[Chimera-users] CHIMERA help - coloring density maps

Thomas Goddard goddard at cgl.ucsf.edu
Mon Feb 2 14:42:00 PST 2004

Hi Padma,

  Chimera does not include code to color surfaces radially yet.  But
Steve Ludke at Baylor College of Medicine has written an extension to
Chimera that does this.  This Chimera extension is part of his EMAN
single particle reconstruction package available at:


I just tried the EMAN 1.50 distribution.  It includes a directory
called chimeraext that includes several Chimera extensions.  The
radial coloring extension is in the FilterKit subdirectory, with code
in Colorizer.py.  If you add the chimeraext directory to Chimera's
list of extension directories using Chimera
Favorites/Preferences/Category Tools/Add locations you will get a
bunch of new extensions under Chimera Tools/EMAN.  Select Isosurface
Colorizer and a dialog will be shown.  You select the isosurface you
want to color at the top of the dialog.  There are a bunch of entry
fields and color buttons in the dialog.  You enter radius values and
corresponding colors.  Then press the Apply button.

  In order for this extension to work you need to add a line of code
to the standard Chimera distribution to chimera/share/VolumeViewer/surface.py,
line 213.  You add the following "if ..." statement.  The line above and
below are already in the code and I provide them just for context.

    self.set_display_style(self.show_mesh, self.mesh_lighting,
                           self.two_sided_lighting, self.flip_normals,
                           self.line_thickness, self.smooth_lines,
                           self.dim_transparency, only_if_changed = 0)

    if hasattr(model,"colorizer"):


This is needed to tell the Colorizer extension when isosurfaces change.

  This is experimental stuff and Isosurface Colorizer is not
documented.  But I just tested it with Chimera 1892 and it is working.

  If you try this you'll probably also want to adjust the volume origin
in the Volume Viewer dialog under the Data panel in order to center the
volume at the origin.  You might also want to adjust the voxel size to
scale the data set to get the correct physical size.  Sometimes the origin
and header information is in the CCP4 file header and Volume Viewer can
read it but often it is not.


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