<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 20/03/12 23:35, Geoffrey Feld wrote:
<blockquote
cite="mid:CAE2HsN6NSj12Pu2-9jhgiBHBT-Wiu62z6ODsT2u6bTh0tEz0VA@mail.gmail.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
Greetings,<br>
<br>
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,
</blockquote>
<br>
<br>
Eeeek! It is not clear to me why you are doing that. I would
simply beam in D amino acids, either with Get Monomer or Search
Monomer Library (if you don't know the TLC). One I have Rted the
new AA into position, I'd merge the individual molecules (into <br>
the first one typically) renumber and change chain ids... You'll
have to delete the peptide hydrogens and OXTs of course. That
(AFAICS) will give you a model that should Just Work with
phenix.refine. I don't follow how you would have problems with GLU
- or that this method would do so.<br>
<br>
HTH, <br>
<br>
Paul.<br>
<br>
<br>
</body>
</html>