User:Eric Martz

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===Eric Martz===
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{| class="wikitable" align="right" width="300"
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|[[Image:Eric 1Day Workshop Osaka2009 small.jpg|300px]]
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|-
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|Teaching at Osaka University, Japan, 2009, in Keiichi Namba's Protonic Nanomachine Group. Photograph courtesy of [[Proteopedia:Scrapbook#Workshops|Akihiro Kawamoto]].
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(See T-shirts below.)
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|}
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<!--[[Image:Eric_Apr08.png|right]]-->
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 +
<!--
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IN PROGRESS/ASSIGNMENTS:
 +
 
 +
 
 +
NEW PAGES NEEDED:
 +
Retractions
 +
PDBRedo (on Quality & Retractions)
 +
Cation-pi interactions
 +
Molecular modeling
 +
Theoretical models (with link to Policies)
 +
 
 +
Add page for high school teachers! List same molecules on BME3D.
 +
 
 +
TRICKS:
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Special:ConfirmAccounts
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 +
Special:LatestUserLogin
 +
 
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http://proteopedia.org/cgi-bin/sandboxReservation
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 +
Special:Allmessages has system messages, and they can be edited.
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MediaWiki:Sitenotice appears only when logged in.
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MediaWiki:Anonnotice appears only when NOT logged in.
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Eran's pop-out demo, test/2q66.html
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MediaWiki:Sitenotice, MediaWiki:Anonnotice
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SCRIPTS:
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View source to see the script URL in a JmolAppletInline() call, e.g.
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http://proteopedia.org/wiki/scripts/Morphs/1osl_19_1l1m_9_morph/2.spt
 +
 
 +
initialize is disabled in state scripts, which disables "reset all", which deletes all user-defined variables.
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For support of color keys below Jmol, a reset for specified variables is inserted into the state script for those variables defined by the SAT.
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UPLOADED SCRIPTS:
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Cannot upload type .spt, but can upload .spt.gz and Jmol gets it.
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NEED WORK:
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The Bacterial Flagellar Hook
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 +
Water in macromolecular models
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 +
TO DO:
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A group/gallery page for Namba, adapting the one I did.
 +
 
 +
http://www.pnas.org/content/105/32/11170.abstract SUPPL MATS.
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http://xtal.nki.nl/perrakis.htm USE OF GALLERY MAKER
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http://oca.weizmann.ac.il/oca-bin/xgalery
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 +
interactive jmol example at Hydrogen bonds: HIV protease? (from FirstGlance)
 +
 
 +
Hydrogen in macromolecular models (linked on Hydrogen bonds page)
 +
 
 +
Help:Copying Firstglance scenes page needs an example, as does the FirstGlance page.
 +
 
 +
1rpu (wayne decatur) has alternate locations for ALL RNA atoms. Ppda shows two RNA's in the same space. Is this what we want? See the configuration command in Jmol.
 +
 
