailed explanation, here is the original publication for the program Reduce: http://www.ncbi.nlm.nih.gov/pubmed/9917408 -Nat On Mon, Nov 21, 2011 at 8:06 AM, Jeff Headd wrote:

Hi Dialing,

For cases where phenix.refine indicates that both conformations of an N/Q/H residue clash, it is likely that some part of the model in the vicinity of the N/Q/H residue is built incorrectly and is trapped in a false-minima. Refinement may not be powerful enough to correct this on its own, so your best course of action is to look at in a model building program such as Coot and correct the problem by hand. It will be best to examine your molecule with hydrogens present so you can see all of the clashes. The MolProbity webserver may also be helpful to you, or if you're using the Phenix GUI, you can launch KiNG from the validation window which will give you the same graphical analysis that you would find in MolProbity.

If you have further questions please let me know.

Thanks, Jeff

On Mon, Nov 21, 2011 at 1:21 AM, Dialing Pretty wrote:

...

Dear All, I am refining a crystal structure with Phenix refine. I have adopted automatically correct N/Q/H errors. During refinement for some residues it writes "both conformations clash, check manually". Will you please tell me what does it mean for "both conformations clash, please check manually",   and how to process it? I am looking forward to getting your reply.

Cheers, Dialing

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