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On Thursday 10 August 2006 12:55 pm, Artem Lyubimov wrote: > I am using SHELX to refine a protein structure where electron density > clearly shows what appears to be a rather strong CH - O hydrogen bond > between two residues (i.e. Met and Asp are within 2.5A of one > another). However, SHELX seems to interpret that as a steric clash > and the two residues are pushed apart (and out of density) in the > refinement. I'm trying different things to convince SHELX that those > atoms indeed belong this close together, but I'd like to ask the pros > for ideas, as well. I would prefer to avoid fixing the coordinates > of the residues, and using BIND to simulate covalent connectivity > between those atoms also seems like a misrepresentation of the > situation. So, is there a way to manually specify an individual > hydrogen bond in SHELX, rather than let the program find it? I can't > find anything about that in the manual. > Alternatively, is there a > way to selectively turn off the anti-bumping restraints for a group > of atoms? Section 7.5 of the manual: "Anti-bumping restraints are generated automatically ...if the atoms have different PART numbers and neither of them is zero no restraint is generated" But that description applies to the non-hydrogen atoms. If your problem is coming from the hydrogen itself, then I don't know of a fix other than to not generate the hydrogen in the first place. -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle WA
