[phenixbb] problems with clashes

Pavel Afonine pafonine at lbl.gov
Sun Jul 29 21:02:57 PDT 2007


In upcoming version of PHENIX there will be more detailed manual for 
Until recently phenix.refine was not using H atoms by default. We 
changed this behavior very recently. In newer version, if you have an 
input PDB file with H atoms (generated for example, with phenix.reduce), 
then phenix.refine will use these hydrogens by default. You don't need 
to do anything special for this.

> I nowadays use phenix.refine almost always in the first stages of the
> refinement and later usually move to refmac. Now I have two modest
> resolution structures which behave much better in phenix than in refmac. 

This is partially because Refmac uses "2nd derivatives' minimizer". 
Saying differently, given a pretty refined model out of phenix.refine 
Refmac can possibly refine it some more to deeper minimum. The downside 
of this is sometime higher Rfree factors.
However, if you have a pretty bad starting model, phenix.refine is more 
powerful than Refmac to bring this model to a reasonably refined state.

> B-factors on
> the other hand seem to be less restrained in phenix.

Here is how B-factors are restrained in phenix.refine (if TLS is not used):

look for "* The Phenix refinement framework *" by Afonine P.V., 
Grosse-Kunstleve R.W, Adams P.D.

It is pretty old text, but reflects some general things. Note that "k" 
and (Bi+Bj) in the ADP restraints target formula  have now different 
empirically found values.

And yes, playing with wxc_scale is definitely good thing to do if you're 
not happy with either Rfree-Rwork gap or stereochemistry.

Analogously to wxc_scale in coordinates refinement, to play with 
B-factors restraints use wxu_scale.

> If I take the phenix refined coordinates, keep the aniso records from TLS and run some refmac 
> cycles, my structure is better than average with regards to the clash scores (69 %). I do not 
> know how valid refinement strategy this is. (Rfree-R = 5.4 %)

Please look another post on phenixbb (Subject: "Re: [phenixbb] R-factor 
problem !!!") regarding how tricky and error prone could be to jump 
between different programs.


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