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. Pavel 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