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

Thomas Goddard goddard at cgl.ucsf.edu
Mon Aug 18 10:28:43 PDT 2008

Hi Chuck,

   Chimera does not have a mode that displays line contours in a plane. 
  This is item 90 on the following Chimera feature request web page:


Elaine's two suggestions show a very thin section of the contour 
surface.  This has some problems.  First if you use the volume planes 
mode you'll want to turn of the "Cap high values at box faces" option in 
the volume dialog Surface and Mesh Options panel.  The thin slab cuts 
out thin ribbons from the surface.  They tend to look better if you tilt 
the plane so you are not viewing it face-on.  This seems to reduce the 
places where the ribbon is viewed edge-on and has zero thickness.  Also 
the appearance is greatly improved if you save a super-sampled image -- 
reducing the jaggedness.  Also the directional lighting on the ribbons 
is unpleasant.  You can reduce it's effects by increasing the brightness 
of the lights with the volume brightness and transparency panel.  All 
this is still a rather unsatisfactory approximation to what you want.

   I think it would be not too difficult to make a Python script to draw 
actual contour lines.  If the slab techniques don't work well enough for 
you let me know and I can try to write such a script.


Elaine Meng wrote:
> 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.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html 
>  >
> I can't think of any way to do the line drawing as opposed to slicing,  
> however.
> I hope this helps,
> Elaine
> -----
> 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
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> 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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