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Dear Jeorge, the refmac logfile should tell you which cif-file it reads in for restraints. Can you compare the atom names in that cif-file with the atom names in your PDB-file? My first guess is that the respective atom is named differently, or that maybe the bond is not specified at all. Best, Tim On Thursday, June 09, 2016 06:30:37 PM jeorgemarley thomas wrote: > Dear all, > I have been encountered a problem when the ligand in the active site is > fitted (it is a modified form of glutamate). After refinement with refmac > the one of the oxygen atom bonded with carbon is always getting lost and no > coordinate is being available afterwards for this bond only, although cif > file of the ligand is used during the refinement. I have used sketcher > (ccp4) to get the cif file of the ligand. please suggest what can be done. > I tried phenix also to generate the cif from elbow but did not work. > Thanks in advance > Jeorge -- -- Paul Scherrer Institut Dr. Tim Gruene - persoenlich - OFLC/102 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A