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

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Patrick J. Loll, Ph. D.

Professor of Biochemistry & Molecular Biology

Director, Biochemistry Graduate Program

Drexel University College of Medicine

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