Andy: First, what version of COOT are you running?
Second, when you say you have a cif file, I presume you mean a cif dictionary file as opposed to just a simple coordinate file in cif format. What tool(program) did you use to generate the dictionary file?
Third, have you imported the cif dictionary file under File->Import CIF dictionary... ?
Fourth, have you checked the cif dictionary file to be sure that it has defined the torsion angles for the ligand and that the torsion angles are labeled var_1, var_2, var_3, etc.? [I am blanking on the designation other than var, but COOT will not be able to rotate torsion angles that are not defined as var].
Fifth, on the Model/Fit/Refine pop-up menu, have you clicked on "Edit Chi Angles" and then clicked on an atom in your ligand?
Steven Andy Dodds wrote:
OK, I have a ligand and I want to move it around in my density. I have a cif file, but coot treats the molecule as a rigid structure and so I can't move a specific part of the structure, without moving the whole thing. I am sort of working around this problem by going into the pdb file of the ligand and renaming parts of it as below. Instead of the whole thing being called DRG, I changed it. ATOM 2501 NAT DRA D 1 N ATOM 2502 CAZ DRA D 1 C ATOM 2503 CAK DRA D 1 C ATOM 2504 CAI DRB D 1 C ATOM 2505 SAV DRB D 1 S ATOM 2506 CBB DRC D 1 C ATOM 2507 CAY DRC D 1 C But, when I come to do Rotate/Translate zone, coot crashes. Does anyone know a good way to achieve what I want, avoiding manipulating the pdb file? cheers
