[phenixbb] minimizing clash score

oleg at quantumbioinc.com oleg at quantumbioinc.com
Fri May 17 13:53:12 PDT 2019

Dear Erron,

We recently demonstrated that the high clash count typically seen with the conventional PHENIX refinement is likely attributed to a particular non bonded restraint function used by phenix.refine. When we employed QM/MM (ONIOM) refinement (Borbulevych et al., Acta Cryst., 2018, D74, 1063               https://doi.org/10.1107/S2059798318012913 ) that resulted in significantly better clashscore and improvements of other metrics. 

QM/MM refinement is available within PHENIX with the DivCon plugin. This plugin is available at no cost to academic users at http://www.quantumbioinc.com/products/software_licensing.


Oleg Borbulevych

Oleg Borbulevych, Ph.D.
Staff Scientist
QuantumBio, Inc.
2790 W. College Ave.
State College, PA 16801
E-mail: oborbulevych at yahoo.com, oleg at quantumbioinc.com
Linkedin Professional Profile: https://www.linkedin.com/in/oleg-borbulevych-b8045422

-----Original Message-----
From: "Titus, Erron" <Erron.Titus at ucsf.edu>
Sent: Friday, May 17, 2019 1:58pm
To: "phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
Subject: [phenixbb] minimizing clash score

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phenixbb at phenix-online.org
Unsubscribe: phenixbb-leave at phenix-online.orgHello,

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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