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.


On Sat, Feb 13, 2010 at 9:48 PM, Sean Law <magicmen@hotmail.com> wrote:

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.


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
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)