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: [EMAIL PROTECTED]
Date: Mon, 24 Nov 2008 21:15:03 -0500
To: [email protected]
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: [EMAIL PROTECTED]> To:
[email protected]> 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>> [email protected]>> http://www.bioinformatics.org/
mailman/listinfo/bbb>>>>>> --> Thanks,> Shreyasee>
_______________________________________________> BBB mailing list>
[email protected]> http://www.bioinformatics.org/mailman/
listinfo/bbb
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