Re: [Chimera-users] Question about using the volume command
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.
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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participants (2)
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Elaine Meng -
Tom Goddard