Hi Albert, Please pay attention to the difference between all-atom RMSD and RMSD after outlier rejection. http://pymolwiki.org/index.php/Align#RMSD
If your "trj" and "pdb1" have identical topology and matching atom identifiers, then you can also use cmd.rms(). http://pymolwiki.org/index.php/Rms Cheers, Thomas On 06 May 2015, at 11:56, Albert Solernou <a.soler...@leeds.ac.uk> wrote: > Terribly useful Carsten! > > I could easily do a loop and get the RMS along the trajectory: > k = [] > for i in range(1,101): k.append(cmd.align("trj","pdb1",mobile_state=i)) > for i in range(100): print k[i][0] > > Cheers, > Albert > > > On 05/06/2015 04:20 PM, Schubert, Carsten [JRDUS] wrote: >> 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 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y _______________________________________________ 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
