[modeller_usage] refining bad backbone & side chain angles

[Irene Newhouse <irenenew AT hawaii.edu>]

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