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 1.2540. Documentation and example images: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.h...

<http://www.cgl.ucsf.edu/chimera/feature_highlights/2gbp-bfactor.png> 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). <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volume...

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 ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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