From: Inbal Tuvi-A. <in...@op...> - 2011-07-06 06:17:54
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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: in...@op... http://telem.openu.ac.il/symmetry <http://telem.openu.ac.il/symmetry> ___________________________ From: Robert Hanson [mailto:ha...@st...] Sent: Tuesday, July 05, 2011 4:48 PM To: jmo...@li... 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 <in...@op...> wrote: It works! What an upgrade to my daily work! Thank you very much. Inbal From: Robert Hanson [mailto:ha...@st...] Sent: Tuesday, July 05, 2011 12:13 AM To: jmo...@li... 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 <in...@op...> 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:ha...@st...] Sent: Sunday, July 03, 2011 8:28 PM To: jmo...@li... 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 <in...@op...> 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 Jmo...@li... 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 Jmo...@li... 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 Jmo...@li... 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 |