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

Jeff Headd jjheadd at lbl.gov
Mon Nov 21 08:06:19 PST 2011

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.


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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