[Chimera-users] How to Create Isopotential Contours, not Surfaces, with Chimera

Elaine Meng meng at cgl.ucsf.edu
Mon Aug 18 09:38:03 PDT 2008

Hi Chuck,
While Chimera does not have an option to do exactly what you want  
(draw isopotential lines in a plane), there are a couple of ways to  
approximate the effect by showing a thin slice of isopotential  
surfaces. The main disadvantage of this slice approach relative to  
true lines are that you must show some finite thickness and different  
places in the surface are angled differently relative to the slice  
plane.  Where the surface is very perpendicular to the slice plane it  
may be barely visible, whereas in other areas it may look like a  
ribbon of the specified thickness.

Given that caveat, here are the slicing approaches:

(a) Volume Viewer "Planes" feature, which you discovered.  Limitations  
are you can only slice along data axes and must use depth at least 2  
planes (at least in my tests), which may be quite thick.

(b) Per-Model Clipping (under Tools... Depiction).  If slicing rather  
than true lines is good enough, I think you want to go this route  
because it affords complete freedom over slab thickness and  
orientation.  (if you were using Volume Viewer planes, first show  
"All")  Start the tool, enable clipping for the ESP map model, turn on  
slab mode, adjust thickness, and turn on "adjust clipping with mouse"  
to allow moving/reorienting the slab interactively.  Takes a bit of  
getting used to, but then you can play all day.

I can't think of any way to do the line drawing as opposed to slicing,  
I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 17, 2008, at 5:47 PM, Charles Letner, Ph.D. wrote:

> Hello all,
> I have a map of electrostatic potentials.  Using volume viewer I am  
> able to display the surfaces at any potential value I would like (as  
> well as multiple values by having multiple bars in the volume viewer  
> histogram).  Now, I would like to be able to take a slice through  
> that potential surface and see a line associated with a given value  
> of the potential in that slice – call that the contour.  I would  
> like to have multiple potential contours, each with a different  
> constant value in that contour (-10 for one contour, -20 for the  
> next, -30 for the third, and so on- call these the iso-potential  
> contours).  This would allow the contours of potential to be seen in  
> a single plane.
> Seems like I am so close using planes but that just isn’t working.   
> Am I approaching this right and if so any hints would be  
> appreciated?  If I am off base with the approach, I sure would  
> appreciate a nudge in the right direction?
> Cheers,
> Chuck

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