I am also looking forward to a tool that could produce high resolution
images from a view designed with Jmol.
I remember a message in last couple of years about writing a JSP script
embedding part of Jmol code in order to do this server side. I don't
know if that idea has been brought forward since then ?
It should be possible with a script recorder to get a list of commands,
and then send this list of command to a server producing the images.
I have also seen a webservice that produces customized high quality
images from a PDB file. You can have a look at :
http://aismig.dkfz.de/
The approach is different : there is no applet nor plug-in used to get
the desired view : all the views are generated in
almost-(not-so-long;)-real time by the server and the webpage is
regenerated each time a new command is issued. PyMol is used to generate
the rough image, and PovRay can be used to generate the high quality
output. Due to the time of actualisation between two views, I find this
system not interactive enough. I believe a previous stage (prior the
settings for the high-resolution output) could be achieve with Jmol and
a script recorder. The last part is as Eric mentioned it, to translate a
Jmol script in a Pymol one...
Paul
PS : about server side application, I read that PHP can run Java
routine. I was wondering if an image generator derived from the Jmol
rendering engine could be embeded in a PHP application. Any idea ?
Eric Martz a écrit :
Dear Miguel and jmol community,
While I was in Japan recently showing off Protein Explorer, and
talking up jmol, there were frequent requests to be able to export
publication quality images. People who learn how to use Protein
Explorer and finally get the view they want would like to be able to
save it in publication quality, not just screen-shot quality. This is
not possible while Protein Explorer uses Chime, but might be possible
when it is ported to jmol applet.
My impression is that MolScripts and Raster3D or Pov-Ray are one of
the most common mechanisms for making publication quality images.
PyMOL is increasingly popular as well.
Is a mechanism to export a MolScript or somesuch under consideration
for Jmol, e.g. the signed applet? If yes, what is the status of it? If
no, is anyone on this user-list knowledgable about how to translate a
jmol view into e.g. a molscript or pymol script?
-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- http://www.umass.edu/molvis/martz
Protein Explorer - 3D Visualization: http://proteinexplorer.org
Workshops: http://www.umass.edu/molvis/workshop
Biochem Structure Tutorials http://MolviZ.org
World Index of Molecular Visualization Resources: http://molvisindex.org
ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm
PDB Lite Macromolecule Finder: http://pdblite.org
Molecular Visualization EMail List (molvis-list):
http://bioinformatics.org/mailman/listinfo/molvis-list
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