Dear all, I might excuse myself for the silly question but it is the first time I solve an x-ray structure.
After modell building in coot and running of refmac with restrained refinement I have the problem that the pdb output file contains distances between e.g. ILE Cb and Cg that are so long that the Cg is displayed as single atom (distance ~1.64 A instead of 1.5 A). This seems to happen to me for aminoacid sidechains where I added an alternative conformation (especially if the 2nd conformation is oriented not far away from the first one) and if I set the occupancy of sidechains like Glu for Cd and further to zero (Here refmac gives a bond break between the last atom with occupancy 0 and the first with occupancy 1). I can adjust it of course in coot back to normal but after the next refmac run the same happens again. The option card in refmac for geometric restraints I kept untouched. Am I missing to set on an option in refmac, or is there something else going wrong? Thanks a lot for the help Marcus
