[phenixbb] phenix.refine: including modifications

[Engin Ozkan]

I don't have access to phenix, ccp4, or any of my files right now (our 
systems are being upgraded), but I'll make some guesses that may help 
you, I might be off the mark.
I think the data_link determines the linkage type, so you should have 
ALPHA1-4 and BETA1-4 for different mannoses in your parameter file.
You can also call alpha and beta mannoses different names, I think MAN 
is usually alpha mannose, and BMA is beta, and give phenix different cif 
files to phenix.

I suggest you look into the cif descriptions, runs a few phenix runs, 
and convince yourself that everything checks out chemically.

Engin

Patrick Loll wrote:
> 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 <mailto:pat.loll at drexelmed.edu>
>
>
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