Irene,
Relaxing the structure in Rosetta may do the trick:
http://www.rosettacommons.org/software/
Also, I would trust Molprobity assessment more than Procheck, since it uses larger and more up-to-date rotamer libraries:
http://molprobity.biochem.duke.edu/
At 04:30 PM 12/8/2010, Irene Newhouse wrote: >Following an earlier message on the topic of refining a homology model, I >just tried a Chimera minimization. The results underwhelm me: Procheck >before minimization had 34/576 residues marked with bad phi, psi angles & >10 with bad chi angles. After minimization, there were 40 residues with >bad phi, psi angles & 11 with bad chi angles. That's NOT the direction I >was looking for! > >The template structure contained 454 residues, of which only 2 were marked >for phi, psi angles by Procheck, and 4 for chi angles. There's only 27% >identity, so that's probably part of the issue. > >Any recommendations? > >Thanks! >Irene Newhouse >_______________________________________________ >modeller_usage mailing list >modeller_usage@salilab.org >https://salilab.org/mailman/listinfo/modeller_usage
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