[phenixbb] to get dihedral angles for a ligand

[Nigel Moriarty]

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
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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
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>>>
>>
>>
>>
>>
>
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-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
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