 +
BUGS:
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 +
TEACHING:
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StudentJava2 (std no 2)
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--------------------------------------------------- -->
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Professor Emeritus, University of Massachusetts, Amherst MA USA
Professor Emeritus, University of Massachusetts, Amherst MA USA
<br>
<br>
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'''emartz ''at'' microbio ''dot'' umass ''dot'' edu'''
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<imagemap>
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Image:Youtube.png|left
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desc none
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default [https://www.youtube.com/channel/UCWNgrSnEfQWaPh3J3mtKhMQ]
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</imagemap>
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&nbsp;
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{{Template:Martz_email}}
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<br clear="left">
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Personal website: [http://martz.molviz.org martz.molviz.org]
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<br>
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[https://scholar.google.com/citations?user=Bb3H0OsAAAAJ&hl=en&oi=ao Publications and Citations]
 +
&nbsp;
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&nbsp;
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&nbsp;
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&nbsp;
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&nbsp;
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&nbsp;
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(([[User:Eric_Martz/Workbench/AccountManagement|quick link for accts]]))
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<br>
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[https://orcid.org/0000-0003-4679-6967 ORCID ID 0000-0003-4679-6967]
-
====Workshops====
+
==Proteopedia Pages to Which I've Contributed==
 +
Unless otherwise indicated, these are pages that I created, and for which I provided the initial content.
 +
<br>
 +
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]]
 +
**[[Proteopedia:Featured SEL/1]]
 +
*[[Drug and peptide transport in humans]]
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** [[Proteopedia:Featured EDU/7]]
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** [[Proteopedia:Featured EDU/8]]
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*[[Flagella, bacterial]] <- [[Flagellum]], [[Flagellar structure]]
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*[[Flagellar filament of bacteria]]
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*[[Flagellar hook of bacteria]]
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*[[Flaps Morph for HIV Protease]]
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*[[Gramicidin Channel in Lipid Bilayer]]
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*[[Influenza hemagglutinin]]: I started a stub; article later written by [[User:Savannah Anderson]] and others.
 +
*[[Lac repressor]]
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*[[Lipase lid morph]]
 +
*[[Major Histocompatibility Complex Class I]]
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*[[Mechanosensitive channels: opening and closing]] included MORPHS
 +
*[[Membrane proteins]]
 +
*[[Metal-Ligand Polyhedra]]
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*[[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]]
 +
*[[Synthetic nanomaterials from standardized protein blocks]]
 +
*[[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|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.)
 +
 
 +
*[[Proteopedia:News#Adoptions_in_College_and_University_Classes|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]]
 +
* [[Molecular Playground/Authoring]]
 +
* [[Molecular Playground/Procedures]]
 +
* [[CBI Molecules]]
 +
::<hr width="10%">
 +
* [[Molecular Playground/HIV Protease Inhibitor]]
 +
**[[Molecular Playground/HIV Protease Inhibitor Enlarged]]
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**[[Molecular Playground/HIV Protease Inhibitor/Enlarged]]
 +
* [[Molecular Playground/Relenza]]
 +
* [[Molecular Playground/Tamiflu]]
 +
 
 +
===Topic Pages - Structural Bioinformatics===
 +
====A-B====
 +
*[[About Macromolecular Structure]]
 +
 
 +
 
 +
*[[AlphaFold/Index]], a list of Proteopedia pages about AlphaFold.
 +
*[[AlphaFold]], an introduction and overview.
 +
*[[AlphaFold2 examples from CASP 14]]
 +
*AlphaFold3:
 +
**[[Converting AlphaFold3 CIF to PDB]]
 +
**[[User:Eric Martz/AlphaFold3 case studies]]
 +
*AlphaFold: [[How to predict structures with AlphaFold|How to predict structures from sequences]]
 +
*AlphaFold: [[FirstGlance/How to get average pLDDT from AlphaFold models|How to get average pLDDT]]
 +
 
 +
 
 +
*[[Alternate locations]] (initiated by Wayne Decatur)
 +
**[[Alternate locations of backbones]]
 +
*[[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:
 +
**[[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]]
 +
 
 +
*[[Chains and Chain IDs]] <- [[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]]
 +
*[[Drug and peptide transport in humans]]
 +
*[[DRuMS]]
 +
*[[Eric Martz's Favorites]]
 +
*[[Electron cryomicroscopy]]
 +
*[[Electron density maps]]
 +
*[[Electrostatic potential maps]]
 +
** [[Proteopedia:Featured EDU/6]]
 +
*[[Empirical models]]
 +
*[[Epitopes]]
 +
*[[Ester protein crosslinks]]
 +
*Evolutionary conservation: see Conservation
 +
*[[Extremophiles]]
 +
 
