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 [email protected]