[Chimera-users] Draw schemas with Chimera ?

Benjamin SCHWARZ schwarz.ben at gmail.com
Wed Feb 20 01:30:37 PST 2013


Thanks a lot Elaine, I'll have a look at these.

@François, I am more skilled with inkscape ;)
And yes, since Chimera doesn't produce SVG, my idea is to produce pictures of each simplified elements of the complex with chimera, then to import separately the bitmaps of each elements in inkscape and rebuild the picture in an SVG format that way :)

    --Ben




Le 19 févr. 2013 à 17:40, Elaine Meng a écrit :

> 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
> 

> Francois Berenger berenger at riken.jp  Tue Feb 19 16:21:07 PST 2013
>
> The part with ellipsoids could easily be drawn with xfig on Linux.




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