Hi Al,
you would need to go through the Python API:
python
rms=cmd.align("mob////CA","tar////CA", quiet=0)
print rms
python end
rms contains a tuple with various parameters related to the superposition. The
first value in the tuple i.e. rms[0] should be the RMS value.
HTH
Carsten
-----Original Message-----
From: Albert Solernou [mailto:a.soler...@leeds.ac.uk]
Sent: Wednesday, May 06, 2015 8:32 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] RMS over a MD trajectory.
Hi,
I am trying to compute the RMS between a PDB file and a Gromacs trajectory. I
can see that "align" does things correctly when:
align trj, pdb1, mobile_state=1
i. e., when I align the first snapshot of the trajectory with the PDB file. I
also understand that PyMOL does compute the RMS along the trajectory if I
simply:
align trj, pdb1
as it is told in:
http://www.pymolwiki.org/index.php/Align
However, I am unable to get the list of RMS values printed out. How could I do
that?
Thanks,
Albert
--
---------------------------------
Dr Albert Solernou
EPSRC Research Fellow,
Department of Physics and Astronomy,
University of Leeds
Tel: +44 (0)1133 431451
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