Carsten, Phenix does do this a little differently and yes it ignores existing ligands (which I like). CCP4 comes with is own library of existing ligand cif files from the pdb which coot also uses. The best way is to try and find a unique code to call your new ligand. That way you can have some say in what it is coded rather than an arbitrary code.
J -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Schubert, Carsten [JRDUS] Sent: Thursday, 27 February 2014 2:22 p.m. To: [email protected] Subject: Re: [ccp4bb] New ligand Hi Louise, for internal use the name of your ligand does not matter as long as you have a .cif file describing the restraints. I am not sure about the behavior of refmac, but in phenix the presence of a defined name in a .cif file takes precedence over any duplicate entry in your monomer library. As far as PDB submission is concerned: it is my experience that they will rename your ligand to some arbitrarily name anyhow upon annotating the entry, so I would not sweat that part too much. HTH Carsten -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Louise Fairall Sent: Wednesday, February 26, 2014 6:14 AM To: [email protected] Subject: [ccp4bb] New ligand Hello, we have a structure with a novel ligand. I used to use LIG for new ligands but now that is taken in the PDB by 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE. Any suggestions for a generic name that is not already used? thanks and best wishes, Louise
