[phenixbb] secondary restraint refinement

Pavel Afonine pafonine at lbl.gov
Wed Dec 17 13:31:25 PST 2014

Hi Charles,

secondary structure (SS) restraints are rather to preserve correct 
secondary structure elements in low-resolution refinement. Refinement 
with SS restraints is unlikely to fold atoms into a SS element starting 
from a conformation that is beyond refinement convergence radius.

This means that if you distort the helix in input structure it may or 
may not fold back into helix after refinement, regardless whether you 
use or do not use SS restraints. The outcome depends on how badly you 
distort it and how good the map is to force it back.

Also, I do not understand the logic of what you are trying to do. Are 
you trying to make the model worse (locally, in that helix place) and 
keep it that way? In this case you can just exclude atoms in question 
from coordinate refinement.


On 12/17/14 10:57 AM, CPMAS Chen wrote:
> 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 conformation.
> 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?
> Thanks!
> Charles

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