[phenixbb] adding hydrogens -> increasing clash score

Nathaniel Echols nechols at lbl.gov
Sat Jul 30 11:56:06 PDT 2011

On Sat, Jul 30, 2011 at 11:35 AM, Tatyana Sysoeva
<tatyanasysoeva at gmail.com>wrote:

> I am almost done repeating fix-rotamers run. First time it gave a way worse
> validation results then before running phenix without fix_rotamers=true.

This method behaves very poorly at low resolution - I ran some tests
recently on a variety of 3.0-4.5A structures solved by molecular
replacement, and while the rotamer fitting usually decreased the R-factor,
it always made the clashscore much worse.  I wouldn't bother using it if you
have worse than 3.0A data.

Model pdb contained the model identical to the control run but with added H
> atoms. I have not add H to the ADP molecules since I did not know how to
> write a correct CIF file for it.

If you use phenix.ready_set, it will handle the ADP molecules.

Interestingly in previous release version the same refinement runs produced:
> without H clashscore = 77.580195/cbeta =8
> with H clashscore = 119.729960/cbeta=330

We increased the weight on the nonbonded restraints 5x in the last few
releases - this always improves the clashscore and Ramachandran statistics
at low resolution, although it doesn't change the R-factors very much.
 Still, 12% is an awful lot of Ramachandran outliers, even at that
resolution.  If you're willing to experiment a little, try adding
"ncs.type=torsion" to the parameters (without hydrogens) and let us know
what happens.

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