[Chimera-users] Movie for various clipping

Hyeong-Tae Jou htjou at kiost.ac
Thu Dec 26 17:37:41 PST 2013

Hi Elaine,

Many thanks for your quick reply.
I'll try some of your suggestions while waiting for other's ideas.
It's holiday season, and I'll take time to get the good solution.
I wish you a Happy New Year.


-----원본 메시지----- 
From: Elaine Meng
Sent: Friday, December 27, 2013 9:50 AM
To: Hyeong-Tae Jou
Cc: chimera-users at cgl.ucsf.edu List
Subject: Re: [Chimera-users] Movie for various clipping

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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