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

[Mike Marchywka]

> From: boris.steipe at utoronto.ca
> Date: Mon, 24 Nov 2008 21:15:03 -0500
> To: bbb at bioinformatics.org
> Subject: Re: [BiO BB] Save protein structure image as an adobe SVG format file
> 
> Meh.
> Simple Z-sorting is not intersecting spheres.
> If it's any non-trivial vector graphic representation you are trying 
> to do, you might consider the following workflow:
> 3D-viewer -> View Matrix -> Molscript -> PS -> ps2svg

there is something called bkchem,
 
http://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Chemistry/Structure_drawing
 
and if you look at discussions the viewers don't obviously have svg output options.
 
Certainly if you can't find direct svg output, conversion from another model-preserving
output format would be great. But, I wouldn't dismiss the script approach immediately
depending on your ultimate goals. A scriptable viewer could generate many views but you
could also write a script without the viewer. 
 
Spheres aren't that hard for z-sorting, 
 
 
http://en.wikipedia.org/wiki/Bounding_volume
 
 
 
 
 
 
 
 
 
> 
> 
> B.
> 
> 
> 
> 
> On 24-Nov-08, at 7:23 PM, Mike Marchywka wrote:
> 
>>
>> I guess the real question is, " what are you trying to do?" You could
>> probably write a perl script to do this. The pdb is ascii, you just 
>> need to project
>> 3D onto 2D and get some atom colors and radii. SVG AFAIK is all ascii
>> XML which is easy to generate from a script.
>> If you take all the atoms, project, sort on Z ( distance from viewer),
>> and generat XML that would probably give you what you need.
>> http://www.w3.org/Graphics/SVG/
>>
>> the code to draw circles is pretty simple,
>> http://www.w3.org/TR/SVG11/shapes.html> Date: Tue, 25 Nov 2008 
>> 07:36:35 +0800> From: shreyasee.pradhan at gmail.com> To: 
>> bbb at bioinformatics.org> Subject: Re: [BiO BB] Save protein 
>> structure image as an adobe SVG format file>> Hi,>> For viewing 
>> PDB files you can use Swiss PDB viewer software. Its free !!!>>> 
>> On Fri, Nov 21, 2008 at 11:14 PM, Xiaowei Jiang 
>> wrote:>>> Hi fellows,>>>> Does anyone 
>> know a PDB viewer software or a way, in which I can save image>> 
>> directly as an adobe SVG format file?>>>> Thanks in advance!!>>> 
>>> Cheers,>> Xiaowei>>>>>>>>>> 
>> _______________________________________________>> BBB mailing 
>> list>> BBB at bioinformatics.org>> http://www.bioinformatics.org/ 
>> mailman/listinfo/bbb>>>>>> --> Thanks,> Shreyasee> 
>> _______________________________________________> BBB mailing list> 
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