Hi Richard, Just yesterday I made the surftransparency command take an optional "frames" argument so you can fade in or out a surface over a specified number of frames. This may be of use to you. Before we would sometimes use twenty surftransp commands in a row in a script to gradually change the transparency. Now a command like surft 100 #2 50 will fade out surface model #2 to full (100%) transparency over 50 frames. To use that you'll need to get a Chimera 1.4 daily build. http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Good luck with movie making. We're trying to make this easier in Chimera but have a long ways to go. Tom Tom Goddard wrote:

Hi Richard,

There is no command equivalent of the multiscale dialog, and other other Chimera commands don't know anything about the multiscale surfaces (none can even change the color or transparency as far as I know).

Maybe the way to go is to not use multiscale, and instead make a PDB file with all the molecule copies (can use multiscale to do that) then use the "molmap" command to create surfaces for the desired chains, and the "volume" command to change colors, and other commands to show/hide ribbons and surfaces as needed. This approach should work for a tetramer, but if you have a virus with 60-fold icosahedral it will be unwieldy because every chain will need separate molmap commands to create the surfaces.

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html

If that isn't practical it is possible to use Python code to do the things the Multiscale dialog does.

Tom

-------- Original Message -------- Subject: [Chimera-users] controling multiscale models from command script From: Marhoefer, R (Richard) To: chimera-users@cgl.ucsf.edu Date: 6/15/09 8:40 AM

...

Dear Chimera Users,

for the production of a movie file I like to control some attributes of a multiscale model e.g. the style and the surface transparency through a Chimera command file. Unfortunately I couldn't find many commands allowing to do so in the documentation. How could that be done?

Kind regards, Richard

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