I have my doubts about supporting NCS restraints of alternative conformations; the two seem to be mutually exclusive. But maybe I don't understand your situtation.

Here are some more details on the refinement situation: it is possible for a piece of duplex DNA to be positioned in two conformations in the crystal, and it appears that both conformations are occupied with roughly the same occupancy. The sequence is not completely palindromic, so at some positions a different base is present depending on the random orientation of the DNA. However, the phosphate and ribose atoms occupy the same positions regardless of the orientation, and I want to enforce this.

I can see that NCS restraints of backbone atoms only are useful, even if the residue names are different. The trouble is that atoms in two chains need to be matched unambiguously while allowing for chain breaks. I could try to simply remove the requirement that the residue names have to match and go by residue sequence number + insertion code only. Would that work in your case?

Yes, that sounds like it would work.

A potential downside is that people have to be careful excluding non-matching sidechain atoms.

Perhaps it could be that there is an override option after an error message. Thanks for your help. -John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ----- Forwarded message from [email protected] ----- Date: Thu, 20 May 2010 11:54:33 -0400 From: John Pascal Reply-To: John Pascal Subject: Restraining altloc related atoms during refinement To: [email protected] Hello All, I would like to restrain the positions of ribose/phosphate atoms of altloc 'A' to the positions of those in altloc 'B'. Problem is, altloc A and altloc B are different residue types, so phenix.refine exits stating that there are no common atoms when I enter the following NCS-type restraint: selection: chain I and altloc A and resid 1 and (phosphate or ribose) restrain: chain I and altloc B and resid 1 and (phosphate or ribose) I am using the phenix GUI. Is there a better place to enter this type of restraint (rather than NCS) that does not care if a P atom is from a Cd or from a Gd residue type? thanks. Best, John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. ----- End forwarded message ----- ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.