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
refinement.
Best regads,
Oleg Sobolev.
On Fri, May 17, 2019 at 11:01 AM Titus, Erron
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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