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 Elaine Meng wrote:

Hi Jeff, Tom Goddard is/will be on vacation June 6-27; I will try to help, but you might have to wait until he gets back.

As you know, the IMOD reader is an experimental feature developed by Tom (not yet included in the Chimera download). Experimental features page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html

Normally I get a lot of experience with a tool after it is included with Chimera in order to write documentation. These experimental separately downloaded features, however, have generally only been tested by the person who wrote them and the users who requested them.

I can only point you to the experimental feature documentation written by Tom; here's the page for the IMOD reader: http://www.cgl.ucsf.edu/chimera/experimental/imod/imod.html

From that, it sounds like one should be able to change the color of any IMOD object that is selected. The only issue I see is that (if I understand correctly) the contour lines and the surface meshes are two different things. Perhaps you are coloring the contour lines instead of the surface meshes. Make sure you are really selecting what you want. That is just a wild guess, however. If you have any example file that is not too huge, you could mail it to me if you would like and I could attempt to use this feature myself.

As Tom mentioned before, nearly everything Chimera does can be done from Python. For noncoders like me, however, that is a last resort! Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

On Jun 6, 2007, at 7:53 PM, William Jeffrey Triffo wrote:

...

hi,

is there a way to control the color of surfaces generated from IMOD meshes in Chimera?

when I select a surface, and pick a new color in the color editor, I notice that the color of the 'IMOD contours' in the Model Panel changes, but that there is no change in the color of the actual rendered surface.

thanks,

--------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488

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-- ------------------------------------------------------------- Jeff Triffo Auer Group, Donner Lab, Lawrence Berkeley National Laboratory Raphael Group, Bioengineering Department, Rice University Medical Scientist Training Program (MSTP), Baylor College of Medicine phone (Berkeley): 510-486-7940 fax (Berkeley): 510-486-6488

Hi Jeff, When you try to color the IMOD contours (volume path tracer model) in Chimera by pressing the color button in the Model Panel dialog it does not change the contour colors as you expect. This is because that color button controls the default color -- the contours are just implemented as a fake "molecule" model. The individual vertices of the contours are atoms of the molecule model which have their own colors that over-ride the default molecule color. This business of atom colors over-riding the default molecule color is confusing. I'd suggest selecting the contours (ctrl click one with mouse and press up arrow key) and then use main menu Actions / Color to color all the "atoms" as desired. To change the colors of the IMOD mesh surface you select them and then use the "co" accelerator as Elaine described in a previous email. Unfortunately the menu entry Actions / Color doesn't work for these mesh surface objects. This is appallingly bad user interface -- I've added fixing it to my to-do list (#95 http://www.cgl.ucsf.edu/chimera/plans.html). Tom