 +
====F-H====
 +
*[[Fadel A. Samatey Group]] also in [[Fadel A. Samatey Group (Japanese)|Japanese]]
 +
*[[Favorites]]
 +
*[[FirstGlance/Index]]
 +
*[[Four levels of protein structure]] -- [[Four levels of protein structure (Spanish)|Los cuatro niveles estructurales de las proteínas]]
 +
*[[Free R]]
 +
*[[Calculating GDT_TS|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]]
 +
*[[Practical Guide to Homology Modeling|Homology Modeling, Practical Guide to]]
 +
*[[Homology modeling servers]]
 +
*[[How to find a protein's best structure]]
 +
*[[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
 +
**[[Introduction to Evolutionary Conservation|Evolutionary Conservation]]
 +
**[[Introduction to molecular visualization|molecular visualization]]
 +
**[[User:Eric Martz/Introduction to Structural Bioinformatics|Structural Bioinformatics]]
 +
*[[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]]
 +
*[[Introduction to molecular visualization|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]]
 +
*[[Lysine-cysteine NOS bonds|NOS bonds]]
 +
*[[Proteopedia:Overview|Overview of Proteopedia]]
 +
*[[PDB identification code]] <- [[PDB code]], [[PDB codes]], [[pdb code]], [[pdb codes]]
 +
*[[Peptide]] (page created by Eran Hodis)
 +
*[[Peptide bond]] <- [[Peptide bonds]]
 +
*[[Personal favorites]]
 +
*[[Tutorial:Ramachandran principle and phi psi angles|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]]
 +
**[[Protein primary, secondary, tertiary and quaternary structure (Spanish)|Los cuatro niveles estructurales de las proteínas]]
 +
*[[Pyrrolysine]]
 +
*[[Quality assessment for molecular models]]
 +
*[[R value]]
 +
*[[Tutorial:Ramachandran principle and phi psi angles|Ramachandran principle and phi psi angles]] (Tutorial) and accompanying [[User:Eric Martz/Ramachandran Principle Quiz|Quiz]]
 +
** [[Proteopedia:Featured EDU/1]]
 +
** See also [[Dihedral/Index]] (initiated by Angel Herráez)
 +
*[[User:Eric Martz/Remarkable Structures|Remarkable Structures]]
 +
*[[RMSD]]
 +
*[[Renumbering PDB files]]
 +
*[[Resolution]]
 +
*[[Retractions and Fraud]]
 +
*[[Ribosomal_A_Site_Binding_Paromomycin:_A_Morph]]
 +
 
 +
====S-Z====
 +
*[[Salt bridges]]
 +
*[[Sculpting protein conformations]]
 +
*[[Molecular sculpture|Sculpture, molecular]]
 +
*[[Selenocysteine]]
 +
*[[Selenomethionine]]
 +
*[[Unusual sequence numbering|Sequence numbering, unusual]]
 +
*[[Sites | Sites, Functional]]
 +
*[[Standard Residues]] and [[Non-Standard Residues]]
 +
*[[User:Eric_Martz/Introduction to Structural Bioinformatics|Structural Bioinformatics, Introduction to]] aka [http://565.molviz.org 565.molviz.org]
 +
*[[Structural bioinformatics servers]]
 +
*[[Structural genomics]]
 +
*[[Structures_Gallery_Generator]]
 +
*[[Structure superposition tools]]
 +
*[[Suggestions for new articles]]
 +
*[[Structure superposition tools|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]]
 +
*[[Unknown amino acids and nucleic residues]]
 +
*[[Unusual sequence numbering]]
 +
*[[Van der Waals radii]]
 +
*[[FirstGlance/Virus Capsids and Other Large Assemblies|Virus Capsids and Other Large Assemblies]]
 +
** Polio: [[Proteopedia:Featured EDU/4]]
 +
** Eastern Equine Encephalitis virus [[Proteopedia:Featured EDU/5]]
 +
** Bacterial gas vesicles [[Proteopedia:Featured SEL/9]]
 +
*[[Introduction to molecular visualization|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)
 +
* [[User:Fadel A. Samatey/FlgA I]] (June, 2016)
 +
** [[Proteopedia:Featured JRN/1]]
 +
*[[Malvankar/1]] (March, 2015)
 +
** Animations of pilus model: [http://proteopedia.org/wiki/images/b/b5/Geobacter_pilus_assembling_animation.gif Assembly], [http://proteopedia.org/wiki/images/0/0f/Geobacter_pilus_assembled_rocking.gif Rocking], [http://proteopedia.org/wiki/images/0/0a/Geobacter_pilus_aromatics_rotating.gif Aromatics].
 +
*[[Malvankar/2]] (April, 2019)
 +
** [[Proteopedia:Featured JRN/3]]
 +
*[[Malvankar/3]] (September, 2021)
 +
** [[Proteopedia:Featured JRN/4]]
 +
*[[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/Biographies===
 +
*[[Richards, Frederic M.]]
 +
*[[Oberholser, Karl]]
 +
 
