Re: [modeller_usage] refining bad backbone & side chain angles

[Mensur Dlakic <mdlakic AT montana.edu>]

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
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| Mensur Dlakic, PhD                | Tel: (406) 994-6576                |
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