[Chimera-users] color zone on command line

Tom Goddard goddard at cgl.ucsf.edu
Tue Jan 27 10:30:46 PST 2009

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.


# 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
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