[PyMOL] Trying to get rms and rms_cur to run

[Evan Kantrowitz]

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 ***@bc.edu
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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[Warren DeLano]

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