Re: [PyMOL] PyMOL-users Digest, Vol 45, Issue 5
On Sun, Feb 14, 2010 at 4:39 PM, David Hall li...@cowsandmilk.net wrote: I don't think DynoPlot can't do this. Are there even callbacks to watch for things like changing state in the Pymol GUI? Maybe that should be a feature request as it would allow for a lot more powerful plugins. Callbacks that we can bind to through TKinter to watch for modifications in the OpenGL window of Pymol like changing state, moving atoms, etc, then we can easily build boxes that reflect these changes. If this is somehow already possible, I would love someone to point me to an example. Check out pymol.importing.load_callback - is that what you were thinking of? (I think I've tried this before, but I can't remember exactly what the behavior was.) -Nat -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev___ 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] PyMOL-users Digest, Vol 45, Issue 5
I don't think DynoPlot can't do this. Are there even callbacks to watch for things like changing state in the Pymol GUI? Maybe that should be a feature request as it would allow for a lot more powerful plugins. Callbacks that we can bind to through TKinter to watch for modifications in the OpenGL window of Pymol like changing state, moving atoms, etc, then we can easily build boxes that reflect these changes. If this is somehow already possible, I would love someone to point me to an example. -David On Sat, Feb 13, 2010 at 10:01 PM, Michael Lerner mglerner+sourcefo...@gmail.com wrote: I don't have any MD trajectories on hand at the moment, but can DynoPlot do this? If not, it might be an easy modification. Cheers, -Michael On Sat, Feb 13, 2010 at 9:48 PM, Sean Law magic...@hotmail.com wrote: Hi, Another idea that came to mind while staring at MD trajectories all day is the ability to display measured values (distance, angle, dihedral, etc) in a localized or boxed in area (maybe even under the list of objects). The main use for a measurement area would be to make it easier to monitor allosteric effects. For example, from an MD simulation, if I have a protein that has two distant binding sites and I want to monitor the effects on site A (perhaps, the cavity of site a changes) when the inhibitor binds to site B. In PyMOL, I could measure the distance between the inhibitor and site B but it may simply be too far away to see the changing value as I flip through the frames since it is so far away from site A. If the measurement was instead displayed in its own distinct area, independent of the molecule viewing pane then this could be helpful (or have it displayed in both a separate location as well as the molecule viewing area). Just a thought. Sean Windows® phone-your Windows stuff, on the go. See more. -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ 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 -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ 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 -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ 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] PyMOL-users Digest, Vol 45, Issue 5
Hi, Another idea that came to mind while staring at MD trajectories all day is the ability to display measured values (distance, angle, dihedral, etc) in a localized or boxed in area (maybe even under the list of objects). The main use for a measurement area would be to make it easier to monitor allosteric effects. For example, from an MD simulation, if I have a protein that has two distant binding sites and I want to monitor the effects on site A (perhaps, the cavity of site a changes) when the inhibitor binds to site B. In PyMOL, I could measure the distance between the inhibitor and site B but it may simply be too far away to see the changing value as I flip through the frames since it is so far away from site A. If the measurement was instead displayed in its own distinct area, independent of the molecule viewing pane then this could be helpful (or have it displayed in both a separate location as well as the molecule viewing area). Just a thought. Sean _ -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev___ 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] PyMOL-users Digest, Vol 45, Issue 5
I don't have any MD trajectories on hand at the moment, but can DynoPlot do this? If not, it might be an easy modification. Cheers, -Michael On Sat, Feb 13, 2010 at 9:48 PM, Sean Law magic...@hotmail.com wrote: Hi, Another idea that came to mind while staring at MD trajectories all day is the ability to display measured values (distance, angle, dihedral, etc) in a localized or boxed in area (maybe even under the list of objects). The main use for a measurement area would be to make it easier to monitor allosteric effects. For example, from an MD simulation, if I have a protein that has two distant binding sites and I want to monitor the effects on site A (perhaps, the cavity of site a changes) when the inhibitor binds to site B. In PyMOL, I could measure the distance between the inhibitor and site B but it may simply be too far away to see the changing value as I flip through the frames since it is so far away from site A. If the measurement was instead displayed in its own distinct area, independent of the molecule viewing pane then this could be helpful (or have it displayed in both a separate location as well as the molecule viewing area). Just a thought. Sean -- Windows® phone-your Windows stuff, on the go. See more.http://go.microsoft.com/?linkid=9708119 -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ 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 -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev___ 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
