[phenixbb] phenix.refine: including modifications

[Patrick Loll]

OK, so I think you are implying that if I feed phenix.refine the MAN- 
a-D.cif, it will assume that any MAN residue it encounters in the PDB  
file is alpha. Is that right?

Does this mean that if you have examples of both alpha and beta  
mannose residues in a structure, you would need to give one of them a  
different residue name?

Thanks,

Pat

On 16 Oct 2008, at 4:52 PM, Engin Ozkan wrote:

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

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