[Chimera-users] Draw schemas with Chimera ?

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 19 08:40:44 PST 2013


Hi Ben,
The short answer is not really, although there are some related possibilities. Chimera doesn't write SVG format, though.

(a) you can create arbitrary 3D objects:
- BILD format
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html>
- "shape" command
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html>

(b) you can create structure-derived 3D objects:
- "measure inertia" command
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia>
- Axes/Planes/Centroids or "define" command
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>

(b) with 2D labels you can place labels including arbitrary symbols.  These do not move along with the Chimera 3D scene, they simply stay wherever in the window you place them.  
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.html>
However, although the symbols include geometric objects, I don't know if there are unicode ellipses/ovals: I only see circle- and square-based and triangular objects, e.g. as in this list <http://jrgraphix.net/r/Unicode/25A0-25FF>

There are probably many tools more suited to this purpose, e.g. Illustrator, PowerPoint, OmniGraffle ...

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

On Feb 19, 2013, at 2:13 AM, Benjamin SCHWARZ wrote:

> Hi list,
> 	I wonder if it is possible to draw "simplified schemas", such as those that can be found in biology publications where a protein complex is represented by a superimposition of ellipses, each ellipse representing a different protein in the complex, and their 2D placement reflects their known interactions in the complex (cf, for instance http://www.erasmusmc.nl/proteomics1/files/PBAP.jpg).
> 	This question triggered several interrogations :
> 	1.) Is it possible in Chimera to draw 2D ellipses that would always reorient towards the screen as the scene rotates the same way the labels do
> 	2.) Is it possible to draw ellipsoids ?
> 	3.) Is it possible to save a picture in SVG format ?
> 
> 	Thanks for your help, and thanks once more for the wonderful tool you provide us
> 
>           --Ben




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