Thanks, Phillip. Yes, I'm starting biomolecules in organic class and thought
this might be of help. We're doing carbohydrates right now, and I think I'll
have fun with the Fischer projection business. Kind of crazy, of course, but
it might be fun. I've souped it up a bit today so that it is better
organized with subcategories. Still some work to do, I think. One
interesting aspect, I think, is that it uses the files from the Klotho site,
but it changes how the molecule loads depending upon its type. For example,
amino acids are depicted with N on the left and C on the right.I'm working
on the pyranoses and furanoses now.
Some nice coding examples in there:
-- determining a structure type using connected()
-- checking for rings using within("branch")
-- setting dihedrals using rotate branch
-- setting orientations using quaternion(center, axisx, vectorxy)
-- using Excel/JavaScript (klotho.xls) to set up a simple database
What should I do with this, do you think?
Bob
On Sat, Apr 18, 2009 at 3:25 PM, Philip Bays <[email protected]> wrote:
> Ok. Got it going by clearing both the cache and the history. Boy this
> is cool. Wish I had had it last week for class:-(
>
> On Apr 18, 2009, at 12:38 PM, Philip Bays wrote:
>
> That is what I observe on mine as well. The applet does not load. So
> let's look at configurations:
> I am running on an intel Mac using OS 10.5.6 and Safari Public Beta 4.
> Link does not work; applet does not download.
>
> On the other hand, I have an old G4 iBook running 10.4.11 and Safari 3.2.1
> on which the link works, albeit a little slow.
>
> Phil Bays
>
>
> On Apr 18, 2009, at 12:15 PM, Frieda Reichsman wrote:
>
> The page does not work on my machine running Safari 3.2.1 - not a beta. The
> applet never finishes loading.
> Frieda
>
> On Apr 17, 2009, at 8:58 PM, Philip Bays wrote:
>
> This page works fine on the Mac using Firefox, but not using the latest
> beta of Safari. Is that a problem with java in this version of Safari?
> Phil
>
> On Apr 17, 2009, at 1:59 PM, Robert Hanson wrote:
>
> One more addition -- that page now rotates bonds to correspond to Fischer
> projections and then reorients the molecule appropriately for that using
> quaternions.
>
> (Select D-glucose and then click the "Fischer Projection" button)
>
> Bob
>
>
> On Thu, Apr 16, 2009 at 11:22 PM, Robert Hanson <[email protected]>wrote:
>
>> I found a nice set of carbohydrate structures and made a little page for
>> them -- could be useful?
>>
>> http://chemapps.stolaf.edu/jmol/docs/examples-11/carbo.htm
>>
>> This page illustrates the use of the calculate "AROMATIC" command. The
>> files don't have any indication of single or double bonding. I think it's
>> pretty close.
>>
>> 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
>>
>
>
>
> --
> 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
>
> ------------------------------------------------------------------------------
> Stay on top of everything new and different, both inside and
> around Java (TM) technology - register by April 22, and save
> $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
> 300 plus technical and hands-on sessions. Register today.
> Use priority code J9JMT32.
> http://p.sf.net/sfu/p_______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> J. Philip Bays
> Professor of Chemistry
> Science Hall 172
> Saint Mary's College
> Notre Dame IN 46556
> (574) 284-4663
>
>
> ------------------------------------------------------------------------------
> Stay on top of everything new and different, both inside and
> around Java (TM) technology - register by April 22, and save
> $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
> 300 plus technical and hands-on sessions. Register today.
> Use priority code J9JMT32.
> http://p.sf.net/sfu/p_______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
> ------------------------------------------------------------------------------
> Stay on top of everything new and different, both inside and
> around Java (TM) technology - register by April 22, and save
> $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
> 300 plus technical and hands-on sessions. Register today.
> Use priority code J9JMT32.
> http://p.sf.net/sfu/p_______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> J. Philip Bays
> Professor of Chemistry
> Science Hall 172
> Saint Mary's College
> Notre Dame IN 46556
> (574) 284-4663
>
>
> ------------------------------------------------------------------------------
> Stay on top of everything new and different, both inside and
> around Java (TM) technology - register by April 22, and save
> $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
> 300 plus technical and hands-on sessions. Register today.
> Use priority code J9JMT32.
> http://p.sf.net/sfu/p_______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> J. Philip Bays
>
> Professor of Chemistry
>
> Science Hall 172
>
> Saint Mary's College
>
> Notre Dame IN 46556
>
> (574) 284-4663
>
>
>
> ------------------------------------------------------------------------------
> Stay on top of everything new and different, both inside and
> around Java (TM) technology - register by April 22, and save
> $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
> 300 plus technical and hands-on sessions. Register today.
> Use priority code J9JMT32. http://p.sf.net/sfu/p
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
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
------------------------------------------------------------------------------
Stay on top of everything new and different, both inside and
around Java (TM) technology - register by April 22, and save
$200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco.
300 plus technical and hands-on sessions. Register today.
Use priority code J9JMT32. http://p.sf.net/sfu/p
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
