Eric Martz

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.
Publications and Citations             ((quick link for accts))

Proteopedia Pages to Which I've ContributedProteopedia 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 PagesMolecules: 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 PagesMolecules: 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 PagesTopic 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 - EducationTopic 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 PlaygroundTopic Pages - Molecular Playground

• Molecular_Playground
• Molecular Playground/Authoring
• Molecular Playground/Procedures
• CBI Molecules

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• Molecular Playground/HIV Protease Inhibitor
  • Molecular Playground/HIV Protease Inhibitor Enlarged
  • Molecular Playground/HIV Protease Inhibitor/Enlarged
• Molecular Playground/Relenza
• Molecular Playground/Tamiflu

Topic Pages - Structural BioinformaticsTopic Pages - Structural Bioinformatics

A-BA-B

• About Macromolecular Structure
• AlphaFold
• AlphaFold2 examples from CASP 14
• AlphaFold, How to predict structures from sequences
• 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-EC-E

• CASP
• Cation-pi interactions (started by Wayne Decatur)

• Cavities:
  • Cavity programs
  • Jmol/Cavities pockets and tunnels
  • PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins
  • User:Eric Martz/Cavities tests
  • User:Eric_Martz/Cavity_Notes

• Chain <- Chains
• Clashes
• Chimera
• Conservation, Evolutionary <- Evolutionary Conservation
  • Introduction to Evolutionary Conservation
  • How to see conserved regions
  • Quick ConSurf Analysis Procedure
• ConSurf/Index
• ConSurfDB vs. ConSurf
• CPK
• Crosslinks:
  • Protein crosslinks
  • FirstGlance/Evaluating Protein Crosslinks
• Cryo-EM
• Crystal contacts
• Cystine
• Density maps
• Disulfide bond
• Domain
• DRuMS
• Eric Martz's Favorites
• Electron cryomicroscopy
• Electron density maps
• Empirical models
• Epitopes
• Ester protein crosslinks
• Evolutionary conservation: see Conservation
• Extremophiles

F-HF-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
• Homology Modeling, Practical Guide to
• Homology modeling servers
• How to predict structures with AlphaFold
• Hydrogen bonds
• Hydrogen in macromolecular models

I-MI-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
  • Evolutionary Conservation
  • molecular visualization
  • Structural Bioinformatics
• Isopeptide bond <- Isopeptide bonds
• Knots in proteins
• Ligand
• Lysine-cysteine NOS bonds <-- NOS Disambiguation
• Membrane proteins
• 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-RN-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
  • Los cuatro niveles estructurales de las proteínas
• Pyrrolysine
• Renumbering PDB files
• Ribosomal_A_Site_Binding_Paromomycin:_A_Morph
• 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
• Renumbering PDB files
• Resolution
• Retractions and Fraud

S-ZS-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
• 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, MolecularArt, 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 Sculpture
• Art:Pentagonal Garden
• Art:Rainbow_Corn
• Art:War of the Worlds

Interactive 3D ComplementsInteractive 3D Complements

• User:Fadel_A._Samatey/FlhBc_I (April, 2013)
• Malvankar/1 (March, 2015)
  • Animations of pilus model: Assembly, Rocking, Aromatics.
• Ke Xiao/1 (March, 2016)

• Interactive 3D Complements in Proteopedia (page started by Jaime Prilusky & David Canner) <- I3DC
  • Samatey, links to I3DC for publications from the Samatey Group.
  • Malvankar, links to I3Dc for publications by Nikhil Malvankar et al.
  • Ke Xiao, links to I3DC for publications by Ke Xiao et al.

Topic Pages: People/BiographiesTopic Pages: People/Biographies

• Richards, Frederic M.
• Oberholser, Karl

SoftwareSoftware

• Molecular modeling and visualization software

JmolJmol

• 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

JSmolJSmol

• 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

FirstGlanceFirstGlance

• 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-JmolNon-Jmol

• CCP4
• Chime
• Java
  • Installing and enabling Java
• Kinemages, Mage and KiNG
• Molecular Workbench
• Protein Explorer
• PyMOL
• RasMol
• Swiss-PDBViewer = DeepView
  • DeepView/Mutating Amino Acids

EMail ListEMail List

• Proteopedia:Email list

Meta PagesMeta Pages

HelpHelp

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.

• User:Eric Martz/Getting email from Proteopedia

• 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

ProteopediaProteopedia

• 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 LegendsProteopedia Pages Using Jmol Color Key Legends

• Gramicidin Channel in Lipid Bilayer
• Metal-Ligand Polyhedra

MediawikiMediawiki

• Special:Prefixindex/Mediawiki:
• Special:Prefixindex/Mediawiki:Sat-tooltip

TemplatesTemplates

• Template:Article_under_development
• Template:Button Toggle Animation used at Lac repressor and Template:Button Toggle Animation2 generally more useful.
• Template:Chemical Components

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Color KeysColor 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".

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• Template:COVID Validation
• Template:EEEV and Template:EEEV-slab

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Green LinksGreen Links

• Template:Green_links_zoom See also adaptation emphasizing rotation of a morph at SARS-CoV-2_protein_S_activation_by_furin
• Template:ClickGreenLinks

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• 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

(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 LikePages 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

WorkshopsWorkshops

• One-day courses in molecular visualization and structural bioinformatics for researchers and educators.

Principal Author or Architect of (Elsewhere):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 QuicklinksPersonal Quicklinks

HelpHelp

• 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
• Template:Button_Toggle_Animation
• User:Eric Martz/Getting email from Proteopedia

PDB ExamplesPDB 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 UploadedFiles Uploaded

• Files Uploaded by Eric Martz

Sandboxes Reserved for TeachingSandboxes 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 CollaborationsSandboxes 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: ProtectedSandboxes: 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 Available
• 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 Available

• User:Eric Martz/liveConnect Test hyperlink to javascript applet.script(...): HTML not interpreted

WorkbenchesWorkbenches

• 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.

CollaborationsCollaborations

SamateySamatey

• Samatey
• Fadel_A._Samatey_Group
  • Fadel A. Samatey Group (Japanese)
• 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.
• File:3b0z-all-chain-a.pdb.gz

Malvankar CollaborationsMalvankar 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
• User:Nikhil Malvankar/Workbench/M4

Ke Xiao CollaborationsKe Xiao Collaborations

• User:Ke_Xiao
• Ke_Xiao
• User:Ke_Xiao/Workbench_1 -> Ke_Xiao/1 -> User:Ke Xiao/Geobacter pilus models

Protected Topic PagesProtected 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 PagesAll Protected Pages

• Special:Prefixindex/User:Eric_Martz
• Search for User:Eric Martz in User Namespace

Other QuicklinksOther Quicklinks

• Special:Wantedpages

Personal To Do ListPersonal To Do List

• Knots

Pages Needing RepairsPages 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.)