[phenixbb] phenix.refine: including modifications

Pavel Afonine PAfonine at lbl.gov
Fri Oct 17 11:29:59 PDT 2008


Hi All,

the file ending with ".geo" has a complete footprint of all the geometry 
restraints used in phenix.refine run. For example, if you want to check 
that atom A is bonded to atom B with given bond length, bond angle, 
corresponding sigmas, and so on, just find the corresponding record in 
".geo" file. If you don't see it there, then it means this particular 
bond (angle, ...) was not restrained.

Pavel.

On 10/16/2008 3:16 PM, Engin Ozkan wrote:
> 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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>>   
>>     
>
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