[Project PE w/ spinning molecule until slides]

SUBJECT: How to visualize 3D protein structure easily
  with Protein Explorer.
  protein-protein, protein-nucleic acid, protein-ligand

PURPOSE of Protein Explorer:
  Make 3D struct widely accessible
    -- concentrate on the protein,
      not how to use the software.
  Yet powerful at largely qualitative level.

METHOD:
  Browser based, using MDL Chime -- free but not open source.
    -- Pros/Cons (Better open source)
    -- Not a long term solution
    -- But could improve access much more quickly w/ Chime

POLL:
  Somewhat familiar w/ RasMol? THEN PE FAMILIAR
    Know some RasMol commands?
      ALL WORK IN PE -- BUT DON'T NEED THEM
  Somewhat familiar w/ MDL Chime plugin?
  Somewhat familiar w/ PE?
  Somewhat familiar w/ SwissPDB-Viewer aka DeepView?
  Somewhat familiar w/ WebLab now Accelrys Viewer?
  Primary workstation unix (incl. SGI Irix, linux)?

proteinexplorer.org -> Alpha -> FIRSTVIEW all steps
  10-20% of crystal water
  hydrogens not resolved with typical protein xtls
    1.01 hydrogens/non hydrogen atom (weighted av AA comp)

FEATURES 1D66
  (Postpone buttons b/c no help here!)
  1USN (sites, ligands)

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QuickViews
  Buttons - top row only, ending 2o
  Automatic help (Zoom, Secondary color scheme)
  Paradigm SELECT -> DISPLAY -> COLOR

  Nucleic, Sticks, ACGTUbb (toggle Background)

  Protein, Spacefill, Polarity2
    Slab
    Only
    Color Charge
  Nucleic, Surface, Transparent
    Note major groove, Zn domain in it

  SITE MAP
  Seq3D
    // Single residues
    // Range, (Hide Surf!), Color Red, Chain A: Backbone
    Single, SF -> B&S, CysGREEN, CenterClickCd

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MAIN SLIDE
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  *** RESET VIEW/NEW SESSION ***

  Chain A, Sticks (Zoom)
    Contacts (hydrophobic, DNA backbone, CGG)

  // Optional: SELECT Clicked, Cyt 13, Stop, Contacts
  //  (enlarge help frame)
  //  Arg charge, Base stacking, Watson-Crick]

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Just say (no demo) Cation-Pi, Salt Br

DISPLAY, Evolution -> ConSurf

Animations

Comparator Snapshot

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//1B07
//  Cartoon, Structure
//  Cation-Pi
//    DISPLAY Clicks, Label
//  Salt Bridges

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