[Chimera-users] IMOD mesh/surface colors

[William Jeffrey Triffo]

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 at 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
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>

-- 
-------------------------------------------------------------
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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