[phenixbb] to get dihedral angles for a ligand

Nigel Moriarty nwmoriarty at lbl.gov
Fri May 14 08:35:22 PDT 2010


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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>>>
>>>
>>
>>
>>
>>
>
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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



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