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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sop.html> <http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html> There is also a volume planes animation example. Elaine On Dec 26, 2013, at 4:37 PM, Elaine Meng <meng@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@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 KIOST
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