[Chimera-users] drawing circles

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 24 09:46:08 PDT 2012

Hi Bala,
You can change the color (including transparency) of planes, axes, centroids by clicking a color well in the table of such objects and using the Color Editor.  However, there is no separate fill, it is just the color of the whole object.
(In recent versions of Chimera you can also just select the plane with mouse Ctrl-click and use the menu, Actions... Color... from editor)

Alternative ways to draw rings:

(1) just add a 2D Label circle symbol, increase font size and color as desired.  You can have multiple labels of different font sizes and colors.  As the name suggests, 2D labels exist only in the 2D plane and do not move along with the 3D Chimera view... however, you can drag each to the desired X,Y location:

You can copy-and-paste into the label field, for example from this page of symbols.  The circle is the top symbol in the "Miscellaneous" column:

(2) create a surface model shaped like a ring by opening the attached python script.  Inner/outer radii and color can be changed by editing the script.  This will exist in 3D, so if you want it to look like a circle be careful to only translate (not rotate) it.

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

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On Sep 24, 2012, at 9:17 AM, Bala subramanian wrote:

> Friends,
> I want to draw concentric circles of increasing sizes around the
> protein. To achieve this, i used the 'define plane' option to draw
> disk choosing I three reference atoms and drew the disks of increasing
> sizes and choose two different color for the inner and outer disk.
> Since the reference atoms are the same. If i change the color of the
> bigger disk, i get a weird appearance of the inner disk. I dnt know
> how to resolve this problem.
> I would like to know if i can do something like making the disk
> transparent/removing the fill color of the disk.
> thanks,
> Bala
> -- 
> C. Balasubramanian

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