[Chimera-users] Question about using the volume command

Elaine Meng meng at cgl.ucsf.edu
Thu Feb 28 14:09:52 PST 2013


Hi Henning,
Best to share with the list (cc'd here)...

One problem with the solid level is that the second number should be between 0 and 1.  However, even when I tried that, I got the same error, so I'm guessing that is a bug.

The second issue may also be a bug: I don't know why the style does not change directly between surface and mesh.  I'll try a simple test case and submit a bug report for that one too.  

Sorry for the problems,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


On Feb 28, 2013, at 12:38 PM, Henning Stahlberg wrote:

> Hi Elaine,
> 
> Yes, you are right with the solid level option.
> But I still don't understand this.
> This here doesn't have any effect, I give the command on the command line:
> volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style surface
> No change of display.
> volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style mesh
> No change of display.
> volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style surface
> No change of display.
> volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style mesh
> No change of display.
> 
> This leads to an error message in the log window:
> volume #5 level 2.30,2.6 color 0.6,0.6,0.6 transparency 0.4 style solid
> No change of display. Error message:
> TypeError: 'NoneType' object is not iterable
>   File "/Applications/Chimera.app/Contents/Resources/share/VolumeViewer/solid.py", line 213, in update_coloring
>     cmap, cmap_range = self.colormap()
> 
> (I just submitted a bug report on the above.)
> 
> 
> And this gives an error message after the "solid" command, but after that the other commands appear to work:
> volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style solid
> Solid level must be <data-value,brightness-level>; no change of display.
> volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style surface
> The display changes to surface view.
> volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style solid
> No change of display. Error message:
> Solid level must be <data-value,brightness-level>
> volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style mesh
> The display changes to mesh view.
> volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style solid
> No change of display. Error message:
> Solid level must be <data-value,brightness-level>
> volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style surface
> The display changes to surface view.
> volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style solid
> No change of display. Error message:
> Solid level must be <data-value,brightness-level>
> volume #5 level 2.30 color 0.6,0.6,0.6 transparency 0.4 style mesh
> The display changes to mesh view.
> 
> Do you have an example how to change the display from "mesh" to "surface"?
> 
> Thanks for your help so far,
> 
> Henning.
> 




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