[BiO BB] Save protein structure image as an adobe SVG format file

[Mike Marchywka]

> From: boris.steipe at utoronto.ca
> Date: Wed, 26 Nov 2008 17:33:39 -0500
> To: bbb at bioinformatics.org
> Subject: Re: [BiO BB] Save protein structure image as an adobe SVG format file
> 
>> Spheres aren't that hard for z-sorting,
> 
> 
> Yes, a collection of atoms can be well approximated with a Z-sorted 
> stack of circles in 2D. But *molecules* are represented by 
> intersecting spheres and the line of intersection is a circle at an 
> arbitrary orientation relative to the viewer. It projects as an 
> ellipse, and part of the ellipse is occluded.
> 
> Think "methane".

I guess when I wrote sphere and posted the bounding volume link, I meant this,
 
http://en.wikipedia.org/wiki/Sphere
 
The rest of that stuff is non-trivial but hardly prohibitive. The intersecting
ones are easy to find, the intersection can be solved with vector manipulation,
( I think this is 3 lines if you write a vector expression for a triangle consrained
by sphere radii and distance, find the normal and radius or intersection- 
if you use vectors the orientation is really not important
http://en.wikipedia.org/wiki/Vector ). 
etc. You could probably write a plugin or modify source for your favorite viewer
if you are sold on this approach.
 
 
 
> 
> (And working with ball and stick models, or even cartoon or mesh 
> representations, you'll start recoding much of what the 3D-viewer is 
> there to do in the first place.)
> 
> BKchem is 2D chemical structure editor.
> 
> 
> Again: Molscript produces postscript output. Postscript can be 
> converted to svg.
> 

Obviously this would capture more of the capabilities of the viewer and you wouldn't
have to guess about the matricies. Even without a program, you could probably
write a script to do this pretty easily too :)
If you are just making a document and don't really have detail at many levels,
there is always ctrl-alt-printscreen. I would strongly suggest the model based
approach where practical but in a pdf document I don't think you can salvage much anyway :)
 
 
 
> 
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