[phenixbb] to get dihedral angles for a ligand

Maia Cherney chern at ualberta.ca
Thu May 13 16:48:43 PDT 2010


I got the error

Gtk-Message: Failed to load module "canberra-gtk-module": 
libcanberra-gtk-module.so: cannot open shared object file: No such file 
or directory
Traceback (most recent call last):
  File "/usr/local/phenix-1.6.1-357/reel/reel/command_line/main.py", 
line 20, in <module>
    reel_frame.ProcessArguments(args, options)
  File "/usr/local/phenix-1.6.1-357/reel/reel/ReelFrame.py", line 1935, 
in ProcessArguments
    overlay=options.overlay,
  File "/usr/local/phenix-1.6.1-357/reel/reel/ReelFrame.py", line 1124, 
in LoadFile
    overlay=overlay,
  File "/usr/local/phenix-1.6.1-357/reel/reel/MoleculeNotebook.py", line 
127, in ReadFile
    if atom1.unique_residue_key==atom2.unique_residue_key:
AttributeError: AtomClass instance has no attribute 'unique_residue_key'

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
>>
>>     
>
>
>
>   



More information about the phenixbb mailing list