 +
===Software===
 +
*[[Molecular modeling and visualization 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.
 +
*[http://firstglance.jmol.org FirstGlance Entry Page] with links to [http://firstglance.jmol.org/whatis.htm Purpose, Pros & Cons] and [http://tinyurl.com/firstglance1 YouTube: Design Goals and Quick Introduction].
 +
*About [[FirstGlance in Jmol]]
 +
*[[FirstGlance/Evaluating Protein Crosslinks]]
 +
*[[FirstGlance in Jmol Literature Citations]]
 +
 
 +
====Non-Jmol====
 +
*[[CCP4]]
 +
*[[Chime]]
 +
*[[Java]]
 +
**[[Installing and enabling Java]]
 +
*[[Kinemages, Mage and KiNG]]
 +
*[[Molecular Workbench]]
 +
*[[Protein Explorer]]
 +
*[[PyMOL]]
 +
*[[RasMol]]
 +
*Samson, see [[Sculpting protein conformations]].
 +
*[[Swiss-PDBViewer = DeepView]]
 +
**[[DeepView/Mutating Amino Acids]]
 +
 
 +
===EMail List===
 +
*[[Proteopedia:Email list]]
 +
 
 +
===Meta Pages===
 +
====Help====
 +
<!--[[Image:Proteopedia pink t-shirt.jpg|right]]
 +
 
 +
{| class="wikitable" width=300px align="right"
 +
|-
 +
|[[Image:Proteopedia_mug.jpeg|150 px]]
 +
|[[Image:Proteopedia_T-shirt.jpeg|150 px]]
 +
|-
 +
| colspan="2" |Proudly show your love for Proteopedia and help spread Proteopedia's wonders with highly coveted mugs and T-shirts from [http://www.cafepress.com/molviz4 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]]
 +
 
 +
====Proteopedia====
 +
*Mugs and T-Shirts: I created these products and set up the non-profit store at [http://www.cafepress.com/molviz4 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====
 +
*[[Gramicidin Channel in Lipid Bilayer]]
 +
*[[Metal-Ligand Polyhedra]]
 +
 
 +
{{Clear}}
 +
===Mediawiki===
 +
*[[Special:Prefixindex/Mediawiki:]]
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*[[Special:Prefixindex/Mediawiki:Sat-tooltip]]
 +
 
