From: Eric M. <em...@mi...> - 2008-04-06 19:49:23
|
http://Proteopedia.Org is a new Jmol-based server developed by Joel L. Sussman (an eminent crystallographer and former Head of the Protein Data Bank), Jaime Prilusky (author of The OCA PDB Browser and Head of the Bioinformatics Unit at the Weizmann Institute), and Eran Hodis (developer of the eMovie PyMol plugin for macromolecular movie making) at the Weizmann Institute in Israel. I think it is one of the most exciting uses of Jmol that I have seen -- perhaps the most exciting. Proteopedia is a wiki on macromolecular structure, so anyone can contribute (as in Wikipedia). Its most exciting innovation is a "Scene Authoring Tool" that makes it easy for those unfamiliar with the Jmol scripting language to develop custom molecular views, or scenes, in Jmol. These scenes are then automatically saved (as state scripts), and played back in Jmol from "green links" in the text. There can be as many applets per page as needed. You are invited to add text about your favorite molecules, to add scenes that show key features, and to suggest ideas for technical improvements to best exploit Jmol. It is expected that, as visitors add content, Proteopedia will develop into one of the most useful on-line reference sites for structural information about macromolecules. Proteopedia already contains an automatically-generated page for each of the nearly 50,000 entries in the Protein Data Bank. This automatic page contains the molecule in Jmol, with green links to display every site and ligand in the PDB file (echoing their full names), the abstract of the paper, and links to a few other particularly useful structure services and resources. Students and Educators can develop macromolecular structure tutorials in Proteopedia far more easily than in any other system at present. Proteopedia can also be used for supplementary materials for journal publications, or laboratory websites. For lecture presentations, supplementary materials or lab websites, those who contribute the content need to be able to guarantee that their pages will not be edited by others. Unlike Wikipedia, Proteopedia provides an easy solution. Each user has the option of creating protected pages that only s/he can edit. Others can copy, edit, and adapt the content from protected pages, since all content (including protected content) is bound to the GNU Free Document License. I recently taught a course to 40-some researchers in which I introduced Proteopedia. I had the entire class try out the scene authoring tools concurrently on their laptops. I assigned each student a number from one to 40 by counting and pointing. Each student then used (or created) a page "Sandbox N", where N is that student's number (for example, "Sandbox 15" for the student assigned number 15). As in Wikipedia, Sandbox pages are places to practice. Their content is periodically cleared. Proteopedia uses MediaWiki, and was greatly facilitated by Nico Vervelle's Jmol Extension. Have fun! -Eric ---- Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US http://www.umass.edu/molvis/martz |
From: Egon W. <ego...@gm...> - 2008-04-06 20:00:37
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On Sun, Apr 6, 2008 at 9:48 PM, Eric Martz <em...@mi...> wrote: > Proteopedia is a wiki on macromolecular structure, so anyone can > contribute (as in Wikipedia). Its most exciting innovation is a > "Scene Authoring Tool" that makes it easy for those unfamiliar with > the Jmol scripting language to develop custom molecular views, or > scenes, in Jmol. These scenes are then automatically saved (as state > scripts), and played back in Jmol from "green links" in the text. > There can be as many applets per page as needed. For long I wished to see Folding@Home with custom views on thing. Exactly like the way this is done. I really like the idea of those green links! Brilliant! Does not work for me, but the idea is brilliant :) java.security.AccessControlException: access denied (java.net.SocketPermission 132.77.150.58:80 connect,resolve) ----line 1 command 1 of file null: script >> "/wiki/scripts/1eve/E2020_close_up_with_84_279/10.spt" << Script completed Firefox 2.0.0.13, Java(TM) Plug-in 1.6.0_05-b13 > You are invited to add text about your favorite molecules, to add > scenes that show key features, and to suggest ideas for technical > improvements to best exploit Jmol. What about the wiki code? That is, are the mediawiki extensions open source? Can we expect to use them in Wikipedia for small molecules too? Egon -- ---- http://chem-bla-ics.blogspot.com/ |
From: Andrew T. <and...@ed...> - 2008-04-07 08:28:27
|
