Tom,
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")
Cheers,
Warren
-----Original Message-----
From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr]
Sent: Wed 10/28/2009 8:09 PM
To: pymol-users@lists.sourceforge.net
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.
thanks,Tom
------------------------------------------------------------------------------
Come build with us! The BlackBerry(R) Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9 - 12, 2009. Register now!
http://p.sf.net/sfu/devconference
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
------------------------------------------------------------------------------
Come build with us! The BlackBerry(R) Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9 - 12, 2009. Register now!
http://p.sf.net/sfu/devconference
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
