Yes, yes, yes. Thank you.

I had modified the wrong list file.  Judit's instructions are perfect.

On May 29, 2009, at 8:45 AM, Judit Debreczeni wrote:

Hello Everyone

Where does coot get monomers from?
Is it my ccp4 distribution? Or the coot distribution (It's a kind of old

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.


Dr. Sue A. Roberts
Biochemistry & Molecular Biophysics
University of Arizona
520 621 8171

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