Jmol 11.3.10 adds some interesting features and fixes a few bugs.
Thanks, Nico, for that release.
bug fixes
---------
# bug fix: dots nn% not operational
# bug fix: molecular dipole in multiple frame environment
(note: you still only get ONE molecular dipole, no matter how many
models you have)
# bug fix: state of multi-polymer protein cannot be restored
# bug fix: application script window using swing thread start not from
event queue
# new feature: molecular dipole for Gaussian files
--------------------------------------------------
Just let us know if you have a file format that shows a molecular dipole
but Jmol is not aware of it.
# new feature: simple calculation of approximate dipole moment
--------------------------------------------------------------
dipole molecular # from file value if provided
dipole calculate molecular # from "center of gravity" of charges
calculation
This is a very crude implementation of molecular dipole. It's just
SUM(charge*position).
# new feature: show frames
--------------------------
show frames
based on models in the current frame set, SHOW FRAMES displays just the
basic information -- file name, model title, and model name -- in a
format that could be executed as JavaScript.
load files "data/caffeine.xyz" "data/1crn.pdb"
show frames
=>
file["1.1"] = "C:\jmol-dev\workspace\Jmol\data\caffeine.xyz"
title["1.1"] = "3"
name["1.1"] = "1"
file["2.1"] = "C:\jmol-dev\workspace\Jmol\data\1crn.pdb"
title["2.1"] = "1CRN"
name["2.1"] = "1"
# new feature: write JPG n "filename"
-------------------------------------
JPG image format allows for a range of quality and, as a result, file
size. Jmol's default is to use the highest quality (100), which creates
quite large files. Jmol 11.3.10 now allows setting of the JPG quality in
the write command:
write JPG 60 "myfile.jpg"
Lower quality is probably what people are more used to seeing in JPG
files. I know MicroSoft Paint, for example, saves JPG files with about a
quality of 50. especially if you are going to make a movie with lots of
JPG files, you will probably want to reduce the quality level to
something like 50-60.
# new feature: application option for web page export
-----------------------------------------------------
A new Jmol application menu and toolbar item, File -- Export -- Export
to Web Page allows very simple creation of two types of web pages.
Pop-In Jmol pages display a set of applets, but all you see initially
is a PNG image "cover" showing the model along with a message and a
link. When the user clicks the link, the applet comes alive (it is
downloaded only then).
<http://jmol.svn.sourceforge.net/viewvc/*checkout*/jmol/trunk/Jmol/src/org/openscience/jmol/app/webexport/pop_in_instructions.html>
ScriptButton Jmol pages display a single resizable applet and a set of
buttons.
<http://jmol.svn.sourceforge.net/viewvc/*checkout*/jmol/trunk/Jmol/src/org/openscience/jmol/app/webexport/script_button_instructions.html>
The idea is to have a very simple set of tools that both HTML novices
and experts can use to build web pages from within the Jmol application.
A single directory is created containing the necessary HTML, SPT, and
PNG files.
John Gutow is developing this. We have a bunch of ideas for how to make
this even better, but we think it is basically functional right now. The
two of us are interested in all feedback you might have.
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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
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