Oh, I see... It looks like I'll need to end up writing a short script that does the loop along the trajectory together with a correct RMS calculation.
Thanks for the tip, Carsten. Cheers, Albert On 05/08/2015 04:11 PM, Schubert, Carsten [JRDUS] wrote: > Hi Al, > > based on my experience running align or super with "cycles=0" has the > tendency to produce inferior alignment results. So depending on how similar > the conformation of your structures are you may end up with skewed > statistics. What I've done in the past and for a paper I'm working on now is > to run the alignment with default parameters to get the best superposition > and then calculate the statistics by hand from the superposed structures. Not > sure if cmd.rms() would do this for all residues w/o outlier rejection, so I > ended up writing code for myself. The colorbyrmsd.py > (http://pymolwiki.org/index.php/ColorByRMSD) script gives a nice illustration > on how to approach this this. > > Carsten > > -----Original Message----- > From: Albert Solernou [mailto:a.soler...@leeds.ac.uk] > Sent: Friday, May 08, 2015 10:04 AM > To: Thomas Holder > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] RMS over a MD trajectory. > > 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 -- --------------------------------- 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
