[Chimera-users] Movie for various clipping

Elaine Meng meng at cgl.ucsf.edu
Thu Dec 26 16:50:08 PST 2013

Ah, I see that the "sop transform" command can be used to grow/shrink an existing surface shape.  It's the last example in the "Clipping and Slicing" (bottom) section of the video mini-examples page:


There is also a volume planes animation example.


On Dec 26, 2013, at 4:37 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Hyeong-Tae,
> I'm not the expert  in this area, but will try to list the possibilities that I know about.  Other people may have better ideas when they return from the holiday break.
> (a) single plane or slab perpendicular to viewer, front-back motion ("global clipping")
> (b) single plane or slab per model, at any angle to viewer ("per-model clipping")
> … commands and more details here ...
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/clipping.html>
> ( c) moving orthogonal planes through the data, for example the "Herpes virus slices" movie about halfway down the Animation Gallery page.  Example command file is linked there.
> <http://www.rbvi.ucsf.edu/chimera/animations/animations.html>
> (d) showing the volume values with coloring on a surface, where that surface can grow/shrink,  for example the movie at the very bottom of the Animation Gallery, "Rice Dwarf Virus".
> <http://www.rbvi.ucsf.edu/chimera/animations/animations.html>
> Certain shapes of surfaces (sphere, icosahedron, etc.) can be created with the "shape" command, and the surfaces can be colored by volume data value with the "scolor" command.   I don't think there is a shape command option to automatically replace a previous shape, so it may be a bit tedious to create new surface, close old surface, color new surface (repeat).  It was probably done with python rather than commands, but that is beyond my skills, sorry.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html>
> Best,
> 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 Dec 26, 2013, at 3:10 PM, "Hyeong-Tae Jou" <htjou at kiost.ac> wrote:
>> Hi,
>> I am trying to animate some clipping motion in volume data.
>> I only find very simple clipping method using plane.
>> I'd like to make a movie for clipping motion using prism or 3-D box
>> (the clipping gear gradually moving deeper into volume data).
>> I have tried mask (by inverse masking) using 3-D box,
>> but it was very inconvenient, and took too much time to make a movie.
>> Are there any other way to make an animation for some fancy clipping?
>> Many thanks,
>> Hyeong-Tae
>> -----------------
>> Hyeong-Tae Jou
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