User:Eric Martz: Difference between revisions

(91 intermediate revisions by the same user not shown)

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<br>

Personal website: [http://martz.molviz.org martz.molviz.org]

~~<br>~~

~~[http://www.bio.umass.edu/micro/faculty/martz.html My page] on my Department's website.~~

<br>

[https://scholar.google.com/citations?user=Bb3H0OsAAAAJ&hl=en&oi=ao Publications and Citations]

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*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]]

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*[[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 protein S priming by furin]]

*[[SARS-CoV-2 spike protein fusion transformation]] -- [[Proteopedia:Featured_SEL/6]]

**[[Proteopedia:Featured_SEL/5]]

*[[SARS-CoV-2 spike protein mutations]] -- [[Proteopedia:Featured_SEL/7]]

*[[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]]

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===Topic Pages - Structural Bioinformatics===

====A-E====

====A-B====

*[[About Macromolecular Structure]]

*[[AlphaFold]]

*[[AlphaFold/Index]], a list of Proteopedia pages about AlphaFold.

*[[AlphaFold]], an introduction and overview.

*[[AlphaFold2 examples from CASP 14]]

*[[How to predict structures with AlphaFold|~~AlphaFold,~~ How to predict structures from sequences]]

*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]] ~~UNIT CELL SCENE NOT WORKING~~

*[[Asymmetric Unit]]

*[[Atomic coordinate file]] <- [[PDB file]], [[PDB file format]]

*[[Backbone representations]]

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*[[Biological Unit: Showing]]

*[[Buried charges detection]]

====C-E====

*[[CASP]]

*[[Cation-pi interactions]] (started by Wayne Decatur)

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**[[User:Eric_Martz/Cavity_Notes]]

*[[Chain]] <- [[Chains]]

*[[Chains and Chain IDs]] <- [[Chain]] <- [[Chains]]

*[[Clashes]]

*[[Chimera]]

*[[Conservation, Evolutionary]] <- [[Evolutionary Conservation]]

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**[[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]]

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*[[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]]

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*[[Extremophiles]]

====F-M====

====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]]

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*[[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]]

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*[[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

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**[[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]]

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*[[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)

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**[[Protein primary, secondary, tertiary and quaternary structure (Spanish)|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]]

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** 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====

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*[[Temperature value vs. resolution]]

*[[Temperature color schemes]]

*[[Theoretical models]] <- [[Theory]], [[Theoretical model]], [[Proteopedia:Featured_SEL/8]]

*[[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]]

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*[[: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]]

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===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)

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*[[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====

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*[[PyMOL]]

*[[RasMol]]

*Samson, see [[Sculpting protein conformations]].

*[[Swiss-PDBViewer = DeepView]]

**[[DeepView/Mutating Amino Acids]]

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*[[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]]

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===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]]

*[[Template:ColorKey_ConSurf]]

*The Templates used on the [[DRuMS]] and [[Help:Color Keys]] pages. All begin "Template:ColorKey".

*[[Template:Protected page banner]]

**Example of use: [[User:Karl Oberholser/Ramachandran Plots]]

*[[Template:Button Toggle Animation]] used at [[Lac repressor]] and [[Template:Button Toggle Animation2]] generally more useful.

<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:~~Green_links_zoom~~]] ~~See also adaptation emphasizing rotation~~ of ~~a morth at~~ [[~~SARS-CoV-2_protein_S_activation_by_furin~~]]

*[[Template:Protected page banner]]

**Example of use: [[User:Karl Oberholser/Ramachandran Plots]]

~~(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: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==

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*[[User:Eric Martz/Sandbox 2]] FGiJ state script -> Proteopedia

*[[User:Eric Martz/Sandbox 3]] '''Miniprotein & microprotein notes'''

*[[User:Eric Martz/Sandbox 4]] ~~'''Available'''~~

*[[User:Eric Martz/Sandbox 4]] Running state scripts for virus capsids and large assemblies

*[[User:Eric Martz/Sandbox 5]] ~~'''Available'''~~

*[[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

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*[[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

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*[[User:Nikhil Malvankar/Cytochrome nanowires]] <- [[Malvankar/2]]

*[[User:Nikhil_Malvankar/Geobacter_pilus_structure_and_function]] <- [[Malvankar/3]]

*[[User:Nikhil Malvankar/Workbench/M4]]

====Ke Xiao Collaborations====

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===Protected Topic Pages===

*[[User:Eric Martz/Cavities tests]]

*[[User:Eric Martz/Entertaining PDB codes]]

