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

Francis E Reyes Francis.Reyes at Colorado.EDU
Wed Dec 14 10:52:24 PST 2011

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>
  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.



Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

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