[phenixbb] question du jour: monomer libs where?

Nathaniel Echols nechols at lbl.gov
Wed Oct 24 11:36:14 PDT 2012

On Wed, Oct 24, 2012 at 9:40 AM, Patrick Loll <pat.loll at drexel.edu> 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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