From emartz at microbio.umass.edu Thu Mar 5 12:44:52 2020 From: emartz at microbio.umass.edu (Eric Martz) Date: Thu, 5 Mar 2020 12:44:52 -0500 Subject: [Proteopedia] Reminder: Use the Proteopedia Email List! Message-ID: I encourage you to use the Proteopedia email list to announce new or updated pages in Proteopedia, or related structural bioinformatics resources. This email list currently has 89 subscribers. There are >4,000 members of Proteopedia but most are inactive, and many of those are students who joined only to complete one assignment. The address of the email list is proteopedialist-for-users at bioinformatics.org The home page for the list is http://www.bioinformatics.org/mm/listinfo/proteopedialist-for-users (If you received this email ONLY ONCE from a proteopedia.org address, and not from a bioinformatics.org address, it means you are not subscribed to the Proteopedia list -- go to the above URL and subscribe!) -Eric -- Eric Martz, Professor Emeritus, Dept Microbiology (he/him/his) 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 Thu Mar 5 13:15:58 2020 From: emartz at microbio.umass.edu (Eric Martz) Date: Thu, 5 Mar 2020 13:15:58 -0500 Subject: [Proteopedia] Flaps morph for HIV protease Message-ID: <0b2b9cc7-051b-b5a7-45dc-9c463832fa76@microbio.umass.edu> Recently I looked for morphs of the flaps of HIV protease opening and closing, as is believed to occur to admit the polyprotein substrate. I did not find any that were quite what I was looking for, so I made one. You can find it here http://proteopedia.org/wiki/index.php/Flaps_Morph_for_HIV_Protease along with some background context. -Eric -- 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: From emartz at microbio.umass.edu Thu Mar 5 13:20:44 2020 From: emartz at microbio.umass.edu (Eric Martz) Date: Thu, 5 Mar 2020 13:20:44 -0500 Subject: [Proteopedia] Sculpting protein conformations Message-ID: <8cf22045-7152-e907-eb48-0eda9db07f91@microbio.umass.edu> Recently I wanted to "re-arrange" some loops on a protein model to explore a hypothesis, ideally just by dragging the loops with the mouse. I stumbled on a FREE software package named Samson that is ideal for this purpose, and also has many other considerable strengths. I made instructional videos that show, step by step, how to drag on proteins to make new conformations in both Samson and PyMOL. http://proteopedia.org/w/Sculpting_protein_conformations -Eric -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaime.prilusky at weizmann.ac.il Sat Mar 7 13:04:33 2020 From: jaime.prilusky at weizmann.ac.il (Jaime Prilusky) Date: Sat, 7 Mar 2020 18:04:33 +0000 Subject: [Proteopedia] Large Structures and Experimental Data Message-ID: <058332B1-62FB-4D60-BF84-AE87F83B3A46@weizmann.ac.il> As a a complement to Jmol, Proteopedia uses now Mol* to render macromolecules with millions of atoms and large Cryo-EM data sets. Mol* is a web-based WebGL 3D molecular viewer that provides access to a wide range of model and volumetric (experimental) data, and makes it possible to see how well the models fit to experimental data, e.g. density maps from X-rays or EM. See for example the full Cryo-EM 3D structure of the Zika virus at https://proteopedia.org/w/5ire or the Herpesvirus capsid at https://proteopedia.org/w/6b43 More information about Mol* is available at https://molstar.org. Jaim -------------- next part -------------- An HTML attachment was scrubbed... URL: From angel.herraez at uah.es Sat Mar 7 13:56:17 2020 From: angel.herraez at uah.es (Angel Herraez) Date: Sat, 7 Mar 2020 18:56:17 +0000 Subject: [Proteopedia] Large Structures and Experimental Data In-Reply-To: <058332B1-62FB-4D60-BF84-AE87F83B3A46@weizmann.ac.il> References: <058332B1-62FB-4D60-BF84-AE87F83B3A46@weizmann.ac.il> Message-ID: <5E63F0DF.27651.6D528A52@angel.herraez.uah.es> Well done! Very efficient. In my laptop, the Zika virus behaves very smoothly although the Herpes is a little jumpy on mouse drag. But very good all in all. The tools are also good. -- El software de antivirus Avast ha analizado este correo electr?nico en busca de virus. https://www.avast.com/antivirus From emartz at microbio.umass.edu Mon Mar 23 15:45:48 2020 From: emartz at microbio.umass.edu (Eric Martz) Date: Mon, 23 Mar 2020 15:45:48 -0400 Subject: [Proteopedia] Art: Cytochrome Wallpaper Message-ID: <223d0a9e-e079-f3bd-ba5a-28e5fe01be69@microbio.umass.edu> See some new molecular art at http://proteopedia.org/w/Art:Cytochrome_Wallpaper It reminds me of the embossed metal ceilings in buildings early last century. Google "embossed metal ceilings" and look at the *images* to see what I mean. Previous molecular art contributions from many different people are listed at http://proteopedia.org/w/Category:PDB_Art -Eric -- Eric Martz, Professor Emeritus, Dept Microbiology (he/him/his) University of Massachusetts, Amherst MA US Martz.MolviZ.Org Proteopedia.Org Administrator User:Eric_Martz -------------- next part -------------- An HTML attachment was scrubbed... URL: