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

Tom Goddard goddard at sonic.net
Wed Sep 11 15:15:49 PDT 2013

Hi Martin,

  Your elemental abundance tomography is interesting.  I'm not sure I understand your Chimera suggestion.  Do you mean there would be a separate window that lists the threshold levels for Zn, Cu, Fe, Mn density maps in type-in fields and adjusting the values would both change the contour level (as is done by the Volume Viewer tool) and update the labels displayed in the graphics window (as with the 2D Label tool)?  Or maybe it doesn't need a separate window -- you might just be able to say display colored labels in the graphics (e.g. "Zn 11" "Cu 47"  "Ca 1500") for several density maps that list both an element name and the current contour level.  You could control those levels using the Volume Viewer dialog and the labels would automatically update.  (By the way, did you know you can display 6 or 10 histograms in the Volume Viewer dialog instead of the normal limit of 3?  Use volume dialog menu Features / Data Display Options and change "Maximum number of Histograms…", and use Features / Save Default Dialog Settings if you want that to be the default for future Chimera uses.)  I don't understand what you mean by "include simple mathematical operations".

  If I understand your basic idea, I think it is specialized enough that only a few Chimera users would use it. I'm not sure I've ever seen a figure like yours with values that correspond directly to density map levels, because usually the density map values have some meaningless normalization.  Most often presentation figure keys need to be created in an entirely custom way appropriate to the content of the figure.  Still I think the feature you suggest would be cool, but given the hundreds of improvements people have requested we try to work on ones that lots of Chimera users (500 or 1000) will benefit from, or requests that allow you to do something that isn't otherwise possible.


On Sep 10, 2013, at 7:56 PM, Martin de Jonge wrote:

> 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).
> thanks
> Martin de Jonge
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