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]>

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