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User:Eric Martz
From Proteopedia
| Teaching at Osaka University, Japan, 2009, in Keiichi Namba's Protonic Nanomachine Group. Photograph courtesy of Akihiro Kawamoto.
(See T-shirts below.) |
Professor Emeritus, University of Massachusetts, Amherst MA USA
Personal website: martz.molviz.org
My page on my Department's website.
Proteopedia Pages to Which I've Contributed
Unless otherwise indicated, these are pages that I created, and for which I provided the initial content.
Below, -> or <- mean that one page redirects to another page.
Molecules: Topic Pages
- I started a stub for Antibody. Article later written by User:David Canner and others.
- Avian Influenza Neuraminidase, Tamiflu and Relenza
- Flagella, bacterial <- Flagellum, Flagellar structure
- Flagellar filament of bacteria
- Flagellar hook of bacteria
- Gramicidin Channel in Lipid Bilayer
- Influenza hemagglutinin: I started a stub; article later written by User:Savannah Anderson and others.
- Lac repressor
- Major Histocompatibility Complex Class I
- Mechanosensitive channels: opening and closing included MORPHS
- Membrane proteins
- Metal-Ligand Polyhedra
- Nitrotyrosine
- Proton Channels, which includes an animated morph.
- Recoverin, a calcium-activated myristoyl switch
- Structure of E. coli DnaC helicase loader (about a homology model)
- SV40 Capsid Simplified
- Thermal motion of peptide
- User:Eric Martz/Nucleosomes (a protected page for lectures), which was copied into Nucleosomes so others can improve it.
Molecules: PDB Code-Titled Pages
- 1hgf Influenza hemagglutinin
- 2ic8 (green links in overview)
- 2rd0 Phosphatidylinositol kinase oncogene: I authored scenes similar to many of the figures from the publication.
Topic Pages: Lists of Other Pages
- About Macromolecular Structure
- High school teachers' resources <- K-12 teachers' resources, Secondary school teachers' resources
- Research Groups and Institutes
- Student Projects
- Teaching Scenes, Tutorials, and Educators' Pages <- Molecule of the Month, MotM, Motm
- See also Topic pages -> Proteopedia: Topic Pages
Topic Pages - Education
(Some of these pages are linked redundantly under other headings on this page.)
- Adoptions in University Classes
- High school teachers' resources <- K-12 teachers' resources, Secondary school teachers' resources
- Molecular Workbench
- Student Projects
- Teaching Scenes, Tutorials, and Educators' Pages <- Molecule of the Month, MotM, Motm
- Teaching Strategies Using Proteopedia
- Technology-Enhanced Science Activities for STEMEd 6 Mar 2010
Topic Pages - Molecular Playground
- Molecular Playground/HIV Protease Inhibitor
- Molecular Playground/Relenza
- Molecular Playground/Tamiflu
Topic Pages - Structural Bioinformatics
A-E
- About Macromolecular Structure
- Amino Acids
- Asymmetric Unit UNIT CELL SCENE NOT WORKING
- Atomic coordinate file <- PDB file, PDB file format
- Biological Unit <- Quaternary structure
- CASP
- Cation-pi interactions was written largely by Wayne Decatur
- Conservation, Evolutionary <- Evolutionary Conservation
- ConSurfDB vs. ConSurf
- CPK
- Crystal contacts
- DRuMS
- Eric Martz's Favorites
- Electron density maps
- Epitopes
- Evolutionary conservation: see Conservation
- Extremophiles
F-M
- Fadel A. Samatey Group also in Japanese
- Free R
- Hetero atoms
- Highest impact structures of all time.
