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User:Eric Martz

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<br>
<br>
Personal website: [http://martz.molviz.org martz.molviz.org]
Personal website: [http://martz.molviz.org martz.molviz.org]
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<br>
 
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[http://www.bio.umass.edu/micro/faculty/martz.html My page] on my Department's website.
 
<br>
<br>
[https://scholar.google.com/citations?user=Bb3H0OsAAAAJ&hl=en&oi=ao Publications and Citations]
[https://scholar.google.com/citations?user=Bb3H0OsAAAAJ&hl=en&oi=ao Publications and Citations]
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====A-B====
====A-B====
*[[About Macromolecular Structure]]
*[[About Macromolecular Structure]]
-
*[[AlphaFold]]
+
*[[AlphaFold/Index]], a list of Proteopedia pages about AlphaFold.
 +
*[[AlphaFold]], an introduction and overview.
*[[AlphaFold2 examples from CASP 14]]
*[[AlphaFold2 examples from CASP 14]]
*[[How to predict structures with AlphaFold|AlphaFold, How to predict structures from sequences]]
*[[How to predict structures with AlphaFold|AlphaFold, How to predict structures from sequences]]
*[[Alternate locations]] (initiated by Wayne Decatur)
*[[Alternate locations]] (initiated by Wayne Decatur)
 +
**[[Alternate locations of backbones]]
*[[Amino Acids]]
*[[Amino Acids]]
*[[Amino acid composition]]
*[[Amino acid composition]]
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**[[User:Eric Martz/Introduction to Structural Bioinformatics|Structural Bioinformatics]]
**[[User:Eric Martz/Introduction to Structural Bioinformatics|Structural Bioinformatics]]
*[[Isopeptide bond]] <- [[Isopeptide bonds]]
*[[Isopeptide bond]] <- [[Isopeptide bonds]]
 +
*[[Joining AlphaFold predictions for halves of a molecule]]
*[[Knots in proteins]]
*[[Knots in proteins]]
*[[Ligand]]
*[[Ligand]]
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*[[Theoretical models]] <- [[Theory]], [[Theoretical model]], [[Proteopedia:Featured_SEL/8]]
*[[Theoretical models]] <- [[Theory]], [[Theoretical model]], [[Proteopedia:Featured_SEL/8]]
*[[Thioester protein cross-links]]
*[[Thioester protein cross-links]]
 +
*[[Thioether protein crosslinks]]
*[[Unusual sequence numbering]]
*[[Unusual sequence numbering]]
*[[Van der Waals radii]]
*[[Van der Waals radii]]
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*[[Art:Five Bakers Dancing]]
*[[Art:Five Bakers Dancing]]
*[[History of Macromolecular Visualization]]
*[[History of Macromolecular Visualization]]
 +
*[[Art:Molecular jacks]]
*[[Art:Molecular Sculpture]]
*[[Art:Molecular Sculpture]]
*[[Art:Pentagonal Garden]]
*[[Art:Pentagonal Garden]]
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*[[PyMOL]]
*[[PyMOL]]
*[[RasMol]]
*[[RasMol]]
 +
*Samson, see [[Sculpting protein conformations]].
*[[Swiss-PDBViewer = DeepView]]
*[[Swiss-PDBViewer = DeepView]]
**[[DeepView/Mutating Amino Acids]]
**[[DeepView/Mutating Amino Acids]]
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*[[Proteopedia:About]]
*[[Proteopedia:About]]
*[[Proteopedia:Guidelines for Ethical Writing]] was started by Jaime Prilusky. I added the sections on ''Content Attribution'' and ''Images''.
*[[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:Languages]]
*[[Proteopedia:Namespaces]]
*[[Proteopedia:Namespaces]]
*[[Proteopedia:News]]
*[[Proteopedia:News]]
 +
*[[Proteopedia:Overview]] <- [[Introduction to Proteopedia]]
*[[Proteopedia:Policy]]
*[[Proteopedia:Policy]]
*[[:Proteopedia:Problems]]
*[[:Proteopedia:Problems]]
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*[[User:Eric Martz/Sandbox 3]] '''Miniprotein & microprotein notes'''
*[[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 4]] Running state scripts for virus capsids and large assemblies
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*[[User:Eric Martz/Sandbox 5]] '''Available'''
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*[[User:Eric Martz/Sandbox 5]] Caption tests
*[[User:Eric Martz/Sandbox 6]] H274Y Tamiflu resistance mutation in N1
*[[User:Eric Martz/Sandbox 6]] H274Y Tamiflu resistance mutation in N1
*[[User:Eric Martz/Sandbox 7]] PyMOL translator notes
*[[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 16]] PNGJ & caption SAT tests
*[[User:Eric Martz/Sandbox 17]] More PNGJ & caption SAT tests
*[[User:Eric Martz/Sandbox 17]] More PNGJ & caption SAT tests
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*[[User:Eric Martz/Sandbox 18]] '''Available'''
+
*[[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
*[[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/Cytochrome nanowires]] <- [[Malvankar/2]]
*[[User:Nikhil_Malvankar/Geobacter_pilus_structure_and_function]] <- [[Malvankar/3]]
*[[User:Nikhil_Malvankar/Geobacter_pilus_structure_and_function]] <- [[Malvankar/3]]
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*[[User:Nikhil Malvankar/Workbench/M4]]
 
====Ke Xiao Collaborations====
====Ke Xiao Collaborations====

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))

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

Proudly show your love for Proteopedia and help spread Proteopedia's wonders with highly coveted mugs and T-shirts from cafepress.com, featuring the original Proteopedia logo by Tali Wiesel. Cafepress is a website that prints custom images on mugs and T-shirts, and is unaffiliated with Proteopedia. Proteopedia collects no money from your purchase.


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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