[phenixbb] to get dihedral angles for a ligand

[Maia Cherney]

Nigel,

I am getting different numbers for dihedrals from reel and from coot or 
pymol. This is one of my ligands, ADP. If you run reel and compare with 
manual measurement, some numbers are the same, but most of them are 
different.
For example, var1 and var2 are the same, but var3 to var6 are different. 
Here is the comparison first number, pymol; second number, reel) 
(hydrogens are removed).

var3 -75.8; 28.6
var4 129.6; -117.6
var5 -169.1; 154.1
var6 136.7; -151.7

etc. What is the problem? Is it a different way to measure the torsions?

Maia


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