[phenixbb] Clashes problem
s.kolstoe at ucl.ac.uk
Mon Feb 11 07:01:12 PST 2008
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
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
>> such clashes. Is this a problem with the version of phenix.refine I
>> 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?
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