*[[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

@@ Line 76: / Line 76: @@
 <br>
 Personal website: [http://martz.molviz.org martz.molviz.org]
-<br>
-[http://www.bio.umass.edu/micro/faculty/martz.html My page] on my Department's website.
 <br>
 [https://scholar.google.com/citations?user=Bb3H0OsAAAAJ&hl=en&oi=ao Publications and Citations]
@@ Line 95: / Line 93: @@
 *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]]
@@ Line 112: / Line 114: @@
 *[[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 protein S priming by furin]]
-*[[SARS-CoV-2 spike protein fusion transformation]] -- [[Proteopedia:Featured_SEL/6]]
+**[[Proteopedia:Featured_SEL/5]]
-*[[SARS-CoV-2 spike protein mutations]] -- [[Proteopedia:Featured_SEL/7]]
+*[[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]]
@@ Line 167: / Line 173: @@
 ===Topic Pages - Structural Bioinformatics===
-====A-E====
+====A-B====
 *[[About Macromolecular Structure]]
-*[[AlphaFold]]
+*[[AlphaFold/Index]], a list of Proteopedia pages about AlphaFold.
+*[[AlphaFold]], an introduction and overview.
 *[[AlphaFold2 examples from CASP 14]]
-*[[How to predict structures with AlphaFold|AlphaFold, How to predict structures from sequences]]
+*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]] UNIT CELL SCENE NOT WORKING
+*[[Asymmetric Unit]]
 *[[Atomic coordinate file]] <- [[PDB file]], [[PDB file format]]
 *[[Backbone representations]]
@@ Line 181: / Line 197: @@
 *[[Biological Unit: Showing]]
 *[[Buried charges detection]]
+====C-E====
 *[[CASP]]
 *[[Cation-pi interactions]] (started by Wayne Decatur)
@@ Line 191: / Line 209: @@
 **[[User:Eric_Martz/Cavity_Notes]]
-*[[Chain]] <- [[Chains]]
+*[[Chains and Chain IDs]] <- [[Chain]] <- [[Chains]]
+*[[Clashes]]
 *[[Chimera]]
 *[[Conservation, Evolutionary]] <- [[Evolutionary Conservation]]
@@ Line 197: / Line 216: @@
 **[[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]]
@@ Line 205: / Line 228: @@
 *[[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]]
@@ Line 215: / Line 241: @@
 *[[Extremophiles]]
-====F-M====
+====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]]
@@ Line 227: / Line 254: @@
 *[[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]]
@@ Line 232: / Line 260: @@
 *[[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
@@ Line 241: / Line 274: @@
 **[[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]]
@@ Line 257: / Line 293: @@
 *[[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)
@@ Line 269: / Line 306: @@
 **[[Protein primary, secondary, tertiary and quaternary structure (Spanish)|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]]
@@ Line 277: / Line 312: @@
 ** 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====
@@ Line 300: / Line 338: @@
 *[[Temperature value vs. resolution]]
 *[[Temperature color schemes]]
-*[[Theoretical models]] <- [[Theory]], [[Theoretical model]], [[Proteopedia:Featured_SEL/8]]
+*[[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]]
@@ Line 311: / Line 356: @@
 *[[: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]]
@@ Line 319: / Line 369: @@
 ===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)
@@ Line 352: / Line 408: @@
 *[[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====
@@ Line 363: / Line 425: @@
 *[[PyMOL]]
 *[[RasMol]]
+*Samson, see [[Sculpting protein conformations]].
 *[[Swiss-PDBViewer = DeepView]]
 **[[DeepView/Mutating Amino Acids]]
@@ Line 404: / Line 467: @@
 *[[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]]
@@ Line 426: / Line 491: @@
 ===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]]
-*[[Template:ColorKey_ConSurf]]
 *The Templates used on the [[DRuMS]] and [[Help:Color Keys]] pages. All begin "Template:ColorKey".
-*[[Template:Protected page banner]]
-**Example of use: [[User:Karl Oberholser/Ramachandran Plots]]
-*[[Template:Button Toggle Animation]] used at [[Lac repressor]] and [[Template:Button Toggle Animation2]] generally more useful.
+<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:Green_links_zoom]] See also adaptation emphasizing rotation of a morth at [[SARS-CoV-2_protein_S_activation_by_furin]]
+*[[Template:Protected page banner]]
+**Example of use: [[User:Karl Oberholser/Ramachandran Plots]]
-(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: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==
@@ Line 523: / Line 612: @@
 *[[User:Eric Martz/Sandbox 2]] FGiJ state script -> Proteopedia
 *[[User:Eric Martz/Sandbox 3]] '''Miniprotein & microprotein notes'''
-*[[User:Eric Martz/Sandbox 4]] '''Available'''
+*[[User:Eric Martz/Sandbox 4]] Running state scripts for virus capsids and large assemblies
-*[[User:Eric Martz/Sandbox 5]] '''Available'''
+*[[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
@@ Line 537: / Line 626: @@
 *[[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
@@ Line 566: / Line 661: @@
 *[[User:Nikhil Malvankar/Cytochrome nanowires]] <- [[Malvankar/2]]
 *[[User:Nikhil_Malvankar/Geobacter_pilus_structure_and_function]] <- [[Malvankar/3]]
-*[[User:Nikhil Malvankar/Workbench/M4]]
 ====Ke Xiao Collaborations====
@@ Line 575: / Line 669: @@
 ===Protected Topic Pages===
 *[[User:Eric Martz/Cavities tests]]
-*[[User:Eric Martz/Entertaining PDB codes]]
+*[[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

User:Eric Martz: Difference between revisions

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