From emartz at microbio.umass.edu Tue Jul 17 11:11:29 2018 From: emartz at microbio.umass.edu (Eric Martz) Date: Tue, 17 Jul 2018 15:11:29 -0000 Subject: [Proteopedia] New Tutorial: Ramachandran Principle & Clashes Message-ID: <7b732163-2b2e-df92-c4a6-1667765de280@microbio.umass.edu> Dear Proteopedians, For years, I have wanted to see protein phi and psi angles rotate smoothly, showing clashes dynamically as they occur between atoms at van der Waals radii. Sure enough, JSmol is quite capable of this. I have made a new tutorial available in three formats: 1. YouTube video (voice explaining): https://tinyurl.com/RamachandranPrincipleYouTube 2. Slideshow: https://tinyurl.com/RamachandranPrinciple The images in the above two formats are *animated*, showing translucent van der Waals-sized atoms rotating smoothly with clashes forming and going away. Those animated clashes are compared side by side with Ramachandran plots. Also included is an animated explanation of dihedral angles. 3. An interactive JSmol tutorial with checkboxes and buttons: http://proteopedia.org/w/Tutorial:Ramachandran_principle_and_phi_psi_angles Please pass this on to websites that will alert educators. There is also a practice *Quiz* with immediate feedback: http://proteopedia.org/w/Dihedral/Ramachandran_Principle_Quiz Angel Herr?ez and I have also made an illustrated list of ten websites that illustrate the Ramachandran principle and plot, and phi/psi dihedral angles in various ways, mostly using JSmol: http://proteopedia.org/w/Dihedral/Index Several of these are available also in *Spanish*, as indicated there. Thanks to Jaime Prilusky for installing this tutorial in Proteopedia, and for providing an easy mechanism for making quizzes. -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 Thu Aug 9 15:11:49 2018 From: emartz at microbio.umass.edu (Eric Martz) Date: Thu, 9 Aug 2018 15:11:49 -0400 Subject: [Proteopedia] New Tutorial: Ramachandran Principle & Clashes (sent again) In-Reply-To: <7b732163-2b2e-df92-c4a6-1667765de280@microbio.umass.edu> References: <7b732163-2b2e-df92-c4a6-1667765de280@microbio.umass.edu> Message-ID: <84eeac41-e9f9-618f-4eef-a8244fb873f8@microbio.umass.edu> I sent this on July 17 but I think there have been problems with the Proteopedia email list, so I am re-sending it in case you missed it (and to see if it goes through promptly). -Eric Dear Proteopedians, For years, I have wanted to see protein phi and psi angles rotate smoothly, showing clashes dynamically as they occur between atoms at van der Waals radii. Sure enough, JSmol is quite capable of this. I have made a new tutorial available in three formats: 1. YouTube video (voice explaining): https://tinyurl.com/RamachandranPrincipleYouTube 2. Slideshow: https://tinyurl.com/RamachandranPrinciple The images in the above two formats are *animated*, showing translucent van der Waals-sized atoms rotating smoothly with clashes forming and going away. Those animated clashes are compared side by side with Ramachandran plots. Also included is an animated explanation of dihedral angles. 3. An interactive JSmol tutorial with checkboxes and buttons: http://proteopedia.org/w/Tutorial:Ramachandran_principle_and_phi_psi_angles Please pass this on to websites that will alert educators. There is also a practice *Quiz* with immediate feedback: http://proteopedia.org/w/Dihedral/Ramachandran_Principle_Quiz Angel Herr?ez and I have also made an illustrated list of ten websites that illustrate the Ramachandran principle and plot, and phi/psi dihedral angles in various ways, mostly using JSmol: http://proteopedia.org/w/Dihedral/Index Several of these are available also in *Spanish*, as indicated there. Thanks to Jaime Prilusky for installing this tutorial in Proteopedia, and for providing an easy mechanism for making quizzes. -Eric -- Eric Martz, Professor Emeritus, Dept Microbiology University of Massachusetts, Amherst MA US Martz.MolviZ.Org From emartz at microbio.umass.edu Sat Sep 22 17:22:54 2018 From: emartz at microbio.umass.edu (Eric Martz) Date: Sat, 22 Sep 2018 17:22:54 -0400 Subject: [Proteopedia] Hemoglobin Molecular Structure Tutorial Message-ID: Dear Proteopedians, I want you to be aware of the newly-revitalized JSmol version of my tutorial on *hemoglobin molecular structure*: http://hemoglobin.molviz.org or simply http://molviz.org and click on hemoglobin. The tutorial is suitable for projection to accompany a lecture, showing a brief explanation and color keys for each view, and/or for use by students. When preparing for a lecture, the lecturer can open /Details /blocks that provide additional details the lecturer may wish to be aware of before lecturing. The tutorial has 7 chapters that include morph animations of the conformational changes induced by oxygen binding, and sickle hemoglobin. Chapters are summarized briefly at https://www.merlot.org/merlot/viewMaterial.htm?id=1377059 (click on /Show More/). Each chapter has somewhat *open-ended questions* (in green text) to challenge understanding. *Answers* are available online. There is also a 17-question *immediate feedback multiple-choice quiz*. Apologies that this is slightly off topic since this tutorial is not implemented in Proteopedia, but in a tutorial "shell" that I developed largely before Proteopedia was mature. However, the immediate-feedback practice quiz is in Proteopedia: http://proteopedia.org/w/User:Eric_Martz/Hemoglobin_Quiz As a historical note, most of the contents of this tutorial go back to a RasMol movie script that I released in 1996. A Chime version was released with in 1997, and a Jmol Java applet version with Frieda Reichsman in 2007. There are, of course, a variety of hemoglobin-related pages in Proteopedia. See http://proteopedia.org/w/Hemoglobin#See_Also -Eric -------------- next part -------------- An HTML attachment was scrubbed... URL: