[Chimera-users] Question about using the volume command

Tom Goddard goddard at sonic.net
Thu Feb 28 16:11:37 PST 2013


Hi Henning,

  I've fixed the bug which prevented switching between "surface" and "mesh" display styles with the volume command.  That bug was introduced 4 months ago when I added orthoplanes display mode -- it was a Python code wrong level of indentation problem.

  The error message when setting the "solid" display style is because the command has to specify 2 or more levels to define a piecewise linear brightness curve.  Specifying one level would show nothing, it shouldn't have thrown an error, and I've fixed that so it merely warns you explaining the problem.  Here's a command that specifies a linear ramp from brightness 0 to 1 over map values 1.2 to 2.3

	volume #5 level 1.2,0 level 2.3,1 color 0.6,0.6,0.6 transparency 0.4 style solid

The fixes will be in tonight's Chimera daily builds and also in a 1.7.1 release if we decide to make that release.

	Tom


On Feb 28, 2013, at 2:09 PM, Elaine Meng wrote:

> 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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