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. http://www.cgl.ucsf.edu/chimera/experimental/experimental.html 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. http://ncmi.bcm.tmc.edu/~stevel/EMAN/doc/ 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 /usr/local/EMAN/chimeraext to the list of locations Chimera looks for extensions in. Here is some documentation I wrote for an older EMANimator version. http://www.cgl.ucsf.edu/chimera/related/emanimator/emanimator.html 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: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/moviecomma... 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. Tom -------------

To: Thomas Goddard <goddard@cgl.ucsf.edu> From: Frank Alber <frank@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