[Chimera-users] Volume planes tool

[Elaine Meng]

Hi Jeff,
Here is another idea, still not exactly what you were asking for, but  
perhaps worth a look.  You can use the Per-Model Clipping tool (under  
Tools... Depiction) to show a thin slab of the data, and you can  
interactively rotate and translate the slab any way you want relative  
to the data with the mouse.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/per-model/ 
per-model.html

Just choose which model to clip, enable clipping, turn on slab mode  
and adjust clipping with mouse.  You may also want to adjust the  
contour level in Volume Viewer.

I tried it on emd_1274.map in the production release (1.2540).  You  
can use it on solid, surface, or mesh volume displays.  Below I  
attach an image of a slab surface display together with an unclipped  
solid display (a second copy of the same data).

There is also a command to control per-model clipping in a script,  
mclip.  It lets you specify location/orientation in the data  
coordinate system or the viewing coordinate system.
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mclip.html

Best,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html

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