[phenixbb] minimizing clash score

Titus, Erron Erron.Titus at ucsf.edu
Fri May 17 10:58:31 PDT 2019


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...



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