Hi, we are refining a low resolution (3A) membrane protein using coot 0.6_pre2228. In alpha helical regions, coot in doing a very good job but we have more trouble in loops or kinks in helices. Typically, in those regions, we just have density for the main chain carbonyls and the CB of the side chains.
My question is how to use real space refinement in those regions? very often, the side chain of large residue (Lys, Arg, Glu, Trp...) is moving either in the main chain density, or in a neighboring density and the refinement is impossible. My way around is to mutate those large residues to Ala and back to the original when i'm happy with the refinement, but that doesn't seem optimum. What i would like is to have coot only take care of the main chain, trying to fit carbonyls and CB in the blobs of the main chain. will *set-refinement-move-atoms-with-zero-occupancy 0* do the trick? is it possible to have a button saying "perform real space refinement only on the main chain + CB" ? (say in the R/RC control box?) thanks very much vincent IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
