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 "[email protected] for help.") RuntimeError: Failed to identify corresponding atoms from sequence alignment. This is probably a bug - contact [email protected] 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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