[phenixbb] phenix.refine: including modifications

Engin Ozkan eozkan at stanford.edu
Thu Oct 16 13:52:41 PDT 2008

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,


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
> pat.loll at drexelmed.edu <mailto:pat.loll at drexelmed.edu>
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