Re: [COOT] can coot get my monomers?
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-polymer12 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
Re: [COOT] can coot get my monomers?
Yes, yes, yes. Thank you. I had modified the wrong list file. Judit's instructions are perfect. Sue 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 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 Dr. Sue A. Roberts Biochemistry Molecular Biophysics University of Arizona 520 621 8171 s...@email.arizona.edu http://www.biochem.arizona.edu/xray
Re: [COOT] can coot get my monomers?
Hi Sue, I usually get SMILES from the software where you draw the molecules, and input SMILES into Coot. Coot will automatically generate a cif library file which can be used for refinement in CCP4. You can find the cif file under the Coot examples directory. Hope it helps. Joe Sue Roberts wrote: 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? Sue Dr. Sue A. Roberts Biochemistry Molecular Biophysics University of Arizona 520 621 8171 s...@email.arizona.edu http://www.biochem.arizona.edu/xray
Re: [COOT] can coot get my monomers?
I don't think you need to add a monomer for working with a ligand in either coot or ccp4. You can use the Dundee PRODRGD server for making CIF and PDB files of the ligand. You can call the ligand whatever you want in the PDB file (we usually leave it as DRG until submission). We typically load the PDB and cif file into coot, and use the find ligand feature to dock it. Kendall -- Kendall W. Nettles, PhD Associate Professor Department of Cancer Biology The Scripps Research Institute 133 Scripps Way Jupiter Fl 33458 On 5/27/09 1:09 PM, Sue Roberts s...@email.arizona.edu wrote: 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? Sue Dr. Sue A. Roberts Biochemistry Molecular Biophysics University of Arizona 520 621 8171 s...@email.arizona.edu http://www.biochem.arizona.edu/xray
