User:Wayne Decatur/Biochem642 Molecular Visualization Sessions

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Contents

Introduction

Viewing Structures

  • Proteopedia: 1d66
    • Spin
    • Quality toggle
    • Popup
    • Conservation: 5cyt, explanation, and see also The ConSurf Database and The ConSurf Server (Note: This is also item IV at MolviZ "Top 5".)
    • FirstGlance in Jmol from 1d66 entry in Proteopedia
      • Views and Convenience buttons
        • How many chains?
        • Spin
        • Hover (special to FirstGlance is ability to click and display identity; hover more general in Jmol. Model number would be shown if more than 1.)
        • Water
        • Labels
        • N→C Rainbow
        • Composition
        • Cartoon
        • Charge/Hydrophobic
        • Slab
        • Turn slab off and hit cartoon again. Where are the Ligands? Be aware when Ligands are on or off; ligands are often interesting moieties in the structure.
      • Center atom
      • Gaps - I'd suggest helpful PDBSum linked to at Proteopedia vs. less clear Sequence at PDB or S2C (compare 2ace)
      • More Views
        • Distance measuring
        • Cation-Pi interactions (salt bridges come up first)
      • Reset, Snapshot Gallery
      • Contacts
  • Polyview-3D for when you need an animation or extremely high-quality (most times the high quality button on Jmol is sufficient) static image. (Note: This is also item V at MolviZ "Top 5".)

Authoring pages and scenes

Resources

Molecular Visualization

Authoring Scenes and Views in Proteopedia and beyond

Class Sandboxes

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Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur

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