Dear Jmol 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 interactive investigation on a publisher's web site (if that site is so equipped) or on their own institutional site.
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
will convince you that we
have made some pretty significant progress along these lines.
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.]
are some differences in that test set, but they are only cosmetic -- a
few sightly different renderings of cartoons, for instance. Jmol, though
it has a PovRAY interface, doesn't interactively do shadows.
Translucency is handled differently. (PyMOL's translucency is
object-based; Jmol's translucency is pixel-based.) The perspective is
exact, though, because both programs use the same perspective model.
Morph-type (not scripted) movies are no problem. Electron density maps
are read. Scenes are cataloged, reproducible, and easily "discovered" by
Of course, the
(sometimes perceptively) slower than C++. That's a given. Don't expect
prime performance on your smart phone.
particularly the PyMOL default solvent-excluded surface, is considerably
caching the session files in Jmol as PNGJ files that allows them to be displayed
This will be released
as Jmol 13.2.0 sometime next week. In the mean time, if you want to
experiment, the link to the compiled
Java and HTML5 versions are:http://chemapps.stolaf.edu/jmol/jmol-13.1.16_2013.05.30c.zip
(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