Hi Patrick, Let me give my best shot, I don't have my files with me. There might be some mistakes. You can give phenix.refine the .cif file on command line for MAN-a-D.cif, which you can get from ccp4 sketcher (and I think under phenix, somewhere close to where you found mon_lib_list.cif). Then you should describe the linkage as an alpha linkage by data_link = ALPHA1-4 if you have 1-4 linkage, by something like this. In the mon_lib_list.cif, I believe they have all recognized linkage types somewhere down the file, where you can see the proper description for ALPHA1-4, ALPHA1-6, BETA1-4, and other common sugar linkages. refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-4 residue_selection_1 = chain X and resname MAN and resid 905 residue_selection_2 = chain X and resname MAN and resid 906 } I also delete hydrogens and the removed O1 in coot before I do refinement in phenix, but I am not sure if this is necessary (Phenix supposedly knows the deletion, it is in the description of the bond). Good luck, Engin Patrick Loll wrote:
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] mailto:[email protected]
------------------------------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb