Re: [phenixbb] question du jour: monomer libs where?

Partick You can run ReadySet! on your model PDB to get accurate D-peptide restraint CIFs. Or you can use REEL to edit the L-peptide restraints. $PHENIX//chem_data/geostd/g/data_GLN.cif etc Or you can run eLBOW with the three-letter code? If the atoms are named in a similar fashion to the L-peptides (C,N,CA,O) then the linking is automatic. Cheers Nigel On Wed, Oct 24, 2012 at 11:36 AM, Nathaniel Echols wrote:

On Wed, Oct 24, 2012 at 9:40 AM, Patrick Loll wrote:

...

Sorry to be thick, but how then can I run a refinement job using an input PDB that contains DGL, DAS, and DPN, when files corresponding to these monomers are not found in either chem_data/mon_lib/d or chem_data/geostd/d? I see that these residues are listed in mon_lib_list.cif, but I can't find the actual restraints files.

I'm hoping to use one or more such files to help inform my efforts to create a modified restraints file, so my questions, albeit annoying, reflect more than mere idle curiosity...

Amino acids (and nucleotides, and some other common monomers) live in chem_data/geostd, e.g. chem_data/geostd/g/data_GLU.cif. I think you could turn this into D-glutamine restraints fairly easily, the key step being changing the chiral center to "positiv". I'm not sure whether anything else needs to be done to get the chain connectivity working properly, however.

Normally what you would do for a residue present in the chemical components but not mon_lib or geostd is run eLBOW with the three-letter code.

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