[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  

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


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.


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

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