Accelrys ViewerLite

[Rzepa, Henry]

It has just come to my attention that Accelrys has withdrawn its excellent free molecular viewing package ViewerLite and now only offers ViewerPro which retails at $299. I would be interested (a) to know the reaction of other users of this software to the news and (b) if there are any alternative freeware applications that offer the same or similar functionality particularly for viewing crystal lattices.


I am somewhat surprised the Lite version has gone; amongst the "embedded"
uses was Scifinder  Scholar, where it was used as a  3D model viewer
(although its activation to work under such was shall we say less obvious;
I had a lengthy exchange with  CAS about this about two months ago
to clarify this aspect).  I say embedded because the need to use Viewer
was apparently hardcoded into the SciFinder application.

The use of  3D viewers on the Web has gotten "messy" to say the least.
Thus if you are viewing in a  Web page,  Chime is still available, but to
a certain extent this is semi-hard coded into the Web page by being invoked
using the  <embed > element, which presupposes that the  Browser is enhanced
with a plugin.  That in turn presupposes that a plugin for your particular OS/browser
combination is available. Those of us who use  eg MacOS X will have noticed
no native Chime (and it sounds as if there never will be one; to be fair there
is a workaround, which is to use the  Classic mode of OS X, and a classic
browser such as  Netscape  4).  I believe that the  Chem3D viewer plugin
is also still available as an alternative to  Chime, although unfortunately the
two plugins do not share quite the identical set of attributes for the
<embed> element that allow Chime and Chem3D to be used interchangeably;
the author of the Web page would normally author for one or the other
and you have to use the one they expected you to use. This by the way
was one of the objections to the use of  <embed> in  XHTML, since
no common schema for defining the allowable attributes of this
element could in reality be specified.

An alternative method was to deploy applets, and for this
something like  the excellent JMol (http://jmol.sourceforge.net)
continues to improve  (being at version 6.  For a deployed example,
see both their page and eg http://www.ch.ic.ac.uk/local/organic/tutorial/ir/ )
There are quite a few others; I did summarise a few months ago at
http://www.ch.ic.ac.uk/rzepa/talks/author/ . Again applets suffer from
the supposition that the author drives how you will view the resulting
molecule in the browser.

There was supposed to be a solution to all this mess via the
<object> element, which can cascade down through a series of
options available to the person viewing the web page (we wrote
an article about this a couple of years ago http://www.ch.ic.ac.uk/rzepa/ijc/hierarchical/ )
but despite this solution having been drafted quite some time ago, few modern
browsers actually implement it well enough to work reliably (the only
one we found two years ago was the iCab browser for the Mac; we have
not tested the recent crop again).

The "ultra modern" solution is to create the appropriate  viewing instructions
"on the fly", either by querying a database directly, or by  carrying
the "chemistry" in its own markup/database  (e.g. CML) and then transforming
eg the molecule to an appropriate screen rendering, which could be
Chime, or  JMol, or  VRML, or SVG etc etc etc. Our  Chimeral
project exemplified that approach; the excellent metalloprotein database
at http://metallo.scripps.edu/current/raw.html shows how a  (MySQL)
database can be queried. I am sure there are many other exemplars.

None of which of  course  answers  David's original question about viewing
crystal lattices. Other than  Viewer,  I believe  Crystalmaker
http://www.crystalmaker.co.uk/  is probably the best, but again  I think that
is commercial with no "Lite" version.
-- 

Henry Rzepa. Imperial College, Chemistry Dept.
+44 0778 626 8220 +44 020 7594 5804 (Fax)

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