Subject: WWW developments

From: [email-masked] (Steven Bachrach)
Date: Wed, 3 Apr 96 07:40:49 -0600

I will probably get flamed for bringing up this subject as being too far 
removed from comp chem but here goes..

I have been very impressed with a number of web developments like the Tripos
fetch and sketch, and the molecular inventor work of SGI. (If you missed the
demo of this at the ACS meeting, make sure to get your SGI rep or an MSI
rep to show it to you!). I would like to use the plug-in Chime from MDL, but
I'm not a windows user.

Anyways, I would like to poll the community towards their attitudes and
desires in terms of how they would like to see chemical displays develop on
the web. The "old" technology was to provide a compound in one of a variety 
of formats (pdb, xyz, etc), attach a MIME type, and then allow the user to 
provide the molecular viewer locally (like Xmol or RasMol). With the
development of Netscape 2, we now have the Java option (like "fetch and 
sketch") and the plug-in option (like chime). These latter options remove 
the user from selecting the visualization tool. While this has advantages: 
everyone now views the structure in the identical way, no need for the user
to have the appropriate viewer; it also removes the freedom to choose - what 
if you don't like the Java applet provided?

Before we all go and reinvent the wheel, and we have 30 different java 
applets to rotate a molecule, can we discuss what's the "best" way to provide
the data to the general community?

Steve

Steven Bachrach				
Department of Chemistry
Northern Illinois University
DeKalb, Il 60115			Phone: (815)753-6863
[email-masked]			Fax:   (815)753-4802

---

From: "Gerald Loeffler" <[email-masked]>
Date: Thu, 4 Apr 1996 11:51:23 -0600

Hi!

On Apr 3,  7:40am, Steven Bachrach wrote:
> Subject: CCL:WWW developments
>
>-- End of excerpt from Steven Bachrach

Here are my $0.02 on that subject:

1) Without doubt, the Java approach of having a Web-site publish the data _and_
the means (i.e., the applet) to view the data is the most intelligent solution
to this whole problem area this far!

2) Nevertheless, I see two problems with that:

	a) It simply takes too long to download data+Applet every time you want
	to have a look at the data.

	b) While the Applet-approach potentially offers the possibility to
	publish every possible type of data (i.e., perfect freedom to choose
	on the publishers side) in practice, many pieces of data will still
	belong to one of the types already available as chemical MIME types.

3) A solution might be, to agree upon and develop _one_ set of Java-classes
commonly needed by chemical data viewers: Handling PDB files, displaying and
manipulating molecules, ... (in short: the handling and displaying of chemical
MIME types.)
This set will be useful to every Java-developer working in chemistry.
As I understand Java, these classes could be stored locally (just like the
classes being part of standard Java are), so that the process of repeatedly
downloading them over the network is not necessary.
Someone putting a PDB file on his Web-page just has to put a tiny Applet along
with the data, that uses these standard chemical Java classes which would
already be available on every chemists machine.
Someone putting more sophisticated data on his page has to spice up his Applet
with non-standard chemical classes, that would have to be downloaded over the
net for every access to the data.

	Gerald
--
Gerald Loeffler
PhD student in Theoretical Biochemistry

EMail: [email-masked]
Phone: +43 1 40480 612
Fax:   +43 1 4028525
SMail: University of Vienna
       Institute for Theoretical Chemistry
       Theoretical Biochemistry Group
       Waehringerstrasse 17/Parterre
       A-1090 Wien, Austria