From jaime.prilusky at weizmann.ac.il Wed Jan 24 13:07:55 2018 From: jaime.prilusky at weizmann.ac.il (Jaime Prilusky) Date: Wed, 24 Jan 2018 18:07:55 +0000 Subject: [Proteopedia] SAT Advanced Comands Input Message-ID: <248FE14A-B24E-4057-BCAB-937E39A0A0D4@weizmann.ac.il> Dear Proteopedians, Advanced users will found now in Proteopedia?s Scene Authoring Tool (SAT), under the JSmol applet, a button to quickly open JSmol Console and a text input field to enter scripting commands and Execute them on the applet (see the attached image). This allows to easily execute additional scripting JSmol commands besides those currently implemented as buttons and pulldowns. This is only one of the great suggestions formulated during the recent Proteopedia 10th Anniversary Conference (20-22 Jan 2018, UMass Amherst, MA) Regards, Jaim [cid:B91BB8D8-E2C8-491E-A58F-DB912C37095D] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: SAT Advanced command input.png Type: image/png Size: 67082 bytes Desc: SAT Advanced command input.png URL: From jaime.prilusky at weizmann.ac.il Fri Jan 26 01:47:42 2018 From: jaime.prilusky at weizmann.ac.il (Jaime Prilusky) Date: Fri, 26 Jan 2018 06:47:42 +0000 Subject: [Proteopedia] Jmol upgraded 14.28.4 Message-ID: Proteopedia runs now on Jmol-14.28.4 Jaim From jaime.prilusky at weizmann.ac.il Tue Jan 30 11:39:52 2018 From: jaime.prilusky at weizmann.ac.il (Jaime Prilusky) Date: Tue, 30 Jan 2018 16:39:52 +0000 Subject: [Proteopedia] Cutting Edge JSmol features Message-ID: You may now have Proteopedia rendering models with the latest version of JSmol. Login Proteopedia, click on the ?my preferences? link (http://proteopedia.org/w/Special:Preferences) , click on the ?Misc? tab and check the option to ?use the latest JSmol version?. Save your preferences. From this time on, any Proteopedia page you browse will use the latest version from https://chemapps.stolaf.edu/jmol/jsmol Jaim -------------- next part -------------- An HTML attachment was scrubbed... URL: From emartz at microbio.umass.edu Tue Jan 30 11:59:06 2018 From: emartz at microbio.umass.edu (Eric Martz) Date: Tue, 30 Jan 2018 11:59:06 -0500 Subject: [Proteopedia] Let's Use This Proteopedia Email List Message-ID: Dear Proteopedia User, Let's make this Proteopedia email list more valuable to us all. Please send email to this list whenever: 1. You have a problem with Proteopedia or need help or can't find something or wonder whether Proteopeda can do X, Y, or Z. You're probably not the only person with the issue and others may benefit from the discussion. 2. You have written a new page in Proteopedia. Send us a link to it. 3. You have made substantial improvements to an existing page. Send us a link to it. 4. You have used Proteopedia in your teaching. We would love to know how you used it, what worked well, what not so well. If you are comfortable with sharing your syllabus or other materials (and your institution allows this), please provide links (whether they are inside or outside Proteopedia). 5. You ran across an article in a Sandbox that deserves to be moved to a permanent title. Send us the link. 6. You have done something unusual. Examples are three-synchronized DNA molecules on one page (B, A, and Z forms), a translucent surface around water colored by electrostatic potential, an animation of a chemical reaction, a complex "story" animation. Links to those 4 examples (not new): http://proteopedia.org/w/Forms_of_DNA Translucent surface, electrostatic potential for Water: http://proteopedia.org/w/User:Eric_Martz/Sandbox_8 Chemical reaction: http://proteopedia.org/w/Ozonolysis Complex "story" animation: http://proteopedia.org/w/Molecular_Playground/HIV_Protease_Inhibitor Sincerely, Eric Martz, Joel Sussman, Jaime Prilusky, Angel Herr?ez for the Proteopedia development team From angel.herraez at uah.es Tue Feb 6 04:06:22 2018 From: angel.herraez at uah.es (=?ISO-8859-1?Q?Angel_Herr=E1ez?=) Date: Tue, 06 Feb 2018 10:06:22 +0100 Subject: [Proteopedia] updated pages: comparison of protein helices and of DNA helices Message-ID: <5A79700E.14790.19CD38F3@angel.herraez.uah.es> Dear Proteopedia enthusiasts, I have just updated two pages that display in parallel the different types of helical conformations: http://proteopedia.org/w/Helices_in_Proteins with alpha, 3-10 and pi helices http://proteopedia.org/w/Forms_of_DNA with A-, B- and Z-DNA In both pages, synchronization now works better and can be driven from any of the 3 JSmol panels. Additonal buttons have been added to change the rendering of the molecule. Enjoy! ? Dr. Angel Herr?ez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcal? E-28871 Alcal? de Henares (Madrid), Spain From jaime.prilusky at weizmann.ac.il Sun Mar 25 04:19:05 2018 From: jaime.prilusky at weizmann.ac.il (Jaime Prilusky) Date: Sun, 25 Mar 2018 08:19:05 +0000 Subject: [Proteopedia] Scenes from PyMOL .pse files Message-ID: <0815598E-AAEF-453E-9BD6-8F0C1D6AB27C@weizmann.ac.il> To create a Proteopedia scene from a PyMOL .pse file, do the following: 1. Open SAT on the page you?re editing, 2. Drag your .pse file and drop it into JSmol Note: the processing of large .pse files will take longer time 3. If needed, modify the scene with SAT tools 4. Save the scene Please report any problem you may find. Regards, Jaim From emartz at microbio.umass.edu Fri Mar 30 16:20:52 2018 From: emartz at microbio.umass.edu (Eric Martz) Date: Fri, 30 Mar 2018 16:20:52 -0400 Subject: [Proteopedia] Visualizing membrane position Message-ID: <0737b084-511a-7df3-c6ed-9abdc5f8fb7c@microbio.umass.edu> I have newly created a page showing and explaining several methods for visualizing the position of a lipid bilayer membrane proximal to a protein integral membrane domain. http://proteopedia.org/w/Jmol/Visualizing_membrane_position Please let me know if you have questions or the page needs clarifications. Or, feel free to edit the page yourself. -Eric Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- Martz.MolviZ.Org * FirstGlance: 3D Molecules in /Nature/: FirstGlance.Jmol.Org * Protein 3D Structure Wiki: Proteopedia.Org * Top Five 3D MolVis Tools: Top5.MolviZ.Org * Education: Biochem in 3D at MolviZ.Org * Find Functional Patches in Proteins: ConSurf * Atlas of Macromolecules: Atlas.MolviZ.Org * Interactive Molecules in Architectural Spaces: MolecularPlayground.Org * Workshops: Workshops.MolviZ.Org -------------- next part -------------- An HTML attachment was scrubbed... URL: