[phenixbb] to get dihedral angles for a ligand

Maia Cherney chern at ualberta.ca
Fri May 14 11:00:29 PDT 2010


Thanks

Nigel Moriarty wrote:
> Maia
>
> I can add a feature to write all the columns in some simple text
> format.  I'll let you know when its in the release.
>
> Nigel
>
> On Fri, May 14, 2010 at 9:19 AM, Maia Cherney <chern at ualberta.ca> wrote:
>   
>> Hi Nigel,
>>
>> I have the ADP and methyl-ATP ligands in my complexes. I see that some
>> torsion angles that are common for both ligands are very different. I want
>> to give a table in my paper with the most changed torsion angles. They
>> should be actual angles after refinement, not from the ideal cif files.
>> Right now I just do screen shots (png files) to save the information from
>> different complexes, but it's very inconvenient. If I could get a list of
>> torsions as a table in a text file that would be most convenient.
>>
>> Maia
>>
>> Nigel Moriarty wrote:
>>     
>>> Maia
>>>
>>> You can save a CIF file from REEL using a pull-down menu under File.
>>> However, I'm a little unclear on what you are trying to achieve.  Can
>>> you elaborate?
>>>
>>> Nigel
>>>
>>> On Thu, May 13, 2010 at 9:25 PM, Maia Cherney <chern at ualberta.ca> wrote:
>>>
>>>       
>>>> Hi Nigel,
>>>> The phenix.reel worked, even with the error message (Gtk-Message: Failed
>>>> to
>>>> load module "canberra-gtk-module": libcanberra-gtk-module.so: cannot open
>>>> shared object file: No such file or directory).
>>>>
>>>> I got all dihedrals in the reel window, now how can I save them?
>>>>
>>>> Maia
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Nigel Moriarty wrote:
>>>>
>>>>         
>>>>> That should be model.pdb, the final model from the refinement.
>>>>>
>>>>> Sorry
>>>>>
>>>>> Nigel
>>>>>
>>>>> On Thu, May 13, 2010 at 4:32 PM, Maia Cherney <chern at ualberta.ca> wrote:
>>>>>
>>>>>
>>>>>           
>>>>>> lig.cif is the cif file from elbow (ideal) that I gave in the
>>>>>> refinement.
>>>>>> How do I get the model.cif?
>>>>>>
>>>>>> Maia
>>>>>>
>>>>>> Nigel Moriarty wrote:
>>>>>>
>>>>>>
>>>>>>             
>>>>>>> As Patrick correctly stated you should look in the .geo.  All the
>>>>>>> geometry information is written there and it is instructive to look
>>>>>>> there.  There is, however, an alternative if you wish to get more info
>>>>>>> about a ligand.  You can type
>>>>>>>
>>>>>>> phenix.reel lig,cif model.cif
>>>>>>>
>>>>>>> choose "Geometry transfer".  You can then compare the ideal and the
>>>>>>> actual values of all of the restraints listed in the CIF restraints
>>>>>>> file. You may have to choose the pull-down menu View->List geometry
>>>>>>> values depending on your version.
>>>>>>>
>>>>>>> Nigel
>>>>>>>
>>>>>>> On Thu, May 13, 2010 at 2:35 PM, Patrick Loll <pat.loll at drexel.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>               
>>>>>>>> ooh ooh ooh--I know this!
>>>>>>>>
>>>>>>>> Look in the .geo file
>>>>>>>>
>>>>>>>> On 13 May 2010, at 5:34 PM, Maia Cherney wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>                 
>>>>>>>>> Dear phenixbb,
>>>>>>>>> how to get listed all dihedral angles from a ligand after
>>>>>>>>> refinement.
>>>>>>>>> (Not ideal cif files, but actual dihedral angles).
>>>>>>>>>
>>>>>>>>> Maia
>>>>>>>>> _______________________________________________
>>>>>>>>> phenixbb mailing list
>>>>>>>>> phenixbb at phenix-online.org
>>>>>>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>                   
>>>>>>>> ---------------------------------------------------------------------------------------
>>>>>>>> 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
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> phenixbb mailing list
>>>>>>>> phenixbb at phenix-online.org
>>>>>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>                 
>>>>>>>               
>>>>>> _______________________________________________
>>>>>> phenixbb mailing list
>>>>>> phenixbb at phenix-online.org
>>>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>>>>
>>>>>>
>>>>>>
>>>>>>             
>>>>>
>>>>>           
>>>> _______________________________________________
>>>> phenixbb mailing list
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>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>>
>>>>
>>>>         
>>>
>>>
>>>       
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>>     
>
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