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On 08/03/2018 17:55, Thomas, Leonard M. wrote: > Hello All, Hello Thomas, > > We have run into a problem recently when working with cif files for ligands that have been either soaked or > cocrystallized with the proteins we are looking at. Most of the ligands cif files have been used previously > and while not in the CCP4 library database are available from the pdb ligand database. Now when we go to > use them, specifically in coot after refinement in Refmac we get an error saying there are no restraints for > the ligand. Coot may be telling the truth. It depends on what you mean by "used previously" - if you mean that you can use these cif files in Refmac without problem then I guess that there's a problem with Coot. As you know, cif files can contain data, models, chemical definition or (more pertinently) ligand restraints. Coot expects cif files with ligand restraints to have a particular format. After reading a cif file that you type as a dictionary as you read it into Coot, you can see what Coot was able to parse from it by looking in Edit -> Restraints. Restraints contain blocks including _chem_comp_angle, _chem_comp_tor, _chem_comp_plan. Chemistry definition cifs don't have these. > We have tried reading the cif file in before and after reading the pdb file in. Either will do. But Coot has special rules for ligand named LIG, INH, and DRG - ligands of these types don't force an auto-load of the Refmac Monomer Library. > > We can put the molecule/ligand and cif file into Phenix and all seems well with coot but when moving back to > CCP4/coot we still have the problem. Phenix uses Coot's API to send it restraints information on your behalf. > Both CCP4 and Phenix are using the same version of coot so I don’t > think it is a version problem with coot. > I agree. Paul.