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

[Boris Steipe]

> 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".

(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.


:-)
B.




On 25-Nov-08, at 9:17 AM, Mike Marchywka wrote:

>> 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>
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