(Sorry if this is dupe -- my email client is acting up...)
the rms_* and fit commands required that the atoms in each selection to have 
matching identifiers: such as chain, resi, segi, resn, etc.  You can use the 
"alter" command to set the identifiers to matching values before issuing such 
alter all, segi=''
alter c321 and chain E, chain='A'
alter c321 and chain I, chain='B'


From: Albert Solernou [mailto:alb...@mmb.pcb.ub.es]
Sent: Thu 4/23/2009 9:42 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] rms_cur, rms, fit - No atoms selected

I'm new at pymol, and I'm trying to use the commands rms and rms_cur.

I have two pdb files, with two proteins in each.
First, I load the files

> load 1acb_321000.pdb, c321
> load 1acb_dock.pdb, dock

then I select the backbone of the B chain of each complex,
> select lc, /c321//b//ca+c+n+o
> select lr, /dock//b//ca+c+n+o

Everything works until here. Each selection is showed on the screen, and
they are 207 atoms each. Now I want to get the rms value without

> rms_cur lc, lr

but it does not work:
ExecutiveRMS-Error: No atoms selected.
It also does not work with rms or fit commands, although it works with

> align lc, lr
 Match: read scoring matrix.
 Match: assigning 69 x 69 pairwise scores.
 MatchAlign: aligning residues (69 vs 69)...
 ExecutiveAlign: 207 atoms aligned.
 ExecutiveRMS: 5 atoms rejected during cycle 1 (RMS=0.01).
 ExecutiveRMS: 2 atoms rejected during cycle 2 (RMS=0.01).
 Executive: RMS =    0.006 (200 to 200 atoms)

I've seen that someone has reported a bug at debian's, under the version


I've tried the 1.0r2-1 version (commming with ubuntu, apt-get), and
compliling the source code from the svn of the current version, 1.2-x.
Same results.

Hope someone can help me,

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