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
Publications and Citations
 
 
 
 
 
 
((quick link for accts))
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
 - Flaps Morph for HIV Protease
 - Gramicidin Channel in Lipid Bilayer
 - Influenza hemagglutinin: I started a stub; article later written by User:Savannah Anderson and others.
 - Lac repressor
 - Lipase lid morph
 - Major Histocompatibility Complex Class I
 - Mechanosensitive channels: opening and closing included MORPHS
 - Membrane proteins
 - Metal-Ligand Polyhedra
 - Nitrotyrosine
 - Nucleosomes: User:Eric Martz/Nucleosomes (a protected page for lectures), which was copied into Nucleosomes so others can improve it.
 - Proton Channels, which includes an animated morph.
 - Recoverin, a calcium-activated myristoyl switch
 - Ribosomal A Site Binding Paromomycin: A Morph
 - SARS-CoV-2 protein S priming by furin -- Proteopedia:Featured_SEL/5
 - SARS-CoV-2 spike protein fusion transformation -- Proteopedia:Featured_SEL/6
 - SARS-CoV-2 spike protein mutations -- Proteopedia:Featured_SEL/7
 - Structure of E. coli DnaC helicase loader (about a homology model)
 - SV40 Capsid Simplified
 - Thermal motion of peptide
 
Molecules: PDB Code-Titled Pages
- 1hgf Influenza hemagglutinin
 - 2ic8 (green links in overview) Author Ya Ha in 2008 believes the BioUnit is a monomer, though in the 2006 publication, they speculated that it was a trimer. The PDB file deems it a monomer.
 - 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
 - Structural bioinformatics servers
 - 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 College and University Classes
 - High school teachers' resources <- K-12 teachers' resources, Secondary school teachers' resources
 - Molecular Workbench
 - Protein 3D Structure Resources for Educators 2016
 - Quizzes
- User:Eric Martz/Antibody Quiz
 - User:Eric Martz/Antibody Answers for open-ended questions provided with the Antibody tutorial at MolviZ.Org
 - User:Eric Martz/Hemoglobin Quiz
 - User:Eric Martz/MHC Quiz
 - User:Eric Martz/MHC Answers for open-ended questions provided with the MHC tutorial at MolviZ.Org
 - User:Eric Martz/Ramachandran Principle Quiz
 
 - 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
 - User:Eric Martz/Introduction to Structural Bioinformatics
 
Topic Pages - Molecular Playground
- Molecular Playground/HIV Protease Inhibitor
 - Molecular Playground/Relenza
 - Molecular Playground/Tamiflu
 
Topic Pages - Structural Bioinformatics
A-B
- AlphaFold/Index, a list of Proteopedia pages about AlphaFold.
 - AlphaFold, an introduction and overview.
 - AlphaFold2 examples from CASP 14
 - AlphaFold3:
 - AlphaFold: How to predict structures from sequences
 - AlphaFold: How to get average pLDDT
 
- Alternate locations (initiated by Wayne Decatur)
 - Amino Acids
 - Amino acid composition
 - Asymmetric Unit
 - Atomic coordinate file <- PDB file, PDB file format
 - Backbone representations
 - Biological Unit <- Quaternary structure
 - Biological Unit: Showing
 - Buried charges detection
 
C-E
- CASP
 - Cation-pi interactions (started by Wayne Decatur)
 
- Cavities:
 
- Chain <- Chains
 - Clashes
 - Chimera
 - Conservation, Evolutionary <- Evolutionary Conservation
 - ConSurf/Index
 - ConSurfDB vs. ConSurf
 - CPK
 - Crosslinks:
 - Cryo-EM
 - Crystal contacts
 - Cystine
 - Density maps
 - Disulfide bond
 - Domain
 - DRuMS
 - Eric Martz's Favorites
 - Electron cryomicroscopy
 - Electron density maps
 - Electrostatic potential maps
 - Empirical models
 - Epitopes
 - Ester protein crosslinks
 - Evolutionary conservation: see Conservation
 - Extremophiles
 
