[phenixbb] to get dihedral angles for a ligand

[Nigel Moriarty]

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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
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>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
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>>>
>>
>>
>>
>>
>
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-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov