Re: [PyMOL] RMS over a MD trajectory.
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(mobCA,tarCA, 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
Re: [PyMOL] RMS over a MD trajectory.
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(mobCA,tarCA, 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 -- 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
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(mobCA,tarCA, 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
[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 -- 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
Re: [PyMOL] RMS over a MD trajectory.
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(mobCA,tarCA, 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
Re: [PyMOL] RMS over a MD trajectory.
Hi Al, you would need to go through the Python API: python rms=cmd.align(mobCA,tarCA, 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 -- 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 -- 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
Re: [PyMOL] RMS over a MD trajectory.
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(mobCA,tarCA, 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 -- 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
