[Chimera-users] reverse "zone" tool?

Thomas Goddard goddard at cgl.ucsf.edu
Thu Nov 29 10:23:49 PST 2007

Gabriel Lander wrote:
> Hi Tom,
> is it possible to somehow make the "zone" tool in the volume viewer do 
> the reverse of what it does?  I have a PDB docked into a density file 
> and I want to remove the density surrounding it so that it's easier to 
> focus on the rest of the structure.
> By the way, I thoroughly enjoyed your demo of the new Chimera features 
> here at the cryo course, I'm sorry I didn't have a chance to chat very 
> much afterwards,
> Cheers,
> -gabe

Hi Gabe,

   One trick would be to use the "Color Zone" tool to color the surface 
near the fit model completely transparent (hence invisible).  Use menu 
entry Actions / Color / From Editor, click the Opacity button and set 
opacity to zero.  Your molecule will be invisible.  Then use Tools / 
Volume Data / Color Zone, select all atoms (Select / Select All) and 
press the color zone dialog Color button.  Then go back and change the 
color of the molecule to something visible.

   Three drawbacks of this approach.  First, it doesn't allow you to 
save the map with the region near the molecule zeroed out -- it is only 
coloring the surface.  Second, having a partially transparent surface 
makes the rendering slower.  Third, Chimera only handles one transparent 
model correctly.  If you try to add a second transparent surface you 
will see odd effects, like the invisible patch blocks the second 
transparent surface.  If these limitations are severe, I can give you a 
bit of Python code that actually makes a copy of the map with the part 
near the molecule erased.


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