[PyMOL] Trying to get rms and rms_cur to run

[Evan K. <eva...@bc...>]

Hi Folks,

     I have two positions of one small molecule.  I am trying to  
determine the RMSD between them without doing an align

I read the molecules into pymol as m1 and m2.  As seen below each has  
23 atoms.  When I do an rms it gives the error: No atoms selected, but  
if I do an align it it fine.  Can anyone help with why the rms does  
not work?

PyMOL>sele a, m1
  Selector: selection "a" defined with 23 atoms.

PyMOL>sele b, m2
  Selector: selection "b" defined with 23 atoms.

PyMOL>rms m2, m1
ExecutiveRMS-Error: No atoms selected.

PyMOL>align m2, m1
  Match-Warning: unknown residue type 'AMP' (using X).
  Match-Warning: unknown residue type 'AMP' (using X).
  Match: read scoring matrix.
  Match: assigning 1 x 1 pairwise scores.
  MatchAlign: aligning residues (1 vs 1)...
  ExecutiveAlign: 23 atoms aligned.
  ExecutiveRMS: 1 atoms rejected during cycle 1 (RMS=0.37).
  Executive: RMS =    0.333 (22 to 22 atoms)

PyMOL>rms m2, m1
ExecutiveRMS-Error: No atoms selected.

-------------------------------------------------------------------
Evan R. Kantrowitz,  
Ph.D                                                                  eva...@bc...
Boston  
College 
                                                                                    Tel 
. 617-552-4558
Department of  
Chemistry 
                                                                   FAX  
617-552-2705
Merkert Chemistry Center, Rm  
239                                                  www2.bc.edu/ 
~kantrow
Chestnut Hill, MA 02467
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