[phenixbb] on Phenix10
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?
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