Eric, Looks like a great wiki but the green links do not work for me either (Firefox 2.0.0.13, Windows XP 2002 SP2). FileManager opening http://proteopedia.org/wiki/scripts/Hemoglobin/Oxysubunitsf/4.spt script ERROR: java.security.AccessControlException: access denied (java.net.SocketPermission 132.77.150.58:80 connect,resolve) eval ERROR: ----line 1 command 1 of file null: script >> "/wiki/scripts/Hemoglobin/Oxysubunitsf/4.spt" << Cheers Andy Eric Martz wrote: > http://Proteopedia.Org is a new Jmol-based server developed by Joel > L. Sussman (an eminent crystallographer and former Head of the > Protein Data Bank), Jaime Prilusky (author of The OCA PDB Browser and > Head of the Bioinformatics Unit at the Weizmann Institute), and Eran > Hodis (developer of the eMovie PyMol plugin for macromolecular movie > making) at the Weizmann Institute in Israel. I think it is one of the > most exciting uses of Jmol that I have seen -- perhaps the most exciting. > > Proteopedia is a wiki on macromolecular structure, so anyone can > contribute (as in Wikipedia). Its most exciting innovation is a > "Scene Authoring Tool" that makes it easy for those unfamiliar with > the Jmol scripting language to develop custom molecular views, or > scenes, in Jmol. These scenes are then automatically saved (as state > scripts), and played back in Jmol from "green links" in the text. > There can be as many applets per page as needed. > > You are invited to add text about your favorite molecules, to add > scenes that show key features, and to suggest ideas for technical > improvements to best exploit Jmol. > > It is expected that, as visitors add content, Proteopedia will > develop into one of the most useful on-line reference sites for > structural information about macromolecules. Proteopedia already > contains an automatically-generated page for each of the nearly > 50,000 entries in the Protein Data Bank. This automatic page contains > the molecule in Jmol, with green links to display every site and > ligand in the PDB file (echoing their full names), the abstract of > the paper, and links to a few other particularly useful structure > services and resources. > > Students and Educators can develop macromolecular structure tutorials > in Proteopedia far more easily than in any other system at present. > Proteopedia can also be used for supplementary materials for journal > publications, or laboratory websites. > > For lecture presentations, supplementary materials or lab websites, > those who contribute the content need to be able to guarantee that > their pages will not be edited by others. Unlike Wikipedia, > Proteopedia provides an easy solution. Each user has the option of > creating protected pages that only s/he can edit. Others can copy, > edit, and adapt the content from protected pages, since all content > (including protected content) is bound to the GNU Free Document License. > > I recently taught a course to 40-some researchers in which I > introduced Proteopedia. I had the entire class try out the scene > authoring tools concurrently on their laptops. I assigned each > student a number from one to 40 by counting and pointing. Each > student then used (or created) a page "Sandbox N", where N is that > student's number (for example, "Sandbox 15" for the student assigned > number 15). As in Wikipedia, Sandbox pages are places to practice. > Their content is periodically cleared. > > Proteopedia uses MediaWiki, and was greatly facilitated by Nico > Vervelle's Jmol Extension. > > Have fun! -Eric > > ---- > Eric Martz, Professor Emeritus, Dept Microbiology > University of Massachusetts, Amherst MA US > http://www.umass.edu/molvis/martz > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by the 2008 JavaOne(SM) Conference > Register now and save $200. Hurry, offer ends at 11:59 p.m., > Monday, April 7! Use priority code J8TLD2. > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- ================================== Dr Andrew R. Turner Research Computing Officer e: and...@ed... t: +44 (0)131 650 7748 w: http://www.eastchem.ac.uk/rcf icq: 370-899-715 p: School of Chemistry University of Edinburgh EH9 3JJ ================================== The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. |
From: Sérgio C. da S. <ce...@cb...> - 2008-04-24 13:08:48
|
Has anyone noticed that after issuing a "set antialiasdisplay true" all the clickable echoes stop responding? Regards Sérgio -- Dr. Sérgio Ceroni da Silva Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005 Porto Alegre, RS - Brasil - 91501-970 ================================================== Tel.: +55 (51) 3316-6091 | Fax: +55 (51) 3316-7309 http://www6.ufrgs.br/bioquimica |
From: Bob H. <ha...@st...> - 2008-04-25 05:44:48
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this is fixed for 11.5.31 Sérgio Ceroni da Silva wrote: >Has anyone noticed that after issuing a "set antialiasdisplay true" all >the clickable echoes stop responding? >Regards >Sérgio > > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 |
From: Bob H. <ha...@st...> - 2008-06-12 17:42:56
|
That's certainly working in the very latest version I have. Sérgio Ceroni da Silva wrote: >Has anyone noticed that after issuing a "set antialiasdisplay true" all >the clickable echoes stop responding? >Regards >Sérgio > > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 |
From: Sérgio C. da S. <ce...@cb...> - 2008-06-12 21:33:08
|
Bob Hanson wrote: > That's certainly working in the very latest version I have. > > Sérgio Ceroni da Silva wrote: > > >> Has anyone noticed that after issuing a "set antialiasdisplay true" all >> the clickable echoes stop responding? >> Regards >> Sérgio Maybe this is the case of an echoing e-mail :-D The original message was sent April 24 and you replied "oops" (<http://sourceforge.net/mailarchive/forum.php?thread_name=4810E013.8010804%40cbiot.ufrgs.br&forum_name=jmol-users>) It's working fine since then. Thanks -- Dr. Sérgio Ceroni da Silva Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005 Porto Alegre, RS - Brasil - 91501-970 ================================================== Tel.: +55 (51) 3316-6091 | Fax: +55 (51) 3316-7309 http://www6.ufrgs.br/bioquimica |