[phenixbb] building a peptide-like polymer with phenix.elbow

Geoffrey Feld gkfeld at berkeley.edu
Tue Mar 20 16:35:17 PDT 2012


I have a co-crystal structure of a protein bound to an interesting polymer
-- poly-D-g-glutamic acid (poly glutamic acid with D chirality and gamma
linked, rather than alpha linked). In the structure, I have density
corresponding to different links, from 1 to 6 (so far). I'd like to build a
ligand that has "residues" much like a polypeptide polymer so that I can
refine each residue individually (hopefully in COOT). Up till now, I've
been using SMILES to generate the different length polymers so I have pdbs
and cif files, and then (painstakingly) modelling them into COOT, building
restraints for refinement, etc. More recently, I used maestro to build a
dimer that at least has the right atom labels you'd expect for a protein.
However, I can't use phenix now to generate cif files because it is
confused by the GLU. Is there a way to use phenix.elbow to make a
multi-residue polymer? I'm also doing some monte carlo minimizations in
macromodel to generate models of the various low energy states and would
like to use them as building blocks, so an easy order-of-operations would
be to generate the files in macromodel and feed them in via pdbs to
phenix.elbow to generate cif restraints. Any help on this would be greatly


Geoffrey K. Feld

Department of Chemistry
492 Stanley Hall
University of California, Berkeley

"Vigilia pretium libertatis"
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