Proteopedia

Eric Martz

Joined 9 October 2007
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===Eric Martz===
{| class="wikitable" align="right" width="300"
|[[Image:Eric 1Day Workshop Osaka2009 small.jpg|300px]]
|-
|Teaching at Osaka University, Japan, 2009, in Keiichi Namba's Protonic Nanomachine Group. Photograph courtesy of [[Proteopedia:Scrapbook#Workshops|Akihiro Kawamoto]].
(See T-shirts below.)
|}
<!--[[Image:Eric_Apr08.png|right]]-->
 
<!--
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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http://proteopedia.org/cgi-bin/sandboxReservation
 
Special:Allmessages has system messages, and they can be edited.
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MediaWiki:Anonnotice appears only when NOT logged in.
 
Eran's pop-out demo, test/2q66.html
 
MediaWiki:Sitenotice, MediaWiki:Anonnotice
 
SCRIPTS:
View source to see the script URL in a JmolAppletInline() call, e.g.
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.
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.
 
UPLOADED SCRIPTS:
Cannot upload type .spt, but can upload .spt.gz and Jmol gets it.
 
NEED WORK:
The Bacterial Flagellar Hook
 
Water in macromolecular models
 
TO DO:
A group/gallery page for Namba, adapting the one I did.
 
http://www.pnas.org/content/105/32/11170.abstract SUPPL MATS.
http://xtal.nki.nl/perrakis.htm USE OF GALLERY MAKER
http://oca.weizmann.ac.il/oca-bin/xgalery
 
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:
 
TEACHING:
StudentJava2 (std no 2)
-->
 
Professor Emeritus, University of Massachusetts, Amherst MA USA
Professor Emeritus, University of Massachusetts, Amherst MA USA
<br>
<br>
'''emartz ''at'' microbio ''dot'' umass ''dot'' edu'''
{{Template:Martz_email}}
<br>
Personal website: [http://martz.molviz.org martz.molviz.org]
<br>
[https://scholar.google.com/citations?user=Bb3H0OsAAAAJ&hl=en&oi=ao Publications and Citations]
&nbsp;
&nbsp;
&nbsp;
&nbsp;
&nbsp;
&nbsp;
(([[User:Eric_Martz/Workbench/AccountManagement|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.
<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]]
** [[Proteopedia:Featured EDU/7]]
** [[Proteopedia:Featured EDU/8]]
*[[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]]
*[[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]]
**[[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]]
*[[How to find a protein's best structure]]
*[[Practical Guide to Homology Modeling|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
**[[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]]
*[[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]]
 
====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"
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| 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.
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*[[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:]]
*[[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.
*[[Template:Chemical Components]]
 
<hr>
=====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".
 
<hr>
*[[Template:COVID Validation]]
*[[Template:EEEV]] and [[Template:EEEV-slab]]
 
<hr>
=====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]]
 
<hr>
*[[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.


====Workshops====
* [[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.)
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