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? Simon 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 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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