From jaime.prilusky at weizmann.ac.il Thu Oct 8 17:19:10 2020 From: jaime.prilusky at weizmann.ac.il (Jaime Prilusky) Date: Thu, 8 Oct 2020 21:19:10 +0000 Subject: [Proteopedia] SAT related improvements Message-ID: <1521AA97-E144-49A7-A561-67636C8441BC@weizmann.ac.il> Dear Proteopedians, Two new features related to Proteopedia scenes: Feature one: on loading a scene there's a message to the user. (Thank you to Karsten Theis for the suggestion and to Angel Herra?z for the explanations.) Feature two: when saving a scene on the Scene Authoring Tool (SAT), you may now choose on "when this scene loads, I want it to" in addition to 'still' and 'spin', for the model to 'rock' and to 'wobble'. Both rock and wobble add movement to the model, for a brief time, to enhance the appearance of 3D representation. Try them. (Thank you to Karsten Theis for the wobble function.) Remember to clear your browser's cache if you encounter that something on Proteopedia stopped working. It could be a consequence of the recent upgrade to Jmol version 14.31.8 Regards, Jaim -------------- next part -------------- An HTML attachment was scrubbed... URL: From emartz at microbio.umass.edu Sat Oct 10 11:45:37 2020 From: emartz at microbio.umass.edu (Eric Martz) Date: Sat, 10 Oct 2020 11:45:37 -0400 Subject: [Proteopedia] New pages and capabilities Message-ID: <28cbcc46-ab90-f40d-2b62-f1929e7d6aa3@microbio.umass.edu> This message is from Karsten Theis. I am sending it to get around technical difficulties. ------------------ Hi All, I wanted to let you know about some new content and some new tutorial pages: *Content:* 1) I made some new carbohydrate pages fairly recently, and they are now all linked on the carbohydrates page (cellulose, amylose). 2) I made some pages concerning stereochemistry . The parent page links to all of them in the "See also" section. These have been great for teaching remotely when it comes to carbohydrate stereochemistry (e.g. Fisher projection). *Tutorials:* There is a viewing guide , and a rubric to evaluate pages and 3D scenes. There are tutorials on the more advanced uses of Jmol, including Jmol/interactivity, Jmol/superposition, and User:Karsten Theis/Electron density. Examples can be found at http://proteopedia.org/wiki/index.php/Talk:Garman_lab:_Interconversion_of_lysosomal_enzyme_specificities and http://proteopedia.org/wiki/index.php/Talk:Schubert_lab:_bacterial_InIC_disrupts_human_Tuba_complexes I also made a tutorial for remixing Proteopedia articles (reusing text and 3D scenes): Remixing *New features:* Jaim and Angel worked on new features in the scene authoring tool (spin on/off expanded to offer rock or wobble) and in the way we can link to scenes: A link like https://proteopedia.org/w/Lysozyme#hydrogen%20bonds goes straight to the "hydrogen bond" green link, shows the opening scene and then switches to the hydrogen bond scene. These new features are also illustrated here: http://proteopedia.org/wiki/index.php/User:Karsten_Theis/Molecular_Interactions and here: http://proteopedia.org/wiki/index.php/User:Karsten_Theis/Favorite_3D_scenes. Take good care, Karsten -- Karsten Theis Chemical & Physical Sciences Department Westfield State College -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaime.prilusky at weizmann.ac.il Tue Oct 13 17:02:08 2020 From: jaime.prilusky at weizmann.ac.il (Jaime Prilusky) Date: Tue, 13 Oct 2020 21:02:08 +0000 Subject: [Proteopedia] other SAT related improvements Message-ID: Dear Proteopedians, Just implemented features related to SAT (Scene Authoring Tool), suggested a long time ago. Your suggestions on http://proteopedia.org/w/Wishlist are important. 1. Representations tab, change set representation to replace representation and add add to representation and remove from representation. This allows, for example, the (sidechains + alpha carbons) of selected residues to be rendered as ball and stick (add representation) without erasing a backbone trace for those alpha carbons. Suggested on 25 January 2011 by Eric Martz. 2. Load Molecule tab, new option to append a molecule. Suggested on 26 January 2011 by Karl Oberholser. 3. Save Scene tab, new option to spin about the z-axis. Suggested on 26 January 2011 by Karl Oberholser. 4. Representations tab, new dialog for slabbing. Suggested on 5 February 2011 by Eric Martz. Regards, Jaim -------------- next part -------------- An HTML attachment was scrubbed... URL: From emartz at microbio.umass.edu Sun Dec 13 15:39:19 2020 From: emartz at microbio.umass.edu (Eric Martz) Date: Sun, 13 Dec 2020 15:39:19 -0500 Subject: [Proteopedia] New tool to locate and visualize pockets, cavities and tunnels Message-ID: A new, free, open-source program is available: PACUPP, Pockets And Cavities Using Pseudoatoms in Proteins. You can see sample results at http://proteopedia.org/w/PACUPP:_Pockets_And_Cavities_Using_Pseudoatoms_in_Proteins There are demonstrations in YouTube and a slideshow. You can find these and download the program at http://molviz.org/pacupp Examples shown include: * Coronoavirus SARS-CoV-2 spike protein cavity that is a potential drug target * Ribosome nascent peptide exit channel * Proteasome * HIV protease (detailed demonstration of PACUPP commands) * Acetylcholinesterase catalytic pocket with inhibitor * DNA, major and minor grooves * Orthogonal tunnels accessing the heme in protoglobin * Oligopeptide-binding protein A with an octapeptide in a buried cavity (detailed demonstration of PACUPP commands) -Eric Eric Martz, Professor Emeritus, Dept Microbiology (he/him/his) U Mass, Amherst -- Martz.MolviZ.Org Guided Exploration of Macromolecules: 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.tau.ac.il 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: From emartz at microbio.umass.edu Wed Dec 23 16:19:00 2020 From: emartz at microbio.umass.edu (Eric Martz) Date: Wed, 23 Dec 2020 16:19:00 -0500 Subject: [Proteopedia] Coronavirus mutations in interactive 3D Message-ID: <7efd094b-5243-f26c-2f7c-0018d5512b76@microbio.umass.edu> Coronavirus mutations reported within the past week by scientists in the UK have raised concern about an increased transmission rate of COVID-19. The report even temporarily closed the borders between the UK, France, and other EU countries, causing huge backups of trucking and supply concerns. See the locations of the 4 most concerning mutations on a rotating 3D model of spike protein with interpretations of their likely consequences at this article posted December 22, 2020: http://proteopedia.org/w/SARS-CoV-2_spike_protein_mutations The article is written to be suitable for high-school students and higher. There are links to additional background material as well as references to reliable scientific publications and news sources. The article offers a downloadable movie of the spike protein, slide presentation-ready, showing the conformational change when it is primed, with the locations of mutations indicated. -Eric Martz Professor Emeritus, Dept Microbiology (he/him/his) University of Massachusetts, Amherst MA US Martz.MolviZ.Org -------------- next part -------------- An HTML attachment was scrubbed... URL: