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/ imod.html: - 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 ----- 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 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