> Hello Everyone > > Where does coot get monomers from? > Is it my ccp4 distribution? Or the coot distribution (It's a kind of old > coot) > > I'd like to use get monomer for a ligand I've created a dictionary for - not > one known to ccp4. > > I can create the cif for the monomer (and the pdb) and give it an unused > 3-letter code. > I put the cif into the ccp4 monomer library directory tree > I added the new monomer to mon_lib.list > > I did this for both the ccp4 and coot distributions. > > I still get a fatal error that the monomer is not found in the library. > > If I read in the cif file, that doesn't work either (but I bet refinement > would work). > > Is there a different index file I need to update? >
If I understood your question correctly, you would like to add some of your frequently used ligands/cofactors to the standard monomer library so that they can be easily loaded with get-monomer and refined without fiddling with a cif file. Following Garib's recent advice, one should 1. copy the cif file into the corresponding directory in $CLIBD_MON, i.e. ligand foo's cif file FOO.cif would go into $CLIBD_MON/f/ 2. add a line to $CLIBD_MON/list/mon_lib_list.cif to describe the ligand, e.g. FOO FOO 'FOO: Fluoro-O-orotyl bar ' non-polymer 12 15 . I'm not sure if this is what you meant by mon_lib.list. There is another mon_lib.list file in $CLIBD_MON, but editing that doesn't seem to do the trick. My coot uses the refmac dictionary -- at least that's where it gets the user-defined ligands from. HTH JED
