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] Someone interested in writing a DSSR plugin for PyMOL?
Hi all, Is anyone interested in writing a DSSR plugin for PyMOL? DSSR is an integrated software tool for Dissecting the Spatial Structure of RNA (http://x3dna.bio.columbia.edu/docs/dssr-manual.pdf). Among other things, DSSR defines the secondary structure of RNA from 3D atomic coordinates in a way similar to DSSP does for proteins. Most of its output could be translated 1:1 into PyMOL selections, making it available for coloring and other selection based features. A PyMOL plugin could act as a wrapper which runs DSSR for an object or atom selection. Xiang-Jun Lu, the author of DSSR, is also working on base pair visualization (see http://x3dna.org/articles/seeing-is-understanding-as-well-as-believing), similar to (but more advanced) what's already available from 3DNA (http://pymolwiki.org/index.php/3DNA). Xiang-Jun would be happy to collaborate with someone who has experience with Python and the PyMOL API for writing an extension or plugin. Please contact me if this sounds appealing to you. Get DSSR from http://x3dna.org/ See it hooked up with JSmol: http://chemapps.stolaf.edu/jmol/jsmol/dssr.htm Cheers, Thomas -- 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] Delete all but one object
Hi Bernhard,
delete strictly operates on object names, not on atom selections. This
difference is unfortunately a common point of confusion.
Here's a delete command which operates on a selection and therefore supports
the not operator:
python
@cmd.extend
def delete_by_sele(selection):
cmd.delete(' '.join(cmd.get_object_list('(' + selection + ')')))
python end
If you paste this in the PyMOL command line or put it in your pymolrc script,
you can do:
PyMOL delete_by_sele not obj_final
Hope that helps.
Cheers,
Thomas
On 08 May 2015, at 14:42, Bernhard Lechtenberg
blechtenb...@sanfordburnham.org wrote:
Hi all,
after an extensive pymol session, I ended up with a lot of intermediate
objects that I now want to delete so I will only keep my final object. Is
there an easy
way to remove all but one object? I tried the delete command, but something
like
delete (not obj_final)
did not work as expected and only deleted obj_final.
Any help is appreciated.
Thanks,
Bernhard
Bernhard C. Lechtenberg, PhD
Postdoctoral Fellow
Riedl Lab
Sanford-Burnham Medical Research Institute
10901 North Torrey Pines Road
La Jolla, CA 92037, USA
Phone: 858.646.3100 x 4216
Email: blechtenb...@sanfordburnham.org
--
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
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[PyMOL] Delete all but one object
Hi all, after an extensive pymol session, I ended up with a lot of intermediate objects that I now want to delete so I will only keep my final object. Is there an easy way to remove all but one object? I tried the delete command, but something like delete (not obj_final) did not work as expected and only deleted obj_final. Any help is appreciated. Thanks, Bernhard Bernhard C. Lechtenberg, PhD Postdoctoral Fellow Riedl Lab Sanford-Burnham Medical Research Institute 10901 North Torrey Pines Road La Jolla, CA 92037, USA Phone: 858.646.3100 x 4216 Email: blechtenb...@sanfordburnham.orgmailto:blechtenb...@sanfordburnham.org -- 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] Delete all but one object
Thanks for the quick reply. That works like a charm.
On May 8, 2015, at 12:37 PM, Thomas Holder thomas.hol...@schrodinger.com
wrote:
Hi Bernhard,
delete strictly operates on object names, not on atom selections. This
difference is unfortunately a common point of confusion.
Here's a delete command which operates on a selection and therefore supports
the not operator:
python
@cmd.extend
def delete_by_sele(selection):
cmd.delete(' '.join(cmd.get_object_list('(' + selection + ')')))
python end
If you paste this in the PyMOL command line or put it in your pymolrc script,
you can do:
PyMOL delete_by_sele not obj_final
Hope that helps.
Cheers,
Thomas
On 08 May 2015, at 14:42, Bernhard Lechtenberg
blechtenb...@sanfordburnham.org wrote:
Hi all,
after an extensive pymol session, I ended up with a lot of intermediate
objects that I now want to delete so I will only keep my final object. Is
there an easy
way to remove all but one object? I tried the delete command, but something
like
delete (not obj_final)
did not work as expected and only deleted obj_final.
Any help is appreciated.
Thanks,
Bernhard
Bernhard C. Lechtenberg, PhD
Postdoctoral Fellow
Riedl Lab
Sanford-Burnham Medical Research Institute
10901 North Torrey Pines Road
La Jolla, CA 92037, USA
Phone: 858.646.3100 x 4216
Email: blechtenb...@sanfordburnham.org
--
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
___
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