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User:Wayne Decatur/UNH Seminar Feb 1st 2011

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m (fixed typo in citrate synthase)
m (→Resources)
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*[http://www.umass.edu/microbio/chime/top5.htm MolviZ "Top 5"]
*[http://www.umass.edu/microbio/chime/top5.htm MolviZ "Top 5"]
*[http://www.umass.edu/microbio/chime/index.html MolviZ.Org]
*[http://www.umass.edu/microbio/chime/index.html MolviZ.Org]
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*[http://molvis.sdsc.edu/fgij/ FirstGlance in Jmol] is very useful for exploring PDB entries or upload structure files.
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*[http://chemapps.stolaf.edu/pe/protexpl/ Jmol Protein Explorer's] powerful Quickviews approach really helps quickly generate usful views. This is building Chime-based Protein Explorer to work with Jmol and a few features may still not yet work.
*[http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/igloss.htm Protein Explorer's Glossary]
*[http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/igloss.htm Protein Explorer's Glossary]
*[http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jmol_app.htm Jmol Application]
*[http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jmol_app.htm Jmol Application]
*[http://pymol.org/ PyMol]
*[http://pymol.org/ PyMol]
*[http://polyview.cchmc.org/polyview3d.html Polyview-3D], fancy [http://pymol.org/ PyMol] views and animations made super easy via a web server with forms.
*[http://polyview.cchmc.org/polyview3d.html Polyview-3D], fancy [http://pymol.org/ PyMol] views and animations made super easy via a web server with forms.
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*[http://chemapps.stolaf.edu/jmol/docs/ Jmol Command Reference Manual] for advanced scene authoring.
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*[http://www.weizmann.ac.il/ISPC/eMovie.html eMovie],a [http://pymol.org/ PyMol] plug-in for macromolecular movie-making.
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*[http://wiki.jmol.org/index.php?title=Main_Page Jmol Wiki]
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===Small Molecule Visualization and Model Kits===
===Small Molecule Visualization and Model Kits===
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*[http://chemapps.stolaf.edu/pe/protexpl/ Jmol Protein Explorer's] powerful Quickviews approach really helps quickly generate particular scenes or ideas for scenes to generate elsewhere. Using the information detailed [[Help:Copying FirstGlance Scenes into Proteopedia|here]] or at [http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jtatdocs.htm#fgijscripting the JTAT site on extracting state scripts], it is possible to go from these views to Proteopedia scenes; however, as the version of Jmol differs there may be discrepancies and issues.
*[http://chemapps.stolaf.edu/pe/protexpl/ Jmol Protein Explorer's] powerful Quickviews approach really helps quickly generate particular scenes or ideas for scenes to generate elsewhere. Using the information detailed [[Help:Copying FirstGlance Scenes into Proteopedia|here]] or at [http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jtatdocs.htm#fgijscripting the JTAT site on extracting state scripts], it is possible to go from these views to Proteopedia scenes; however, as the version of Jmol differs there may be discrepancies and issues.
*[http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/index.htm Jmol Tutorial-Authoring Template (JTAT)] describes and works for developing and viewing scenes offline or developing and viewing privately.
*[http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/index.htm Jmol Tutorial-Authoring Template (JTAT)] describes and works for developing and viewing scenes offline or developing and viewing privately.
 +
*[http://chemapps.stolaf.edu/jmol/docs/ Jmol Command Reference Manual] for advanced scene authoring.
 +
*[http://wiki.jmol.org/index.php?title=Main_Page Jmol Wiki]
*[[Morphs|Morphing]] allows displaying the visual transition between two molecular conformations.
*[[Morphs|Morphing]] allows displaying the visual transition between two molecular conformations.
*[http://polyview.cchmc.org/polyview3d.html Polyview-3D], fancy [http://pymol.org/ PyMol] views and animations made super easy via a web server with forms.
*[http://polyview.cchmc.org/polyview3d.html Polyview-3D], fancy [http://pymol.org/ PyMol] views and animations made super easy via a web server with forms.
-
*[http://www.weizmann.ac.il/ISPC/eMovie.html eMovie],a [http://pymol.org/ PyMol] plug-in for macromolecular movie-making.
+
 
 +
 
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===Modeling===
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*See the end of [http://www.umass.edu/molvis/workshop/umass11.htm Eric Martz's recent workshop syllabus] where he covers homology (more accurately, comparative) modeling.
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*[http://www.biotechniques.com/news/biotechniquesNews/biotechniques-309517.html A Feb. 1st 2011 news item about Yang Zhang and his work].

Revision as of 15:47, 3 February 2011

Contents

Introduction

  • Overview of the talk
    • My Recent Research
    • Cursory coverage of several free (and mainly open-source) options for molecular visualization


Yeast snoRNAs

  • Introduction to snoRNAs - most modify and are not-essential to yeast
  • Nobel prizes 2009 studies of the structure and function of the ribosome structure
    • Jmol
      • The Application
      • The Java Applet - Demonstration
    • Locations of the modifications in the context of the functional ribosome
    • Yeast snoRNA database
    • Turns out of you remove clusters of modifications or modifications at critical locations and examine processing of pre-rRNA and properties of mature ribosome, find effects.

Jmol

Protein Data Bank

Proteopedia

  • Proteopedia - interactive 3D encylopedia of macromolecular structures and structural biology resources to which scientists contribute and use to share structural biology content
  • People behind Proteopedia

Types of Proteopedia pages

Topic Pages

User Pages

  • Other users cannot edit pages in this space

PDB Entry Pages

  • Proteopedia has an entry for every PDB entry (over 70,000) with interactive scene links and links to useful resources

FirstGlance in Jmol

  • Views and Convenience buttons
    • How many chains? - Use 3pla
    • Key Resources:
      • Biological Unit
      • Missing pieces?; PDBsum link on Proteopedia entry pages helpful for this as well

Structural Biology for Non-structural Biologists


Proteopedia Page Authoring

  • Model of a wiki
  • Sandbox - there is a "student" login that can be used by groups for editing these for teaching purposes
  • Conveniences
    • Buttons for 3D structure windows and other commonly used items
    • Since a large amount of references are from Pub-Med, PMID all that is needed for references


Proteopedia Scene Authoring

  • Scene Authoring Tools
    • Load a structure 2zi0 or previous scene
    • Set your scene. Undo/Redo features.
    • Save your scene
    • Add the scene to the page
  • Try it out and then add and improve. Repeat.

Acknowledgements

  • closing slides

 

Time permitting


Resources

Macromolecular Visualization


Small Molecule Visualization and Model Kits

Topic Pages - Education

Authoring Scenes and Views in Proteopedia and beyond


Modeling

Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur

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