From emartz at microbio.umass.edu Wed Jan 9 13:56:10 2019 From: emartz at microbio.umass.edu (Eric Martz) Date: Wed, 9 Jan 2019 13:56:10 -0500 Subject: [Proteopedia] Uploading to FirstGlance is Fixed Message-ID: Recently there were problems uploading PDB files to FirstGlance in Jmol. This is fixed in a new version 2.74 released on January 6. http://FirstGlance.Jmol.Org or google FirstGlance (no space!) Uploading is useful for homology models, or any PDB file not in the Protein Data Bank, or published PDB files that have been modified. At the index.htm page of FirstGlance (the one where you specify a PDB code), look for "Upload your own PDB file". Thanks to Jaime Prilusky for implementing uploads on a different server to solve this problem. -Eric -- Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US Martz.MolviZ.Org Proteopedia.Org Administrator User:Eric_Martz -------------- next part -------------- An HTML attachment was scrubbed... URL: From emartz at microbio.umass.edu Fri Jan 11 11:11:26 2019 From: emartz at microbio.umass.edu (Eric Martz) Date: Fri, 11 Jan 2019 11:11:26 -0500 Subject: [Proteopedia] Electron cryomicroscopy Message-ID: <3c5aeec9-a99f-9c52-6ff7-acfc567a58a6@microbio.umass.edu> I started an article on cryo-EM http://proteopedia.org/w/Electron_cryomicroscopy It includes links to an excellent silent 3-min video that explains the principles. It would be great if people with expertise help to improve this article. -Eric -- Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US Martz.MolviZ.Org -------------- next part -------------- An HTML attachment was scrubbed... URL: From emartz at microbio.umass.edu Tue Jan 29 14:05:31 2019 From: emartz at microbio.umass.edu (Eric Martz) Date: Tue, 29 Jan 2019 14:05:31 -0500 Subject: [Proteopedia] Tutorials by Educators, Syllabi, Quizzes Message-ID: <1d798917-d071-70f9-6a2e-818fe08e3bb8@microbio.umass.edu> The Proteopedia page "Teaching Scenes, Tutorials, and Educators' Pages" (link ) had not been updated for many years. I have done a major revision and expansion of this page, dividing "Pages by Educators" into the sections Concepts, Molecules, Syllabi, and Quizzes. I also added a new section, "Art". http://proteopedia.org/w/Teaching_Scenes%2C_Tutorials%2C_and_Educators%27_Pages#Concepts I have tried to limit the page to basic introductory material, excluding many more technical concepts (excluding for example pages on asymmetric unit/biological unit, resolution, atomic coordinate files, electron density maps, methods such as X-ray, cryo-EM, theoretical modeling, free R, homology modeling, etc. etc. etc.). The comprehensive list that includes pages on all such concepts is http://proteopedia.org/wiki/index.php/About_Macromolecular_Structure Please help by adding appropriate links to these pages. Sincerely, Eric Eric Martz, Professor Emeritus, Dept Microbiology 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 * 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 Tue Jan 29 17:03:24 2019 From: emartz at microbio.umass.edu (Eric Martz) Date: Tue, 29 Jan 2019 17:03:24 -0500 Subject: [Proteopedia] Student Projects in Proteopedia & Adoptions Message-ID: The page "Student Projects" http://proteopedia.org/wiki/index.php/Student_Projects had not been updated for a long time. I have added many entries to show that there is ongoing and current vibrant, creative and extensive student participation in authoring of well-developed articles in Proteopedia. The pages I included are all vetted/edited by the faculty teaching those students. As mentioned there, many have been featured in the IUBMB journal /Biochemistry and Molecular Biology Education/. Please help by adding links to other well-developed pages where students have been involved in authoring. The section "Adoptions in College and University Classes" surely also needs much updating. I have not tackled that one. If you are assigning use of Proteopedia to your students, or if you know of such use, please make sure such uses are listed there! http://proteopedia.org/w/Proteopedia:News#Adoptions_in_College_and_University_Classes Thanks very much, -Eric -- Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US Martz.MolviZ.Org -------------- next part -------------- An HTML attachment was scrubbed... URL: From emartz at microbio.umass.edu Sat Feb 2 17:02:37 2019 From: emartz at microbio.umass.edu (Eric Martz) Date: Sat, 2 Feb 2019 17:02:37 -0500 Subject: [Proteopedia] New page Jmol/Index Message-ID: <49da0c50-8044-7f57-924b-a2d5790ace20@microbio.umass.edu> I started a new page http://proteopedia.org/w/Jmol/Index in which I have attempted to gather links to all pages in Proteopedia that are "about Jmol or JSmol", plus a few links to key external resources about Jmol. As always, feel free to contribute improvements. -Eric -- Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US Martz.MolviZ.Org -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaime.prilusky at weizmann.ac.il Sun Feb 3 03:14:40 2019 From: jaime.prilusky at weizmann.ac.il (Jaime Prilusky) Date: Sun, 3 Feb 2019 08:14:40 +0000 Subject: [Proteopedia] Morphing on Proteopedia Message-ID: You can now Morph protein structures on Proteopedia and easily use them for creating scenes. The Morph-On-Proteopedia feature is fully active , it works great and enables easy interaction with SAT for scenes development. Start at http://proteopedia.org/w/Special:Morph , provide two structures (either PDB ids, upload files or a combination or both) and optional chain selection and click [Morph]. Morphing takes place between a few minutes, thanks to PyMOL and SCHRODINGER, and you?ll be able to directly upload the resulting morph to Proteopedia for SAT scene development, or download a PDB or .pse file. Please let us know if you encounter any problem or unexpected results. Regards, Jaim -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaime.prilusky at weizmann.ac.il Tue Feb 5 12:38:53 2019 From: jaime.prilusky at weizmann.ac.il (Jaime Prilusky) Date: Tue, 5 Feb 2019 17:38:53 +0000 Subject: [Proteopedia] XML error: Mismatched tag Message-ID: For some time we have on Proteopedia the page Help:Errors, to explain users how to overcome the problem of "XML error: Mismatched tag?, caused by unbalanced tags or ?<>? characters. Starting today, the error page includes an active link to that page, as shown below. XML error: Mismatched tag at line 1 See Help:Errors Jaim -------------- next part -------------- An HTML attachment was scrubbed... URL: From emartz at microbio.umass.edu Wed Feb 13 11:52:28 2019 From: emartz at microbio.umass.edu (Eric Martz) Date: Wed, 13 Feb 2019 11:52:28 -0500 Subject: [Proteopedia] FirstGlance alternate servers Message-ID: It appears to me that bioinformatics.org has been down for an unprecedented 12 hours. That is the primary host for FirstGlance in Jmol, accessed via FirstGlance.Jmol.Org. Until service is restored, FirstGlance can be accessed at either of these locations*: https://proteopedia.org/wiki/fgij/ https://oca.weizmann.ac.il/oca-docs/fgij/index.htm In January, FirstGlance was used on average 379 times/day. -Eric * Thanks to Jaime Prilusky, the Weizmann Institute, and the Proteopedia team. From emartz at microbio.umass.edu Thu Feb 21 14:29:44 2019 From: emartz at microbio.umass.edu (Eric Martz) Date: Thu, 21 Feb 2019 14:29:44 -0500 Subject: [Proteopedia] Searching for retractions etc. Message-ID: The page http://proteopedia.org/w/Retractions_and_Fraud has been updated with links to RetractionWatch, where you can search for retractions (or document them), and PubPeer, a post-publication review site where commenters may express concerns about published structures. -Eric