 |
 |
Dear Marcus The most likely reason is that geometry is a bit loose. You need to tighten it a bit. You can do by decreasing weight using weight matrix option on the interface. You need also check the electron density to make sure that ILE is in electron density. Please let me know if you have any further difficulty. regards Garib On 17 Jan 2011, at 09:28, Marcus Fislage wrote: > 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