F-H
- Fadel A. Samatey Group also in Japanese
 - Favorites
 - FirstGlance/Index
 - Four levels of protein structure -- Los cuatro niveles estructurales de las proteínas
 - Free R
 - GDT_TS, calculating
 - Header of PDB file
 - Hetero atoms
 - Highest impact structures of all time.
 - Histidine-tyrosine protein crosslinks
 - History of Macromolecular Visualization
 - Homology modeling
 - How To Find A Structure
 - Homology Modeling, Practical Guide to
 - Homology modeling servers
 - How to predict structures with AlphaFold
 - Hydrogen bonds
 - Hydrogen in macromolecular models
 
I-M
- Improving published models
 - Index pages
 - Influenza
 - Interface analysis servers
 - Interpreting ConSurf Results
 - Intrinsically Disordered Protein authored largely by User:Tzviya Zeev-Ben-Mordehai
 - Introductions to
 - Isopeptide bond <- Isopeptide bonds
 - Joining AlphaFold predictions for halves of a molecule
 - Knots in proteins
 - Ligand
 - Lysine-cysteine NOS bonds <-- NOS Disambiguation
 - Membrane proteins
 - Missing residues and incomplete sidechains
 - Molecular modeling and visualization software
 - Molecular Playground
 - Molecular sculpture
 - Molecular visualization, introduction to
 - Morphs of conformational changes of macromolecules <- Morph
 - Multiple Protein Sequence Alignment Display with MSAReveal
 
N-R
- Nitrotyrosine
 - NMR Ensembles of Models <- NMR
 - Nobel Prizes for 3D Molecular Structure
 - Non-Standard Residues
 - NOS bonds
 - PDB identification code <- PDB code, PDB codes, pdb code, pdb codes
 - Peptide (page created by Eran Hodis)
 - Peptide bond <- Peptide bonds
 - Personal favorites
 - Phi and psi angles
 - Post-translational modification <- Post-translational modifications, Posttranslational modification, Posttranslational modifications
 - Protein <- Proteins
 - Protein crosslinks
 - Protein Data Bank <- PDB
 - Protein primary, secondary, tertiary and quaternary structure
 - Pyrrolysine
 - Quality assessment for molecular models
 - R value
 - Ramachandran principle and phi psi angles (Tutorial) and accompanying Quiz
- Proteopedia:Featured EDU/1
 - See also Dihedral/Index (initiated by Angel Herráez)
 
 - Remarkable Structures
 - RMSD
 - Renumbering PDB files
 - Resolution
 - Retractions and Fraud
 - Ribosomal_A_Site_Binding_Paromomycin:_A_Morph
 
S-Z
- Salt bridges
 - Sculpting protein conformations
 - Sculpture, molecular
 - Selenocysteine
 - Selenomethionine
 - Sequence numbering, unusual
 - Sites, Functional
 - Standard Residues and Non-Standard Residues
 - Structural Bioinformatics, Introduction to aka 565.molviz.org
 - Structural bioinformatics servers
 - Structural genomics
 - Structures_Gallery_Generator
 - Structure superposition tools
 - Suggestions for new articles
 - Superposition tools
 - Teaching Strategies Using Proteopedia
 - Temperature value <- B value, Disorder, Temperature factor, Temperature
 - Temperature value vs. resolution
 - Temperature color schemes
 - Theoretical models <- Theory, Theoretical model, Proteopedia:Featured_SEL/8
 - Thioester protein cross-links
 - Thioether protein crosslinks
 - Unusual sequence numbering
 - Van der Waals radii
 - Visualization, molecular, introduction to
 - Water in macromolecular models
 - World Index of BioMolecular Visualization Resources
 - X-ray crystallography <- X-ray diffraction
 
Art, Molecular
- Category:PDB_Art
 - Art:Cytochrome_Wallpaper
 - Art:Deconstructing 2GTL
 - Art:Dodecapod
 - Art:Faberge Eggs
 - Art:Five Bakers Dancing
 - History of Macromolecular Visualization
 - Art:Molecular jacks
 - Art:Molecular Sculpture
 - Art:Pentagonal Garden
 - Art:Rainbow_Corn
 - Art:War of the Worlds
 
Interactive 3D Complements
- User:Fadel_A._Samatey/FlhBc_I (April, 2013)
 - Malvankar/1 (March, 2015)
 - Ke Xiao/1 (March, 2016)
 
