[Chimera-users] Viewing mode

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 19 08:54:59 PST 2008

Hi James,
It is a shortcoming of raytracing from Chimera that the global (Side  
View) clipping is not included, as listed in the Limitations here:

However, you may be able to get what you want by using Per-Model  
Clipping (under Tools... Depiction):

You would have to turn this on for each model individually that you  
want to clip, and it takes a little practice moving the plane around  
with the mouse.  It is especially useful when you want to clip one  
model but not another, but if you do want to clip them all with the  
same plane, there is an option to "align plane" of one model with  
that for another.  Experiment a little and you will see what I  
mean...  If you are clipping surfaces, you may also want to use  
Surface Capping (if you aren't already).

Finally, if you are using the production release from November, you  
might also want to try a newer build.  After the November release, we  
changed the default lighting in Chimera to give a brighter appearance  
in raytraced images.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 18, 2008, at 9:28 AM, James Fethiere wrote:

> Hi,
> I'm trying to save an image of an EM map with atomic models fitting  
> in and can't get pov-ray to write-out the displayed image.  Using  
> the side view panel, I cut out part of the surface and models to  
> get the view I want. When I save the image without pov-ray, I get  
> what is displayed but when I try using the pov-ray option, I get  
> the full map and models without the clipping I imposed using the  
> side view mode.  What would be the right procedure?
> Thanks
> James

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