Hi Lukas, There is no Chimera command to set the volume contour surface threshold or color. We plan on adding this command. For now, I have four suggestions. You can use "Volume Series" tool available on the Chimera Experimental Features web page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html This page contains plugins that are not yet distributed with Chimera. You download a zip file and put the new directory in with your existing Chimera to use it. The Volume Series tool lets you play a series of volume data sets perserving thershold level and color settings just as you want: http://www.cgl.ucsf.edu/chimera/experimental/volume_series/volume_series.htm... There is no Chimera command for this tool either so to make a movie you would start Movie recorder (menu entry Tools / Utilities / Movie Recorder or use Chimera movie command) then press the Play button on the volume series dialog. A second approach is to use the EMANimator animation tool http://www.cgl.ucsf.edu/chimera/related/emanimator/emanimator.html It is a Chimera extension included with the EMAN single particle reconstruction package. It provides a time-line user interface for composing animations and has a specific capability for playing a sequence of volume data sets just as you want. A third approach is to use some Python code in Chimera to script your movie. This is a bit more complicated than using just Chimera commands. But you can easily use all Chimera commands in a Python script and you additionally can control all of the volume settings. I include an example at the bottom of this email. You simply open the Python file to run the script. A fourth approach is to get the Animation Commands package http://www.cgl.ucsf.edu/chimera/experimental/transition/transition.html from the Chimera experimental features page. It includes a command to change the contour level of a volume map from one value to another over a set number of frames. You could use it to set the contour level. But there is not a command in this package to set the volume color. Tom ------------ Example seriesmovie.py Python script follows. Tested in Chimera 1.2309. directory = '/usr/local/src/chimera-demos/volume/dna_blur' # Volume file location files = ['1enn_00.mrc', '1enn_05.nc', '1enn_10.nc', '1enn_15.nc', '1enn_20.nc', '1enn_25.nc', '1enn_30.nc', '1enn_35.nc', '1enn_40.nc', '1enn_45.nc', '1enn_50.nc'] movie_path = '/usr/local/src/staff/goddard/1enn.mov' threshold = 0.12 color = (.5, .7, 0) # red, green, blue delay = 10 # movie frames per volume def set_volume_threshold_and_color(threshold, rgb): import VolumeViewer d = VolumeViewer.volume_dialog() r = d.focus_region r.set_parameters(surface_levels = [threshold], # Set threshold level. surface_colors = [color]) # Set color rgb or rgba. d.show_region(r, 'surface') from chimera import runCommand runCommand('cd %s' % directory) runCommand('movie record') for filename in files: runCommand('open %s' % filename) set_volume_threshold_and_color(threshold, color) runCommand('wait %d' % delay) runCommand('close #0') runCommand('movie stop') runCommand('movie encode mformat mov output %s' % movie_path)