(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 commands:
 
alter all, segi=''
 
alter c321 and chain E, chain='A'
 
alter c321 and chain I, chain='B'
 
etc.
 
Cheers,
Warren

From: Albert Solernou [mailto:albert@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
superimposing:

> 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:

> 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
0.99rc6:

http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=486254


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,
albert

------------------------------------------------------------------------------
Stay on top of everything new and different, both inside and
around Java (TM) technology - register by April 22, and save
$200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
300 plus technical and hands-on sessions. Register today.
Use priority code J9JMT32. http://p.sf.net/sfu/p
_______________________________________________
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users