Hi Tom, thanks for your suggestion. I have managed a reproducible movie with color zone in the following way: upload map and pdb start rolling start ColorZone (at least this you can do from the command line) wait n record movie wait n color whatever pdb part wait n color another pdbpart ecc in this way, i get the color zone window opened up before the movie starts and i just keep pressing color so that colors on the map will appear quite immediately after the command "color part of the pdb" has been executed, while the map is rolling. I needed to show the map getting colored in a movie, and the pdb getting colored in the same way in another movie, the 2 movies to be shown together in a slide. This method worked. Giulia ---- Original message ----
Date: Tue, 27 Jan 2009 10:30:46 -0800 From: Tom Goddard <goddard@cgl.ucsf.edu> Subject: Re: [Chimera-users] color zone on command line To: Giulia Zanetti <giulia@strubi.ox.ac.uk> Cc: chimera-users@cgl.ucsf.edu
Hi Giulia,
Unfortunately there is no command equivalent of the color zone dialog. The color zone operation can be invoked by opening a file containing Python code as shown below. One of the main limitations of using Chimera to make animations is that there are no command equivalents for many dialog actions. Another approach is to use the Movie Recorder dialog (Tools / Utilities menu) and stop recording, then use the dialog to add some color, continue recording, then stop and adjust again with the dialog. Tedious but maybe simplest.
Tom
# # Color zone the first surface using the selected atoms and radius set below. # from chimera import selection as s, openModels as om from _surface import SurfaceModel radius = 5 surface = om.list(modelTypes = [SurfaceModel])[0] xform_to_surface = surface.openState.xform.inverse() atoms = s.currentAtoms() bonds = s.currentBonds() import ColorZone as cz points, colors = cz.points_and_colors(atoms, bonds, xform_to_surface) cz.color_zone(surface, points, colors, radius, auto_update = True)
Giulia Zanetti wrote:
Hi all, I would like to make a movie in which areas of my map are coloured while the surface is rotating.
Any idea how to use color zone from the command line?
thanks
Giulia _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users