[phenixbb] to get dihedral angles for a ligand

Maia Cherney chern at ualberta.ca
Fri May 14 09:19:15 PDT 2010


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
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>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>>
>>>>
>>>>         
>>>
>>>
>>>       
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>>
>>     
>
>
>
>   



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