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.
