[Chimera-users] Scale_bar Gradient Color

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 22 14:05:29 PDT 2008

Hi Andy,
I don't think there is any reasonable way to gradient-color the Scale  
Bar, but...

I suspect the new "Color Key" tool is what you really want.  It is  
integrated with other tools such as Surface Color (for example, it can  
automatically generate a color key to match your current radial  
coloring scheme).  You need to get a recent version of Chimera to use  
this feature, as it was not included in the July production release  

Documentation and example images:

The Color Key is like 2D Labels - you can think of it as only in the  
plane of the screen, with no Z-coordinate.  Scale bar is different and  
actually exists in 3D.  I have not heard of any measurement errors,  
but since it is in 3D, it could look relatively larger or smaller in  
perspective when placed further in front of or behind the part of the  
map you are viewing.  You could also check on the scaling of your map  
by looking in the "Coordinates" section of the Volume Viewer dialog  
(see its Features menu).

If you wanted to make the Color Key bar to scale, you could first use  
Scale Bar (assuming that shows the length you want) and then drag out  
a color key bar of matching length, then hide the scale bar.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 22, 2008, at 1:15 PM, Anindito Sen wrote:

> Hi All
> A simple question-
> How do I color the  scale bar (in a gradient form).
> Also Has anyone experienced the problem of  scale bar giving an  
> incorrect
> measurement when a density map in .dat format is displayed in Chimera?
> Best
> Andy
> Dr. Anindito Sen (Ph.D)
> Research Associate , Dept. of Biochemistry and Molecular Genetics  
> University
> of Virginia
> Box 800733 Charlottesville, VA 22908

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