Evan,
Normally, fit, rms, and rms_cur require that all atom identifiers match.
However, we're trying to increase flexibility by supporting alternate
pairwise "matchmakers"...assuming (A) that you're running 1.2 beta 3 and
(B) that the atom names match:
rms_cur m1, m2, matchmaker=4
may work. To visualize the mapping (for verification):
rms_cur m1, m2, matchmaker=4, object=alignment
Cheers,
Warren
________________________________
From: Evan Kantrowitz [mailto:[email protected]]
Sent: Tuesday, March 10, 2009 7:59 AM
To: [email protected]
Subject: [PyMOL] Trying to get rms and rms_cur to run
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
[email protected]
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
-------------------------------------------------------------------
