[Chimera-users] IMOD mesh/surface colors

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 7 11:39:15 PDT 2007

Hi Jeff,
Thanks for sending the example file.
Happily, I can change the IMOD surface color with the procedure  
outlined by Tom in http://www.cgl.ucsf.edu/chimera/experimental/imod/ 

- select the surface w/ Ctrl-click
- turn on accelerators (Tools... General Controls... Accelerators On)
- type the "co" accelerator which will bring up the Color Editor and  
adjust the selected surface's color as you change the Color Editor color

This was with 1.2416 on Mac and I tried it with both contours = False  
and contours = True.

I could not figure out any way to do it without accelerators, which  
take a little getting used to (I keep forgetting to turn them off and  
then get weird behavior when I try to type commands).  If you are not  
an accelerators aficionado, turn them off afterwards (Tools...  
General Controls... Accelerators Off).

With contours = True, two models are generated when you open  
trial2.mod.  The contours are implemented as a molecule model and can  
be treated (colored etc.) just like molecule atoms/bonds or like  
Volume Path tracer markers/links.  The mesh is a surface model and I  
don't see any "hook" into coloring other than the accelerators, since  
as you mentioned, it doesn't have a color well in the Model Panel or  
in its attributes panel.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 7, 2007, at 10:54 AM, William Jeffrey Triffo wrote:

> thanks Elaine,
> here's an IMOD file attached. it includes contours (lines /  
> connected points, in this case each contour lying completely in a z- 
> plane) and a meshed surface that was generated from those contours  
> using IMOD's command 'imodmesh'.
> if you set the Contour flag in the .py file to True (see subheading  
> 'Contours and Points' at http://www.cgl.ucsf.edu/chimera/ 
> experimental/imod/imod.html), this will load the underlying  
> contours as a Volume Path Tracer marker file, along with the  
> surface mesh. I believe the default, with "contours = False", would  
> just load the mesh. To replicate what I am seeing, that flag would  
> need to be set to 'True'.
> When I load the file (trial2.mod), the Model Panel shows 2 models -  
> 'trial2.mod trial2 contours' and 'trial2.mod mesh'. The mesh is  
> colored aqua, which I cannot figure out how to change. (I can  
> select the mesh/surface with cntrl-button1). I do notice that there  
> is a color box by the 'contours' model, but not by the 'mesh' one.  
> I am able to change the color of the markers from the non-meshed  
> contours by using Volume Path Tracer.
> It may be that I just don't know the right function/tool to use to  
> change the color of a general surface; I am usually only changing  
> the display of isosurfaces in volume maps. I tried poking around  
> the menus for a bit before emailing the list, but it is likely I am  
> just missing something.
> I'm using build 2416.
> thanks,
> -Jeff

More information about the Chimera-users mailing list