I'm well aware of Dean Johnston's website - it is certainly one of the
best symmetry websites I know of. In fact, several years ago his site
inspired me to develop our own symmetry website in which we let students
draw online their mental model of a symmetry element - and then compare
to the true symmetry using Jmol "draw pointgroup" script
(http://telem.openu.ac.il/symmetry). We also developed another website
to calculate the deviation of a certain structure from perfect symmetry
using Avnir's continuous symmetry measures
(http://telem.openu.ac.il/symmetry/csm). Here we start with a distorted
structure and find the closest structure with perfect symmetry.
Currently, this site uses an older version of Jmol and only works with
pdb files, but will be updated soon. Then, the "draw pointgroup" script
will be used to visualize the symmetry of the calculated structure and
check if the correct symmetry element was found.
Thank you Bob and Dean for developing this cool feature!
All the best,
Inbal
___________________________
Dr. Inbal Tuvi-Arad
Department of Natural Sciences
The Open University of Israel
1 University Road., POB 808
Raanana 43107
ISRAEL
Tel: 09-7781773
Fax: 09-7780661
Email: [email protected]
http://telem.openu.ac.il/symmetry <http://telem.openu.ac.il/symmetry>
___________________________
From: Robert Hanson [mailto:[email protected]]
Sent: Tuesday, July 05, 2011 4:48 PM
To: [email protected]
Subject: Re: [Jmol-users] Drawing symmetry elements across models
Nice to see draw pointgroup being used. That was a fun addition to make
to Jmol -- the result of a "Bob Challenge" at the Biennial Conference on
Chemical Education a three years ago. (The challenge for the crowd was
to come up with a new idea for Jmol that I would then take on as a
challenge to have implemented before the end of the conference.) Dean
Johnston was the winner with the idea of doing point group analysis, and
we spent long nights that week getting it working. (He was then
responsible for keeping me awake and supplied with nourishment while
coding and also supplying the inorganic chemist's logic for point group
assignment. All I had to do was code. It was great fun.) I only had to
make a few minor tweaks on that since. Dean has done a fabulous job
putting it in context with his pages at http://symmetry.otterbein.edu/.
Bob
On Tue, Jul 5, 2011 at 2:47 AM, Inbal Tuvi-Arad <[email protected]>
wrote:
It works! What an upgrade to my daily work!
Thank you very much.
Inbal
From: Robert Hanson [mailto:[email protected]]
Sent: Tuesday, July 05, 2011 12:13 AM
To: [email protected]
Subject: Re: [Jmol-users] Drawing symmetry elements across models
frame first;while (true) {draw pointgroup;if (_modelNumber ==
_lastframe){break};frame next}
On Mon, Jul 4, 2011 at 1:01 AM, Inbal Tuvi-Arad <[email protected]>
wrote:
Dear Bob,
Thank you for your answer. If I understand correctly, once the bug is
fixed - if I have 10 models in my file I would need to type 10 lines in
order to display the symmetry elements on all models. It would be nice
to have the possibility to type something similar to "set
measureAllModels ON" and then type "draw pointgroup" in order to get the
job done.
Best wishes,
Inbal
From: Robert Hanson [mailto:[email protected]]
Sent: Sunday, July 03, 2011 8:28 PM
To: [email protected]
Subject: Re: [Jmol-users] Drawing symmetry elements across models
That's a bug. Thank you for letting us know about it.
Fixed for 12.0.47 and 12.1.51 See
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
Make sure also that you select just the atoms of one model and also go
to that model's frame before issuing the draw command.
frame 1.1;select 1.1;draw pointgroup
frame 1.2;select 1.2;draw pointgroup
...
like that. Please let me know if that works or not.
Bob Hanson
On Sun, Jul 3, 2011 at 2:28 AM, Inbal Tuvi-Arad <[email protected]>
wrote:
Hello to all,
I'm working with xyz files that contains several models of the same
molecule. I'd like to be able to present the symmetry elements of all
models so that navigation between them will keep the symmetry elements.
"Draw pointgroup" only works for the current model. Is there a command
that draws the same symmetry elements for all models?
Sincerely,
Inbal
------------------------------------------------------------------------
------
All of the data generated in your IT infrastructure is seriously
valuable.
Why? It contains a definitive record of application performance,
security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
_______________________________________________
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
------------------------------------------------------------------------
------
All of the data generated in your IT infrastructure is seriously
valuable.
Why? It contains a definitive record of application performance,
security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
_______________________________________________
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
------------------------------------------------------------------------
------
All of the data generated in your IT infrastructure is seriously
valuable.
Why? It contains a definitive record of application performance,
security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
_______________________________________________
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
------------------------------------------------------------------------------
All of the data generated in your IT infrastructure is seriously valuable.
Why? It contains a definitive record of application performance, security
threats, fraudulent activity, and more. Splunk takes this data and makes
sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-d2d-c2
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
