[phenixbb] secondary restraint refinement

CPMAS Chen cpmasmit at gmail.com
Wed Dec 17 10:57:16 PST 2014

Dear Phenix Users,

How do I force some residues in a non-helix conformation?

I have a 3A data, and have the protein model refined. But in some region,
3~4 residues are in the helix conformation, and the density fit is good.
Anyway, let me say this, I want to force these residues in a non-helix

I tweaked the model a little bit and load them in VMD, and make sure they
are not helix anymore.

I turn on secondary-structure-restraint in phenix, take out the helix
remarks for these residues in the def file. but once the refinement is
done, they are still in a helix region (phenix automatically secondary
structure analysis, or viewed in VMD).

Is there a feasible way to keep them away from helix conformation?





Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

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