Thanks Thomas, I was already printing k[i][3] (RMSD before refinement) instead of k[i][0] (RMSD after refinement) but your "cycles=0" looks cleaner.
Cheers, Albert On 05/06/2015 05:14 PM, Thomas Holder wrote: > 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 -- --------------------------------- Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 ------------------------------------------------------------------------------ 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
