What format to use for 3d Molecular Viewing?

Andreas Zankl andreas.zankl at hospvd.ch
Wed Mar 17 07:43:51 EST 2004


How about Quicktime-VR? Here is an example:
http://www.apple.com/hardware/gallery/ibook_g4_oct2003_480.html
I don't think it's very common in bioinformatics, but its quite common 
on the web in general.

Hope that helps
Andreas.


In article 
<8O03c.152634$ah.29355 at twister01.bloor.is.net.cable.rogers.com>,
 "Mathew Donovan" <mathewdonovan at yahoo.com> wrote:

>  Hi
> 
>
I have recently started putting together a website
> which includes illustrations of biological molecules
> that I get in PDB format from RCSB (http://www.rcsb.org). I
> also want to include 3D animations and would like to
> know if there are any 3D formats that are an "accepted
> standard" in the industry.
> 
> Let me just qualify the above statement further -
> although applications like rasmol
> (http://www.umass.edu/microbio/rasmol/index2.htm) are
> great for visualizing molecules in different modes and
> colors, it doesn't export to any real 3D format. I am
> using kvizpro (http://www.kalsaya.com) for exporting to real
> 3D formats because this is the only tool (I am pretty
> happy with it) that could do the trick of getting my
> molecules into Maya. I am then rendering and animating
> my molecules in Maya - which simply can't be beaten in
> 3D (it was even used in Lord of the Rings so I am sure
> it can produce better 3D graphics than any biotech or
> chemistry software applications that may be out
> there).
> 
> This gives me excellent animations but they rendered
> to AVI and MOV which are only movie formats. However,
> I would also like to allow people at my website to
> also navigate my molecules in 3D.
> 
> What I would like is an answer to is the following -
> are there and standard "3D visualization formats" that
> are used predominantly in the biotech industry? I have
> heard certain applications that output VRML, but I am
> not sure how widely used it is or how good they are.
> 
> Another question: does anyone know of a website where
> I can get more information on visualization of
> molecules for e-learning and illustrative purposes?
> Both rasmol and kvizpro are great tools but more are
> always welcome!
> 
> My preferences are tools that "get the job done"
> without me knowing that they're there - I dislike
> wasting all my time on trying to babysit software
> which continually crashes or has obscure hidden
> features which are 10 menu-levels deep! :-)
> 
> Thanks in advance
> Mathew
> 
> 
>





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