[Chimera-users] clip planes

Elaine Meng meng at cgl.ucsf.edu
Fri May 8 13:15:41 PDT 2015


Dear Bharat,
Maybe you were using global clipping (such as in the Side View) and showing a cap. There is another clipping tool that allows clipping at different angles, and only clipping certain models. Take a look at Per-Model Clipping (in menu under Tools… Depiction).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/clipping.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-model.html>

Here’s another example image of a per-model-clipped surface:
<http://www.rbvi.ucsf.edu/chimera/ImageGallery/entries/kchan/kchan.html>

If you really wanted to cut the protein with a flat plane and then show both sides, you would need to:

(1) open the structure
(2) enable per-model clipping  on that structure (or show surface, then enable per-model clipping on that surface)
   (2a) adjust clipping with mouse, then do other things (coloring etc.) as desired for the image
(3) save image
(4) flip plane 180 degrees (there is a button for this in the dialog)
(5) rotate structure so you can see the cut side  (could use command “turn x 180” to rotate 180 degrees, more precise than trying to do it with the mouse)
(4) save another image

The two images could be separate panels or you could use some standard image-edting program to combine them into a single image file.

In the case of non-planar splitting (for example, showing the interface between protein chains), see the “opened interface image tutorial”
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 8, 2015, at 8:45 AM, Bharat Lakhani <blakhani at wesleyan.edu> wrote:
> 
> Dear All
> I want to visualize the core of my protein, Is it possible to slice the protein right into two half in order to visualize the core of the protein. I tried using chimera pre-capping model but it has not been work out well. Any suggestion on this would be great.
> Thanks




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