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

[Nathaniel Echols]

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 <jjheadd at lbl.gov> 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 <hdc123hdc123 at yahoo.com> 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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>>
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