On Sun, Mar 13, 2011 at 10:35 AM, Yuri wrote:

I am new to phenix and I am trying to probe two residues that are putative H-bond partners, after refinement they seem to be put in orientations that would make it impossible for them to be interacting with a ligand. My SA composite omit map may suggest that one of the Asn could be in a different position. My question: If I manually change its conformation is it wise to keep its position fixed during refinement to see what the new maps would look like? If so where would I do that under the real space or individual sites tab on GUI phenix? I am not sure what these 2 tasks accomplish exactly. Any guidance would be appreciated.

I don't know whether this is advisable - I suspect not - but for future reference, the way to do this is: 1. Select "Individual sites" or "Real space" from the "Modify selections for:" drop-down menu in the Refinement Settings tab. 2. Enter the atom selection you want to refine - by default this will be blank, which means "everything", but in your case, you probably want something like this: not (chain A and resseq 205) assuming that the Asn of interest is A205. The captions here are perhaps a little confusing - "Individual sites" means "Refine XYZ using reciprocal-space target", while "Real space" means "Refine XYZ using real-space [map] target". Because they modify the same set of parameters, there is a single atom selection for both strategies, which may not be obvious in the GUI. I'll add a caption to clarify this. -Nat