[Chimera-users] color zone on command line

Giulia Zanetti giulia at strubi.ox.ac.uk
Wed Jan 28 03:08:01 PST 2009

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

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.



---- Original message ----
>Date: Tue, 27 Jan 2009 10:30:46 -0800
>From: Tom Goddard <goddard at cgl.ucsf.edu>  
>Subject: Re: [Chimera-users] color zone on command line  
>To: Giulia Zanetti <giulia at strubi.ox.ac.uk>
>Cc: chimera-users at 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 
>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 at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

More information about the Chimera-users mailing list