Hi, I'm running into trouble when trying to add an alternative conformation to a non-standard residue type and subsequently trying to do real-space refinement. I am working on the structure of a fluorescent protein that cyclizes three residues in the middle of an alpha-helix. So the chromophore is connected to the protein still, but I have to list it as a separate residue type with a .cif dictionary. I have managed to get it all working, except for real space refinement of a chromophore with alternative conformations in Coot. I can real-space refine in Coot when I only have one conformation with no problem. I can run refinement in Phenix with no problem on the alternative conformations. But when I try to real-space refine a zone (the alpha helix containing the chromophore) in Coot with the alternative conformations of the chromophore present, Coot seems to forget that there is a chromophore and refines the surrounding residues but not the chromophore (it even wants to move the surrounding alpha helical residues down into the density filled by the chromophore!).
I'd appreciate any help and can provide cif dictionaries and all of that if it would be of help. Thanks in advance! Tim
