At 1/9/06, Bob Hanson wrote:
<script type="text/javascript"
src="http://fusion.stolaf.edu/chemistry/jmol/loaddata.js";></script>
[snip]
The only catch is that it's a bit indirect, as it uses our server here at
St. Olaf College to do the transfer.
I tested this method extensively for possible use in firstglance.jmol.org.
I ruled it out because very large PDB files cannot be handled with Bob's
code as written (maybe it could be modified?). In our tests, even
medium-sized PDB files could not be transferred to Jmol using Bob's method
in mozilla firefox on linux (knoppix was what I tested).
The Apache server rewrite rules recommended by Miguel have worked
flawlessly for firstglance.jmol.org, which includes all of his instructions
-- for setting them up -- in its documentation (see
bioinformatics.org/firstglance).
Incidentally, firstglance.jmol.org implements use of the unsigned applet,
the signed applet (click Advanced Options on the main page), and can load
any URL using an Apache rewrite rule. For security reasons, we limited that
rewrite rule to filenames ending ".pdb" or a few other cases. The present
version of FirstGlance (0.96) does not provide a URL slot, but will accept
PDB file URL's in links as illustrated here
http://molvis.sdsc.edu/fgij/links.htm
The forthcoming version (0.97) will have a URL slot on the main page, as
well as a slot for PDB codes.
The entire firstglance.jmol.org code can be downloaded from
bioinformatics.org/firstglance. The controls on which mechanisms a given
installation uses, and how, are in the file config.js.
The disadvantage is that I chose not to use jmol.js in FirstGlance because
I would like to understand better what jmol.js attempts to do and the
possible consequences, before I use it -- perhaps we can develop better
documentation for jmol.js in the near future, and then I can incorporate it.
I will be happy to answer any questions about the implementation of
FirstGlance, and to add the answers to its already extensive documentation.
It is intended to be an open-source project, so I hope others will be
inspired to contribute to it.
----
Eric Martz, Professor Emeritus, Dept Microbiology
University of Massachusetts, Amherst MA US
http://www.umass.edu/molvis/martz
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