[phenixbb] phenix.refine: including modifications
Patrick Loll
pat.loll at drexel.edu
Thu Oct 16 13:36:33 PDT 2008
Hi all,
I'm starting to use phenix.refine and have some questions about
defining modifications during refinement:
I want to refine a structure that includes several alpha-D-mannose
residues.
I see that mon_lib_list.cif contains, under the "LIST OF RECOGNIZED
MODIFIED MONOMERS," the following line:
MAN-a-D MAN-b-D SUG-a-D MAN alpha_D_mannose D-pyranose
Question:
Where/how do I invoke this modification? I.e., how do I tell the
refinement program that a particular sugar is an alpha, and not a
beta, mannose?
Clearly I can't label the residue MAN-a-D in the PDB file, as this
would step on the chain identifier.
I'm guessing that I label each sugar MAN in the PDB file, and then
insert some instructions about applying the modification in the CIF
file that I supply to the refinement program. However, I'm not able
to find an example of the appropriate syntax.
Thanks,
Pat Loll
------------------------------------------------------------------------
---------------
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102-1192 USA
(215) 762-7706
pat.loll at drexelmed.edu
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20081016/2eab5836/attachment-0003.htm>
More information about the phenixbb
mailing list