Re: [PyMOL] Start PyMOL session in web browser

[Jason V. <jas...@sc...>]

Hi Martin,

On Sun, Dec 19, 2010 at 7:37 AM, Martin Hediger <ma...@bl...> wrote:
> Dear all
> Is it possible to start a PyMOL viewer through a web browser? What I
> mean by this is, is it possible to view a protein over the internet
> where the viewing features are provided by some "limited" PyMOL server?
> The only thing able to do that right now is Jmol, but i think its very
> inconvenient to use when viewing large structures such as proteins.

Luckily, your peers have given you quite a few options so you can
weigh the pros/cons against your necessities and proposed platform
(eg. Java vs JavaScript+AJAX vs ActiveX vs HTML5).  As a developer I'd
also consider the following.  First, do you need something that can
launch a viewer from the browser or a plugin that embeds the content
inside the browser window?  If the former, Carsten noted the "p1m"
format, which you can associate with PyMOL.  If the latter, then I'd
next consider platforms (stability, speed, future):

HTML5/WebGL:
 * looks promising as the technology develops, but may be too new for
your users to quickly adopt and performance might not be what you want
(yet).

Java:
 * been around for ages, but Apple just deprecated their JVM
(http://developer.apple.com/library/mac/#releasenotes/Java/JavaSnowLeopardUpdate3LeopardUpdate8RN/NewandNoteworthy/NewandNoteworthy.html#//apple_ref/doc/uid/TP40010380-CH4-SW1)
 * Jmol and JyMOL both work well for their intended uses:
  -- Jmol is good software with a small footprint, fewer dependencies
than JyMOL, a large user base, and is open source in case you need to
modify the Jmol source
  -- JyMOL has PyMOL graphics, speed, and is free-to-academics, but
needs JOGL or LWJGL and is proprietary--which means you cannot modify
JyMOL itself

ActiveX:
  * Consistent cross platform deployment would be my largest concern

Use whatever's best for your project.  Hope this helps and good luck!

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120