Hello, PyMOL users,
The driving force behind these last four months of Jmol/JSmol development has
been e-publication. The goal has been to produce a means of e-publishing
working interactive biomolecular models that are ubiquitously
accessible (i.e. no Java, no WebGL). We achieved that goal for Jmol late last year,
with the introduction of "JSmol" -- a fully HTML5-based identical
renderer for Jmol. See http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
Today, I'm letting you all know that we have
that for PyMOL as well, basically. Authors can produce all the beautiful
PyMOL images they want for regular publication purposes and then have
them available for general viewing on a publisher's web site (if that site is so equipped) or on their own institutional site.
This works because Jmol now has a pretty decent PyMOL session file reader. It's a work in progress, but we are reproducing our complete set of test files (104 to date) fully now, with quite a wide variety of features. It's a work in progress, of course, and we are handling issues as they arise. But I think one look at http://ispcsrv3.weizmann.ac.il/a2jmolb/browse
will convince you that we have made some pretty significant progress along these lines.
[That server is having significant issues just this week, so pardon the "Failed" signs. Those aren't real problems; just some sort of unidentified server issue at the Weizmann Institute.]
This will be released as Jmol 13.2.0 sometime next week. In the mean time, if you want to experiment --- realizing that most of you do not do anything with Jmol right now, right? -- that's understandable --- the link to the compiled Java and HTML5 versions are:
(Java, including stand-alone Jmol.jar and JmolData.jar and applet files)
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900