[Molvis-list] Jmol is superceding Chime

[Eric Martz]

At 12/3/2004, Judy Voet wrote:
>Is there now (or will there be soon) an open source version that can be 
>used on new browsers? Or are the existing exercises importable to 
>java-based viewers? How are people getting around the problem of having to 
>use outdated and unsupported browsers?


Hello, Judy,

Here are answers to some of your questions. Hopefully others can add more, 
especially about Jmol.

1. MDL plans never to open the source of Chime. They have announced that by 
approximately 2006, the present Chime will likely be phased out. The 
replacement from MDL may not be free.

2. Thanks largely to the efforts of Miguel Howard and others, the 
OPEN-SOURCE Jmol java applet now supports essentially all RasMol and Chime 
commands. Thus Jmol (which has both stand-alone application and applet 
forms) appears to me to be by far the simplest and best existing or 
near-term solution to making existing Chime-based tutorials cross platform 
and cross browser.

Also Jmol seems to me to be the simplest and best alternative to Chime for 
new tutorials (and Frieda Reichsman, Tim Driscoll and I are working on our 
first). "Simplest" because existing Chime command scripts will work with 
minimal changes, and simpler for those who already know some of Chime's 
command language. I, myself, have no experience using Jmol yet, though I 
expect to begin porting Protein Explorer to Jmol sometime within the coming 
year. I hope others on this list can offer help in porting. You may also 
wish to subscribe to the Jmol Users email list (available at Jmol Home, 
http://jmol.sourceforge.net aka http://www.jmol.org).

3. Jmol already works in more browsers than Chime, and works on linux as 
well as Windows, Mac OS 9 and native OS X. There are some issues related to 
java support in each browser/platform. Perhaps Miguel Howard or Tim 
Driscoll can give us an updated list?

4. Meanwhile, it is possible to make existing Chime-based tutorials work in 
the CURRENT versions of Mozilla and Netscape 7.x. I am working to do this 
for Protein Explorer in the near future, thanks to hard groundwork by 
Enrique Castro. I or someone else (Enrique?) may get around to documenting 
the tricks for others to use. One trick is that since the Chime installer 
doesn't look for these browsers, you have to copy npchime.dll into their 
plugins directory. This one file was sufficient in my limited tests, even 
tho the Chime installer puts several other small files in IE or Netscape 4.

5. I sent a looooooong message to jmol-users yesterday about the concept of 
using Protein Explorer's soon-to-be-released script recorder to record 
scripts for Jmol-based tutorials.

http://sourceforge.net/mailarchive/message.php?msg_id=10219516

One big advantage will be that you don't have to learn the command language 
in order to author tutorials. Another is that the resulting scripts are 
inherently matched to the capabilities of Chime (unlike the "save script" 
command) and efficient (ditto). But you may have to learn a few differences 
between Jmol and Chime for optimal results. Jmol already has many 
significant enhancements compared to Chime, both in its capabilities and in 
its command language.

If anyone wants to try the Script Recorder immediately, contact Tim 
Driscoll who can put a pre-release on molvisions.com.

6. Following release of Protein Explorer with Script Recorder, I plan to 
release Protein Explorer with support for Presentations in Protein Explorer 
(PiPE). The mechanism will be to put the entire content of the presentation 
into the headers of the PDB files involved. One advantage of this is that 
all such presentations will be automatically downloadable as nothing more 
than a PDB file (or set of PDB files) directly from Chime or Jmol, and will 
run as a presentation in the matching version of PE. A demo of this scheme 
(with a downloadable pre-release of PE usable now for developing such 
PiPE's) is available at
http://www.umass.edu/microbio/chime/beta/pipes/pe_pre2.15/index.htm
download from
http://www.umass.edu/microbio/chime/beta/pipes/download/

This scheme for PiPE's should work in the planned PE-Jmol as well as in the 
existing PE-Chime. Thus, PiPE tutorials created now will have a fully 
open-source future.

-Eric


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Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst MA US  413-545-2325/FAX 413-545-2532
               http://www.umass.edu/molvis/martz
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