 +
===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.
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*[[Template:Chemical Components]]
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<hr>
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=====Color Keys=====
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*[[Template:ColorKey_ConSurf]]
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*[[Template:ColorKey_N2CRainbow]]
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**Example of use: [[NMR_Ensembles_of_Models#Display_of_NMR_Models_by_Proteopedia]]
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*The Templates used on the [[DRuMS]] and [[Help:Color Keys]] pages. All begin "Template:ColorKey".
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<hr>
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*[[Template:COVID Validation]]
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*[[Template:EEEV]] and [[Template:EEEV-slab]]
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<hr>
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=====Green Links=====
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*[[Template:Green_links_zoom]] See also adaptation emphasizing rotation of a morph at [[SARS-CoV-2_protein_S_activation_by_furin]]
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*[[Template:ClickGreenLinks]]
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<hr>
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*[[Template:Homology Modeling Intro]]
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*[[Template:Jmol application instructions]]
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*[[Template:Martz email‎]]
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*[[Template:Molecular Playground animation description]]
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*[[Template:MP masthead]]
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*[[Template:Murthy_fraud]]
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*[[Template:PDBMapViewers]]
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*[[Template:Possible_fraud]]
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*[[Template:Protected page banner]]
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**Example of use: [[User:Karl Oberholser/Ramachandran Plots]]
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*[[Template:Sandbox Reserved Eric Martz]]
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*[[Template:Sandbox Reserved Eric Martz 2]]
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*[[Template:Sandbox Reserved Eric Martz 3]]
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*[[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==
* [http://workshops.molviz.org One-day courses] in molecular visualization and structural bioinformatics for researchers and educators.
* [http://workshops.molviz.org One-day courses] in molecular visualization and structural bioinformatics for researchers and educators.
-
====Principal Author or Architect of:====
+
==Principal Author or Architect of (Elsewhere):==
-
* [http://firstglance.jmol.org FirstGlance in Jmol], a general-purpose molecular visualization tool which has been adopted by [http://www.nature.com/nature ''Nature''] (see the ''3D View'' links), [http://consurf.tau.ac.il the ConSurf Server], and [http://firstglance.jmol.org/adoption.htm other journals and structural bioinformatics servers].
+
* [http://firstglance.jmol.org FirstGlance in Jmol], a general-purpose molecular visualization tool which has been adopted by [http://www.nature.com/nature ''Nature''] (see the ''3D View'' links), [http://consurf.tau.ac.il the ConSurf Server], and [http://firstglance.jmol.org/adoption.htm other journals and structural bioinformatics servers]. Available 2005-present.
-
* Visualization for the [http://consurf.tau.ac.il the ConSurf Server] developed by Nir Ben-Tal, Fabian Glaser, Elana Erez and others, which colors amino acids by evolutionary conservation, completely automatically.
+
* Visualization for the [http://consurf.tau.ac.il 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.
-
* [http://top5.molviz.org Top Five 3D Molecular Visualization Technologies for the Rest Of Us].
+
* [http://top5.molviz.org Top Five 3D Molecular Visualization Technologies for the Rest Of Us]. Page available 2007-present.
-
* [http://molviz.org MolviZ.Org] with tutorials in Jmol and molecular visualization resources for educators and students.
+
* [http://molviz.org MolviZ.Org] with tutorials in Jmol and molecular visualization resources for educators and students. Included is a [http://dna.molviz.org DNA Structure Tutorial] started in 1996, and now (in collaboration with [http://biomodel.uah.es/personal/inicio.htm Angel Herráez]) available in 5 languages.
-
* [http://molvisindex.org World Index of Molecular Visualization Resources].
+
* [[World Index of BioMolecular Visualization Resources]]. Available 2000-2012.
-
* [http://atlas.proteinexplorer.org Atlas of Macromolecules].
+
* [http://atlas.proteinexplorer.org Atlas of Macromolecules]. Available 2002-present.
-
* With [http://bip.weizmann.ac.il/staff/jaime_prilusky.html Jaime Prilusky], the [http://pdblite.org PDB Lite] search interface for students and beginners to find published macromolecular models.
+
* With [http://bip.weizmann.ac.il/staff/jaime_prilusky.html Jaime Prilusky], the [http://pdblite.org PDB Lite] search interface for students and beginners to find published macromolecular models. Available 1998-2010 (decommisioned).
 +
* An incomplete [http://history.molviz.org History of Macromolecular Visualization] which includes a list of the earliest macromolecules solved by X-ray crystallography. Available 1997-present.
 +
* [http://www.bioinformatics.org/mailman/listinfo/molvis-list molvis-list], founded in 1995 as the ''RasMol List''. Maintained largely by [http://molvisions.com Tim Driscoll/molvisions.com] since 2004.
 +
 
