[Chimera-users] automatically calculated labels for quantitative tomography data

Martin de Jonge Martin.deJonge at synchrotron.org.au
Tue Sep 10 19:56:33 PDT 2013

Hi all,

this might sound like a strange feature, but I use Chimera to render quantitative tomography data.  I typically render somewhere between 2 and 6 separate elements (i.e., Zn, Cu, Fe, Mn, etc) and present these with a colour key, along with a numerical value to indicate the threshold concentration (typically in mmol or similar unit).  There is an example of such data in: http://www.pnas.org/content/107/36/15676/F1.expansion.html

When exploring such data it is very useful to adjust the display threshold, as various anatomical features appear at very different concentration levels.  My suggestion  / request is to have a numerical field in the colour key that can be linked to (eg) the per-model thresholds to indicate the concentration threshold at that moment.  This would be particularly useful for making movies for presentations and articles.

Some thoughts on useful properties of this numerical field:

- it should inherit the colour of the colour-key label that it is associated with (or be able to select to be inheritable)
- it could include simple mathematical operations, for when there is a simple relationship between the data and the reportable concentration eg, *, /, +, -
- one should be able to specify the format of the number (using the usual formatting codes).


Martin de Jonge

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