The complication with cmd.align() is that it is doing a whole lot more than a simple alignment.  The first number is in fact the RMS, but it covers only the subset of the input atoms remaining after refinement is completed. The count of aligned atoms is the second field.

If you're looking for exact RMS fit values over a well-defined set of atoms, try using cmd.pair_fit(sele1, sele2) instead, for example:

load $TUT/1hpv.pdb

create loopA, A/46-55/

create loopB, B/46-55/

show sticks, loop*

print cmd.pair_fit("loopA////CA", "loopB////CA")


-----Original Message-----
From: Thomas Evangelidis []
Sent: Wed 10/28/2009 8:09 PM
Subject: [PyMOL] how to get RMSD from align command

Simple question, it must have been answered before but couldn't find 
it so far:

how can I get the RMSD value from the align command in a python 
script? cmd.align() returnes a tuple of 8 numbers and none of them is 
the actual RMSD value I get when I align these 2 structures manually.


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