- Interactive 3D Complements in Proteopedia (page started by Jaime Prilusky & David Canner) <- I3DC
 
Topic Pages: People/Biographies
Software
Jmol
- Jmol
 - Jmol/Index <- About Jmol About JSmol Help:Jmol Help:JSmol
 - Jmol/Application
 - Jmol/Visualizing large molecules
 - Jmol/Visualizing membrane position: lipid bilayer boundaries.
 - Jmol/Cavities pockets and tunnels
 - Jmol/Depth from surface
 - Jmol/PDB file editing with Jmol
 - FirstGlance in Jmol
 
JSmol
- How JSmol Works and User:Eric Martz/How JSmol works.
 - User:Eric Martz/JSmol Notes <--- TABLE OF EXAMPLE SIZES
 - JSmol/Rotation Speeds
 - using pspeed to maintain tranlucency, see User:Jaime_Prilusky/platformSpeed
 
FirstGlance
- FirstGlance/Index lists related resources within Proteopedia and elsewhere.
 - FirstGlance Entry Page with links to Purpose, Pros & Cons and YouTube: Design Goals and Quick Introduction.
 - About FirstGlance in Jmol
 - FirstGlance/Evaluating Protein Crosslinks
 
Non-Jmol
- CCP4
 - Chime
 - Java
 - Kinemages, Mage and KiNG
 - Molecular Workbench
 - Protein Explorer
 - PyMOL
 - RasMol
 - Samson, see Sculpting protein conformations.
 - Swiss-PDBViewer = DeepView
 
EMail List
Meta Pages
Help
| Proudly show your love for Proteopedia and help spread Proteopedia's wonders with highly coveted mugs and T-shirts from cafepress.com, featuring the original Proteopedia logo by Tali Wiesel. Cafepress is a website that prints custom images on mugs and T-shirts, and is unaffiliated with Proteopedia. Proteopedia collects no money from your purchase. | |
- Help:Color Keys
 - Help:Coloring text
 - Help:Copying FirstGlance Scenes into Proteopedia
 - Help:Editing
 - Help:Getting Started in Proteopedia
 - Help:How to Insert a ConSurf Result Into a Proteopedia Green Link
 - Help:Language Translation
 - Help:Making animations for Powerpoint
 - 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.
 - User:Eric Martz/Proteopedia:Introduction
 - Proteopedia:Languages
 - Proteopedia:Namespaces
 - Proteopedia:News
 - Proteopedia:Overview <- Introduction to Proteopedia
 - 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
To find all templates contributed by a user, at the user's page, click User contributions (at left), then set the namespace to Templates.
- Template:Article_under_development
 - Template:Button Toggle Animation used at Lac repressor and Template:Button Toggle Animation2 generally more useful.
 - Template:Chemical Components
 
Color Keys
- Template:ColorKey_ConSurf
 - Template:ColorKey_N2CRainbow
- Example of use: NMR_Ensembles_of_Models#Display_of_NMR_Models_by_Proteopedia
 
 - The Templates used on the DRuMS and Help:Color Keys pages. All begin "Template:ColorKey".
 
Green Links
- Template:Green_links_zoom See also adaptation emphasizing rotation of a morph at SARS-CoV-2_protein_S_activation_by_furin
 - Template:ClickGreenLinks
 
- Template:Homology Modeling Intro
 - Template:Jmol application instructions
 - Template:Martz email
 - Template:Molecular Playground animation description
 - Template:MP masthead
 - Template:Murthy_fraud
 - Template:PDBMapViewers
 - Template:Possible_fraud
 - Template:Protected page banner
- Example of use: User:Karl Oberholser/Ramachandran Plots
 
 - Template:Sandbox Reserved Eric Martz
 - Template:Sandbox Reserved Eric Martz 2
 - Template:Sandbox Reserved Eric Martz 3
 - Template:Theoretical model
 - Template:Unsigned applets
 
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.
- Ozonolysis
 - 2fbw has a comment (correction) by a user, illustrating how a banner alerts users about comments in the discussion tab.
 - Proteopedia:Comments on Published Structures
 
