Re: [PyMOL] PyMOL-users Digest, Vol 45, Issue 5

[Sean Law]

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
  
_

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Re: [PyMOL] PyMOL-users Digest, Vol 45, Issue 5

[Michael Lerner]

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

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