[phenixbb] Clashes problem
Schubert, Carsten [PRDUS]
CSCHUBER at prdus.jnj.com
Mon Feb 11 07:07:38 PST 2008
I saw you fixed your wxc_scale to 0.1. What happens to the clashes if you let the program refine this parameter?
> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org
> [mailto:phenixbb-bounces at phenix-online.org]On Behalf Of Simon Kolstoe
> Sent: Monday, February 11, 2008 10:01 AM
> To: PHENIX user mailing list
> Subject: Re: [phenixbb] Clashes problem
> Are there not restraints to prevent steric clashes? In cns I seem to
> recall that the energy terms went through the roof if atoms got too
> close together.
> Secondly, if I remove the clashes through model building and
> then run
> phenix.refine both my R and Rfree go up, and phenix actually
> puts some
> of the clashes back again - does the community accept
> deposited pdb's
> with such obviously poor chemistry?
> On 11 Feb 2008, at 14:51, Peter Zwart wrote:
> >> I am slightly concerned that a refinement program seems happy to
> >> allow
> >> such clashes. Is this a problem with the version of
> phenix.refine I
> >> am
> >> running, or is there a more obvious explanation that I have missed?
> > Clash scores are not really used directly in refinement, so the
> > refinement program doesn't really care about this. Adding hydrogens
> > could improve the situation a bit, as would some model building do.
> > How does your starting model look?
> > HTH
> > Peter
> >> Thanks,
> >> Simon
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