David, my replies below.
On Tue, Nov 3, 2009 at 5:39 AM, David Leader <d.lea...@bio.gla.ac.uk> wrote:
> Robert Hanson gave a long and obviously carefully thought-out reply to my
> message regarding the division between coders and interface designers. (I
> didn't mean to say I spoke *for* one of the camps - I speak for myself *as*
> a member of one the camps.) I will not quote all of Robert's message, but am
> interested that he clarifies his philosophy to the applet in this way:
>
> The general philosophy behind the applet, as I see it, is minimalist. Give
> the web page developer a black box and let them customize it.
>
>
> This is very useful to know. I would even say it's a realistic attitude
> given the usability problems that the pull-down menus have. I certainly have
> used JavaScript to add my own controls for the user in the website I use it
> for.
>
>
The more I thought about this after replying last time, the more I thought
that this is in fact the key -- the Jmol applet is, in itself, not hugely
useful. It's all about context, and any discussion of interface must include
that context. So the real question is how to augment the applet in ways that
make for an appropriate use -- obviously this depends upon the particular
use, and that is Jmol's strength -- that it allows the web page developer to
introduce whatever design features they desire to make it more useful for
their particular purpose.
> I do find it a little sad that the potential Jmol had for replacing Rasmol
> as a standalone program that undergraduate biochemists could use in a
> reasonably intuitive manner has never been realized. However I don't teach
> such students any more, so it's water under the bridge.
>
>
I'm sorry you are sad about that. I'm very pleased to see how this area is
evolving. Of course, that stand-alone Rasmol replacment has become Pymol. I
think Warren has mostly taken care of that for us, and I am fully supportive
of that project. If a group really wanted to go after interface improvements
for that particular community, I would recommend working with Warren.
In addition, some years ago we made the explicit choice to support the
Bioclipse project in not duplicating their work in this respect -- basically
saying that in the bioinformatics and cheminformatics area Bioclipse is the
standalone "version" of Jmol appropriate for the task. There are some very
nice aspects of the Jmol application, but mostly to date the excitement has
been about the applet.
Jmol has a far broader reach than either Bioclipse or Pymol, which makes it
harder to design a universally acceptable user interface in the stand-alone
department. That's a major challenge.
> PS Get them to take the test first:
> http://www.news.com.au/perthnow/story/0,21598,22492511-5005375,00.html
>
She was turning clockwise for me, but then as soon as I read the piece, she
started turning anticlockwise. Oh, now she's turning clockwise again.... Do
you know what study this is from? Or it is just a cute optical illusion gone
popular by the press? A little more digging might be in order. There's some
evidence that such a claim is nonsense --
http://www.theness.com/neurologicablog/?p=27 -- but I have no reason to
claim that's authoritative, either.
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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