Aonghus,
> I would consider a 20^3 configuration (~ 8000 atoms) to be small- but
> jmol would not handle much larger than this.
Is it the case that you are still using the released jmol version 5?
If so, I would appreciate it if you could test out the development
version of jmol on one of these *smaller* molecules :)
I would like your feedback on the performance of the new version.
To make it easier for you to test I have put a prerelease copy of the
current jmol.jar file on the sourceforge web site:
http://jmol.sf.net/prerelease6
There is one file there. Just download/save the file jmol.jar
You can then run it by typing
java -jar jmol.jar
> In contrast- VMD works smoothly with
> those sizes.
Can you give me a URL for more info about VMD?
> It would be great to be able to display such
> configurations on the web, using the jmol applet.
The jmol applet code is a subset of the application code. The rendering
code is exactly the same. So, the v6 applet will perform just like the
aforementioned v6 jmol.jar
> I realise java will
> never compete with native opengl code- what kind of improvement could
> you achieve with your performance enhancements?
Hmmm ... well, I *hope* that jmol v6 is noticably faster.
However, the 3D things I am talking about adding will slow it down, not
speed it up. May not be good news for those who want to work with
proteins.
But take a look at this version and tell me what you think.
>>
>> There may even be postscript output ... I am somewhat embarassed to
>> say that I don't know.
Have you tried the povray export in Jmol?
File -> Export -> Render in pov-ray
Hold it -- there seems to be a bug in the version I just built and
uploaded for you ... so don't try it out there.
> The best thing about jmol is the ability to run it as an applet- so
> you should try to keep it small and fast.
Good.
> It should also be possible
> to load modules as required- eg. to do protein specific
> visualisations, charge fields etc. If it was quick enough it would be
> nice to connect to the output of a simulation- perhaps you could view
> the evolution of your simulation over the web?
When you say "output of a simulation" what kind of file format are you
talking about?
Do you have any interest in RasMol/Chime scripting for animating your
molecules?
Miguel
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