[Chimera-users] Chimera movie commands

Thomas Goddard goddard at cgl.ucsf.edu
Tue May 16 18:25:45 PDT 2006

Hi Frank,

  There are currently no Chimera commands for volume surfaces, and
there are not commands to control per-model clipping.  We wish to
add these commands and others so that movie making is more powerful.
Currently we are writing a renewal of our major 5-year grant due
June 1 so it will probably not be possible for me to add these commands
before then.

  Here is what is available now.

  There is a command for changing isosurface threshold level.  It is
part of "Animation commands" on the Chimera experimental features page.


It is not part of any Chimera distribution but can be downloaded separately
and use with your current Chimera.

  The most practical way to gradually change from a surface to mesh would
be to open the model twice, then gradually change the mesh color from
completely transparent to opaque, then gradually change the surface from
completely opaque to completely transparent.  You can't do those two steps
simultaneously because Chimera unfortunately does not correctly display two
transparent models -- only one at a time.  There are no commands to do
volume surface color fades.

  You can do the color fades though using the Chimera animation editor called
EMANimator distributed with EMAN.


Get the latest EMAN distribution (nightly build) because it also is able
to move per-model clip planes.  To use EMANimator you install EMANimator
the use Chimera menu Favorites / Preferences, category tools and add the
EMAN chimeraext directory


to the list of locations Chimera looks for extensions in.  Here is some
documentation I wrote for an older EMANimator version.


This is not an entirely trivial tool to use.  It lets you create a timeline
of transitions and preview them, and record a movie.  The drawback is that
it only supports a limited set of smooth transitions, mostly related to
volume data display.  It does not for instance handle 2D labels.  Maybe
you could add those in an external movie editor.

  Using EMANimator is a totally separate option from using Movie Recorder
and commands.  If you want to know all the current Chimera commands with
"frame" options that can do transitions it is a short list:


  Unfortunately our animation tools are quite primitive now and you will
need to make compromises if you want to use them.

  We are proposing to significantly improve animation capabilities in our
new grant and will work on it even before then.  So feedback about what
is important to you is welcome.



> To: Thomas Goddard <goddard at cgl.ucsf.edu>
> From: Frank Alber <frank at salilab.org>
> Subject: chimera movie question
> Date: Tue, 16 May 2006 17:39:15 -0700
> Hi Tom,
> I have a question about chimera. I need to make some movies with 
> chimera in which I like to switch on and off different models (using 
> the volume viewers volume densities) maybe introduce per-model clipping 
> and add and remove 2d labels during the movie. I figured out how to 
> rotate scale and move the model around based on command lines commands 
> that I read in as a file. Also, how to switch the model in the model 
> panel on and off.
> But is it possible to use volume viewer commands on the command line? 
> So I could use them in a command file? For example switch the 
> representation of model 1 from surface to mesh. If so, is it possible 
> to change representations over a number of frames, so that they blur 
> into each other? Like the 'visibility show frames 100' option in the 
> 2dlabels command? I couldn't find such options in the manuel but I am 
> not sure if I looked careful enough.
> In case, do you know anybody who I could ask for some cmd files (used 
> for moviemaking) that actually do similar stuff and which I could look 
> at as template examples? That would be great starting point to see what 
> commands could be useful for making movies.
> I found an example on the web page, but it didn't have volume viewing 
> options there.
> Thanks a lot!
> Frank
> ---
> Frank Alber
> Andrej Sali Lab
> California Institute for Quantitative Biomedical Research
> University of California at San Francisco
> QB3, Box2552
> 1700 4th Street, Room 501
> San Francisco, CA 94143-2552 (CA 94158 for courier delivery), USA
> Phone: +1 (415) 514 4258
> Fax: +1 (415) 514 4231

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