[Chimera-users] measure volume area request

Tom Goddard goddard at cgl.ucsf.edu
Mon May 12 11:19:09 PDT 2008

Edward Brignole wrote:
> Tom,
> I have a request for display of the measure volume area tool - can it 
> be moved from "tools" to "features" such that it is displayed in the 
> volume viewer along with color, voxel size, etc.  The problem I have 
> is that frequently I have 30 or so volumes to open at once and then 
> need to independently go through them and set density thresholds.  
> It's really a pain to have to select the volume once in the volume 
> viewer and then again select the same volume in the measure tool then 
> go back to the viewer and adjust threshold.  After doing this 30 
> times, you'll find that most of the effort is spent making sure to 
> select the same volume in both menus so that the selected volume that 
> you are adjusting is the same volume being measured.
> Thankfully, I did however find a python script that you emailed a year 
> ago that I can steal a few lines out of to adjust the thresholds 
> automatically so that the enclosed surface of each model has the 
> appropriate volume in A^3.  BTW, I really like your hidedust.py as 
> well, however once I've executed that script adjusting the threshold 
> in the volume viewer does nothing to the displayed or measured volumes 
> - I'm using the snapshot from a week or so ago.
> Ed
> Ed Brignole
> Asturias Lab, CB227
> The Scripps Research Institute
Hi Ed,

  I agree it would be helpful to have a measured volume/area panel in 
the volume dialog.  I'll add that to our requested features list.


It still needs to be a separate dialog too because it works on surfaces 
that are not from volume data (e.g. molecular surfaces).

  The hidedust.py script hides connected components smaller than a 
specified volume.  But the Measure Volume and Area dialog displays 
values for the entire surface, hidden or not.  So those values don't 
change.  Currently there is no provision in the volume/area measurement 
to exclude the hidden part of the surface.  You also say that changing 
the contour level does not change the displayed surface.  As soon as you 
change the contour level the whole surface is replaced.  The hidedust.py 
script only acts on the surface that is shown at the time you run it, 
not on future surfaces, so all the dust should come back.  You seem to 
say this is not what happens in your use.  I've attached the hidedust.py 
script to this email in case you are using a different version.


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