- History of Macromolecular Visualization
- Homology modeling
- Homology modeling servers
- Hydrogen bonds
- Hydrogen in macromolecular models
- Improving published models
- Influenza
- Intrinsically Disordered Protein authored largely by User:Tzviya Zeev-Ben-Mordehai
- Ligand
- Membrane proteins
- Morphs of conformational changes of macromolecules
N-R
- NMR Ensembles of Models <- NMR
- Nobel Prizes for 3D Molecular Structure
- PDB identification code <- PDB code, PDB codes, pdb code, pdb codes
- Peptide (page created by Eran Hodis)
- Personal favorites
- Post-translational modification <- Post-translational modifications, Posttranslational modification, Posttranslational modifications
- Protein Data Bank <- PDB
- Pyrrolysine
- Ribosomal_A_Site_Binding_Paromomycin:_A_Morph
- Quality assessment for molecular models
- Remarkable Structures
- R value
- Resolution
S-Z
- Salt bridges
- Selenocysteine
- Sites, Functional
- Standard Residues and Non-Standard Residues
- Structural alignment tools
- Structural genomics
- Structures_Gallery_Generator
- Teaching Strategies Using Proteopedia
- Temperature value <- B value, Disorder
- Temperature value vs. resolution
- Temperature color schemes
- Theoretical models <- Theory, Theoretical model
- X-ray crystallography <- X-ray diffraction
Interactive 3D Complements
- Interactive 3D Complements in Proteopedia (page started by Jaime Prilusky & David Canner) <- I3DC
- Samatey, links to I3DC for publications from the Samatey Group
Topic Pages: People/Biographies
Software
- CCP4
- Chime
- FirstGlance in Jmol
- Java
- Jmol
- Jmol/Application
- Jmol/Visualizing large molecules
- Kinemages, Mage and KiNG
- Molecular Workbench
- Protein Explorer
- PyMOL
- RasMol
- Swiss-PDBViewer = DeepView
EMail List
Meta Pages
Help
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- Help:Color Keys
- Help:Copying FirstGlance Scenes into Proteopedia
- Help:Editing
- Help:How to Insert a ConSurf Result Into a Proteopedia Green Link
- Help:Language Translation
- Help:Plain text editors
- Help:Protected Pages
- Help:Quiz
- Help:Sandboxes
- Help:Snapshots
- Help:Uploading molecules
Proteopedia
- Mugs and T-Shirts: I created these products and set up the non-profit store at cafepress.com/molviz4.
- News (disambiguation)
- Proteopedia:About
- Proteopedia:Guidelines for Ethical Writing was started by Jaime Prilusky. I added the sections on Content Attribution and Images.
- Proteopedia:Languages
- Proteopedia:Namespaces
- Proteopedia:News
- Proteopedia:Policy
- Proteopedia:Problems
- Proteopedia:Scrapbook
- Proteopedia:Subdirectories
- Proteopedia:Supplementary materials
- Proteopedia:Topic Pages
- Proteopedia:What's New <- What's New?, What's New, what's new, What's New in Proteopedia?
- Proteopedia:Wishlist
Proteopedia Pages Using Jmol Color Key Legends
Mediawiki
Templates
- Template:Article_under_development
- Template:ColorKey_N2CRainbow
- Example of use: NMR_Ensembles_of_Models#Display_of_NMR_Models_by_Proteopedia
- Template:ColorKey_ConSurf
- The Templates used on the DRuMS and Help:Color Keys pages. All begin "Template:ColorKey".
- Template:Protected page banner
- Example of use: User:Karl Oberholser/Ramachandran Plots
- Template:Button Toggle Animation used at Lac repressor.
(To find all templates contributed by a user, at the user's page, click User contributions (at left), then set the namespace to Templates.)
Pages by Others That I Especially Like
This is not a complete list -- it is a just a few that I want to be able to find easily in case I forget.
Workshops
- One-day courses in molecular visualization and structural bioinformatics for researchers and educators.
Principal Author or Architect of (Elsewhere):
- FirstGlance in Jmol, a general-purpose molecular visualization tool which has been adopted by Nature (see the 3D View links), the ConSurf Server, and other journals and structural bioinformatics servers. Available 2005-present.
- Visualization for the the ConSurf Server developed by Nir Ben-Tal, Fabian Glaser, Elana Erez and others, which colors amino acids by evolutionary conservation, completely automatically. Available 2002-present.
- Top Five 3D Molecular Visualization Technologies for the Rest Of Us. Page available 2007-present.
- MolviZ.Org with tutorials in Jmol and molecular visualization resources for educators and students. Included is a DNA Structure Tutorial started in 1996, and now (in collaboration with Angel Herráez) available in 5 languages.
- World Index of Molecular Visualization Resources. Available 2000-present.
- Atlas of Macromolecules. Available 2002-present.
- With Jaime Prilusky, the PDB Lite search interface for students and beginners to find published macromolecular models. Available 1998-2010 (decommisioned).