 +
And in an earlier era
 +
 
 +
* [http://proteinexplorer.org Protein Explorer] 1998-present.
 +
* [http://rasmol.molviz.org The RasMol Classic Site] (formerly the ''RasMol Home Page'') founded 1996. (The current RasMol Home Page is at [http://rasmol.org RasMol.Org] by Herbert Bernstein, available since 1999.)
 +
 
 +
==Personal Quicklinks==
 +
===Help===
 +
*[[Special:Prefixindex]]
 +
*&lt;span style="font-size:150%"&gt;Samatey Group&lt;/span&gt;
 +
*<nowiki>{{Clear}}</nowiki>
 +
*<nowiki><table align="right" width="" style="margin: 10px 10px;"><tr><td>[[Image:]]</table></table><tr><td>Caption</td></tr></table></nowiki>
 +
*<nowiki>[[Image:wiki.png|frame|Wikipedia Encyclopedia]]</nowiki>
 +
*[[Help:Editing]]
 +
*[http://en.wikipedia.org/wiki/Help:Wiki_markup#Images Images: Basic Markup] &nbsp; / &nbsp; [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Full Image Syntax]
 +
*[http://en.wikipedia.org/wiki/Help:Table Tables]
 +
*[[Proteopedia:Cookbook]]<small>
 +
**Rectangular Jmol
 +
**Image Maps
 +
**Theoretical Model Template
 +
**Floating Quote Box
 +
**Links in Applet Caption
 +
**Flash .swf</small>
 +
*[[Template:Button_Toggle_Animation]]
 +
*[[User:Eric Martz/Getting email from Proteopedia]]
 +
 
 +
===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===
 +
 
 +
*[http://proteopedia.org/wiki/index.php?limit=100&title=Special%3AContributions&contribs=user&target=Eric+Martz&namespace=6&year=&month=-1 Files Uploaded by Eric Martz]
 +
 
 +
===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===
 +
*[http://www.proteopedia.org/wiki/index.php?title=Special%3APrefixindex&from=User%3AEric+Martz%2FWorkbench&namespace=0 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]]
 +
**[[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.
 +
*[[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====
 +
*[[User:Ke_Xiao]]
 +
*[[Ke_Xiao]]
 +
*[[User:Ke_Xiao/Workbench_1]] -> [[Ke_Xiao/1]] -> [[User:Ke Xiao/Geobacter pilus models]]
 +
 
 +
===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 [[User:Eric Martz/Introduction to Structural Bioinformatics I|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===
 +
*[[Special:Prefixindex/User:Eric_Martz]]
 +
*[http://proteopedia.org/wiki/index.php?title=Special:Contributions&limit=500&contribs=user&target=Eric+Martz&namespace=2 Search for User:Eric Martz in User Namespace]
-
and in an earlier era
+
===Other Quicklinks===
 +
*[[Special:Wantedpages]]
-
* [http://proteinexplorer.org Protein Explorer].
+
===Personal To Do List===
 +
<font color="red">
 +
*Knots
 +
</font>
 +
====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.)

Current revision

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))
ORCID ID 0000-0003-4679-6967

Contents

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

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

Topic Pages - Education

(Some of these pages are linked redundantly under other headings on this page.)

Topic Pages - Molecular Playground

Topic Pages - Structural Bioinformatics

A-B



C-E

F-H

I-M

N-R

S-Z

Art, Molecular

Interactive 3D Complements


Topic Pages: People/Biographies

Software

Jmol

JSmol

FirstGlance

Non-Jmol

EMail List

Meta Pages

Help


Proteopedia

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.

Color Keys
Green Links

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):

And in an earlier era

Personal Quicklinks

Help

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

Sandboxes for Collaborations

Sandboxes: Protected


Workbenches

Collaborations

Samatey

Malvankar Collaborations

Ke Xiao Collaborations

Protected Topic Pages



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.)

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Eran Hodis

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