[phenixbb] on Phenix10

Pavel Afonine pafonine at lbl.gov
Mon Sep 28 07:53:06 PDT 2015

Typically, if clashes don't get resolved automatically it means bits of 
model where clashes occur are trapped in local minima that cannot be 
escaped by gradient-driven minimization. Try SA refinement or fix 
manually, then re-run your usual refinement.

On 9/27/15 18:21, Smith Lee wrote:
> Dear All,
> With the EM cryo data, I have compared the function of 
> phenix.real_space_refine of Phenix10 and Phenix1.9-1692. For the 
> Ramachandran favored, the new version is about 90%, the old version is 
> about 92%. For the clashscore by Molprobity, the new version is about 
> 30, the old version is about 20. Molprobity indicated the clashing 
> atoms were systematically existing in the whole molecule, rather than 
> on specific parts of the protein which may be indication of bad modelling.
> Clearly the clashscore of 30 is unacceptable. Will you please give 
> some advise on how to improve the function of new version of Phenix, 
> considering adding H was not suitable as for the resolution was poorer 
> than 4.0 A?
> Smith
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