[phenixbb] minimizing clash score

Oleg Sobolev osobolev at lbl.gov
Fri May 17 18:08:17 PDT 2019

Hi Erron,

You can try the following:
- put hydrogens on you model;
- inspect particular clashes and rebuild model where necessary;
- set nonbonded_weight parameter to a bigger value (default is 100).

"clash_guard" is to prevent models with terrible clashes from getting into

Best regads,
Oleg Sobolev.

On Fri, May 17, 2019 at 11:01 AM Titus, Erron <Erron.Titus at ucsf.edu> wrote:

> Hello,
> In order to improve model geometry of my x-ray structure, I am using
> real-space refinement together with reciprocal space refinement in
> phenix.refine.
> I like this, because it works very well to fix a lot of geometry issues.
> But clashes are a problem. Clashes tend to keep coming back.
> I found a clunky way to selectively use reference restraints to prevent
> most of the clashes from coming back, but I am wondering if there is
> another way of addressing this. I don't want to up-weight geometry
> globally, because 1) there are major regions of the x-ray map that are
> quite good, and 2) I don't have problems with other geometry, just clashes.
> I couldn't find much documentation on the "clash_guard" keyword...
> Thanks.
> Erron
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