Dear All, I have a ligand-protein complex and I wish to calculate different kinds of omit maps (say, composite omit maps, simulated annealing maps, other unbiased fo-fc maps ). I wish to omit the ligand and 3.5 angstrom 3D space around it. I have tried phenix for this purpose but get this error message consistently. "Fatal problems interpreting model file: no of atoms with unknown nonbonded energy type symbols: 15 Please edit the model file to resolve the problems and/of supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary." This error occurs despite supplying the CIF file for the ligand. I have tried to remake the CIF/PDB files from SMILES strings, by drawing the molecule in both ccp4 (acedrug) as well as phenix (elBOW and Readyset go). Nothing seems to work. 1. Is there something I have missed out that can solve this issue?2. Is there a program in CCP4i that can be used to generate the required omit maps? 3. In general, how do I omit 3.5 ang of the space around the ligand during this map calculations? Thank you so much for your time. Hari
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