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 BioMolecular Visualization Resources. Available 2000-2012.
 - 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
- Special:Prefixindex
 - <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] 1-10 May-July 2015 Osaka Univ
- Formerly 1-40 May-July 2014 Osaka Univ
 - Formerly May-July 2013 Osaka Univ
 - Formerly May-July 2012 Osaka Univ
 - Formerly May-July 2011 Osaka Univ
 - Formerly Apr-Jun 2010 Osaka Univ
 
 - Template:Sandbox Reserved Eric Martz 2 41-100 Jan-Mar 2011 UMass
- Formerly 41-100 Feb-Mar 2010 Israel and extra 151-161
 
 - Template:Sandbox Reserved Eric Martz 3 [101-150] 101-125 May-July 2015 Okinawa Inst Sci Tech, Samatey
- Formerly Oct-Dec 2013 UMass Chem-Bio Interface Thompson
 - Formerly 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 Movie tests
 - 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 Miniprotein & microprotein notes
 - User:Eric Martz/Sandbox 4 Running state scripts for virus capsids and large assemblies
 - User:Eric Martz/Sandbox 5 Caption tests
 - 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 Jmol 12.2 Tests
 - User:Eric Martz/Sandbox 15 Ramachandran references
 - User:Eric Martz/Sandbox 16 PNGJ & caption SAT tests
 - User:Eric Martz/Sandbox 17 More PNGJ & caption SAT tests
 - User:Eric Martz/Sandbox 18 Saving from SAT removes FILTER command
 - User:Eric Martz/Sandbox 19 PACUPP analysis of porin
 - User:Eric Martz/Sandbox 20 Available
 - User:Eric Martz/Sandbox 21 Available
 - User:Eric Martz/Sandbox 22 Available
 
- User:Eric Martz/liveConnect Test hyperlink to javascript applet.script(...): HTML not interpreted
 
Workbenches
- All Eric Martz Workbenches (search using Prefixindex)
 - User:Eric Martz/Workbench/AccountManagement
 - User:Eric Martz/Workbench tests
 - User:Eric Martz/Workbench/Workbench01
 - User:Eric Martz/Workbench 02 is for testing read access to users given permission.
 
Collaborations
Samatey
- Samatey
 - Fadel_A._Samatey_Group
 - User:Fadel A. Samatey has links to Samatey Workbenches
 - User:Fadel_A._Samatey/FlhBc_I <- Samatey/1 was not used in Acta Cryst D paper.
 - User:Fadel_A._Samatey/FlgA_I <- Samatey/2 linked in paper in SciRep.
 - User:Fadel A. Samatey/FlgE I <- Samatey/3 linked in paper in SciRep.
 - User:Fadel A. Samatey/FlgE II/Complete Flagellar Hook Structure <- Samatey/4 linked in paper in NatComm.
 - Image:3b0z-all-chain-a.pdb.gz
 
Malvankar Collaborations
- User:Nikhil Malvankar
 - Malvankar
 - User:Nikhil Malvankar/Geobacter pilus <- Malvankar/1
 - User:Nikhil Malvankar/Cytochrome nanowires <- Malvankar/2
 - User:Nikhil_Malvankar/Geobacter_pilus_structure_and_function <- Malvankar/3
 
Ke Xiao Collaborations
Protected Topic Pages
- User:Eric Martz/Cavities tests
 - User:Eric Martz/Entertaining PDB codes (amusing, humor)
 - User:Eric Martz/Remarkable Structures
 - User:Eric Martz/Nucleosomes (cf. Nucleosomes)
 - User:Eric Martz/Introduction to Structural Bioinformatics and 2012
 - User:Eric Martz/Virus capsid resources
 
- User:Eric Martz/Molecular Playground/Tamiflu
 - User:Eric Martz/Molecular Playground/HIVDrug
 - User:Eric Martz/Molecular Playground/Authoring
 
- User:Eric Martz/5eon cf. pili
 
All Protected Pages
Other Quicklinks
Personal To Do List
- Knots
 
Pages Needing Repairs
- Lac repressor some scenes broken
 - Structural alignment tools: the morph green link hangs JSmol (2/2021) but morph green links work on other pages (tested: Lac repressor, recovering, mechanosensitive, avian influ.)
 