- An incomplete History of Macromolecular Visualization which includes a list of the earliest macromolecules solved by X-ray crystallography. Available 1997-present.
- molvis-list, founded in 1995 as the RasMol List. Maintained largely by Tim Driscoll/molvisions.com since 2004.
And in an earlier era
- Protein Explorer 1998-present.
- The RasMol Classic Site (formerly the RasMol Home Page) founded 1996. (The current RasMol Home Page is at RasMol.Org by Herbert Bernstein, available since 1999.)
Personal Quicklinks
Help
- <span style="font-size:150%">Samatey Group</span>
- {{Clear}}
- <table align="right" width="" style="margin: 10px 10px;"><tr><td>[[Image:]]</table></table><tr><td>Caption</td></tr></table>
- [[Image:wiki.png|frame|Wikipedia Encyclopedia]]
- Help:Editing
- Images: Basic Markup / Full Image Syntax
- Tables
- Proteopedia:Cookbook
- Rectangular Jmol
- Image Maps
- Theoretical Model Template
- Floating Quote Box
- Links in Applet Caption
- Flash .swf
PDB Examples
- Sites (after 2nd remediation): 1uu1 (AC1); 1fws (AC1-6); 1sid (AC1-9, BC1-9, all "binding sites"); 1pop (AC1-AC9, BC1-BC9, CC1-CC6 all "binding sites" + CAT "CAT"); 1zzz (CAT "Active Site");
Files Uploaded
Sandboxes Reserved for Teaching
- Created by Eric: 1-161
- Template:Sandbox Reserved Eric Martz 1-40 May-July 2011 Osaka Univ
- Formerly Apr-Jun 2010 Osaka Univ
- Template:Sandbox Reserved Eric Martz 2 41-60 Jan-Mar 2011 UMass
- Formerly 41-100 Feb-Mar 2010 Israel and extra 151-161
- Template:Sandbox Reserved Eric Martz 3 101-150 May-Jul 2010 UMass
- Template:Sandbox Reserved Eric Martz 4
Sandboxes for Collaborations
- Sandbox Eric Martz (not protected) DeShais Collaboration
- Sandbox2 Eric Martz (not protected) ConSurfDB Collaboration
- Sandbox3 Eric Martz (not protected) (deleted; was Samatey)
- Sandbox4 Eric Martz (not protected) (available)
- Sandbox 5 Eric Martz (not protected) Heme Morph (Prilusky)
- Sandbox6 Eric Martz (not protected) Penghua Wang cas pa se 12
- Sandbox7 Eric Martz (not protected) (available)
Sandboxes: Protected
- User:Eric Martz/Sandbox scrolling division test
- User:Eric Martz/Sandbox 0 Knots in Proteins - see Methods in Sandbox 11
- User:Eric Martz/Sandbox 2 FGiJ state script -> Proteopedia
- User:Eric Martz/Sandbox 3 ConSurf mockup, also SandboxC
- User:Eric Martz/Sandbox 4 Quiz testing
- User:Eric Martz/Sandbox 5 News item mockup for *OLD* main page
- User:Eric Martz/Sandbox 6 H274Y Tamiflu resistance mutation in N1
- User:Eric Martz/Sandbox 7 PyMOL translator notes
- User:Eric Martz/Sandbox 8 Water
- User:Eric Martz/Sandbox 9 Tunnel
- User:Eric Martz/Sandbox 10 hbonds
- User:Eric Martz/Sandbox 11 knot methods
- User:Eric Martz/Sandbox 12 links that perform searches
- User:Eric Martz/Sandbox 13 Sequence Alignment Tools
- User:Eric Martz/Sandbox 14 (available)
- User:Eric Martz/liveConnect Test hyperlink to javascript applet.script(...): HTML not interpreted
Workbenches
Protected Topic Pages
- User:Eric Martz/Molecular Playground/Tamiflu
- User:Eric Martz/Molecular Playground/HIVDrug
- User:Eric Martz/Molecular Playground/Authoring
All Protected Pages
Other Quicklinks
Personal To Do List
-Email other educators, see google/wave.
-Brewer's educational game project: structure-function-drug design as part of the challenges?
-Draft email to pdb-l about either metal-ligand polyhedra or oleg's paper on "suppl mats"
-See Comments
-Enlarged HIV script
-Knots
