[phenixbb] phenix.superpose_pdbs and nucleic acids.. does it work?

[Pavel Afonine]

Hi Francis,

it is supposed to work for nucleic acids no problems... Can you send me 
the PDB files and I will have a look?

Pavel

  On 12/14/11 10:52 AM, Francis E Reyes wrote:
> Hi phenixer's.
>
> I  need to do a superposition of two pdbs. I guess phenix.superpose_pdbs  is my jiffy but it doesn't seem to work for nucleic acids (tried selection = 'name P' or selection = 'all'). LSQKAB seems to have the same limitation. They are the exact same PDBs (1 to 1 atom/residue mapping) but just shifted and rotated relative to the other. I need a superposition or the transformation matrix for all atoms.
>
>
> Traceback (most recent call last):
>    File "/usr/local/phenix-1.7.1-743/phenix/phenix/command_line/superpose_pdbs.py", line 450, in<module>
>      run(args=sys.argv[1:])
>    File "/usr/local/phenix-1.7.1-743/phenix/phenix/command_line/superpose_pdbs.py", line 434, in run
>      m = manager(params.extract(), log)
>    File "/usr/local/phenix-1.7.1-743/phenix/phenix/command_line/superpose_pdbs.py", line 171, in __init__
>      selection_moving     = self.selection_moving)
>    File "/usr/local/phenix-1.7.1-743/phenix/phenix/command_line/superpose_pdbs.py", line 306, in _alignment
>      "bugs at phenix-online.org for help.")
> RuntimeError: Failed to identify corresponding atoms from sequence alignment.  This is probably a bug - contact bugs at phenix-online.org for help.
>
>
>
> I may just strip it down to phosphate's and rename the residues to ALA but a quick phenix jiffy would be great.
>
> Thanks!
>
> F
>
>
>
> ---------------------------------------------
> Francis E. Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
>
>
>
>
>
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