[Chimera-users] Movie for various clipping

[Hyeong-Tae Jou]

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.

Hyeong-Tae.

-----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:

<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 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
>> KIOST
>
>
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