[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) ---------------------------- 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 ------------------------------ MAIN SLIDE ------------------------------ *** 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] ------------------------------ Just say (no demo) Cation-Pi, Salt Br DISPLAY, Evolution -> ConSurf Animations Comparator Snapshot ------------------------------ //1B07 // Cartoon, Structure // Cation-Pi // DISPLAY Clicks, Label // Salt Bridges ------------------------------