[Chimera-users] Movie for various clipping

Elaine Meng meng at cgl.ucsf.edu
Thu Dec 26 16:37:26 PST 2013

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 ...

( 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.

(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".
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.

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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