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Structure Visualization

Structure Visualization. General overview + RasMol. Topic 4. Structure Visualization. Common representation schemes. Surface + ball-n-stick. Ribbon + ball-n-stick (het). Ribbon + ball-n-stick (all). Spacefill. Mix of styles. Visualizing electrostatic surfaces.

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Structure Visualization

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  1. Structure Visualization General overview + RasMol Topic 4

  2. Structure Visualization

  3. Common representation schemes Surface + ball-n-stick Ribbon + ball-n-stick (het) Ribbon + ball-n-stick (all) Spacefill Mix of styles

  4. Visualizing electrostatic surfaces

  5. Protein-substrate complexes MHC Class II Protein

  6. Molecular visualization software Many options: PyMOL, RasMol, Jmol, iMol, VMD, Chime, Chimera, etc. List= http://en.wikipedia.org/wiki/List_of_molecular_graphics_systems PyMOL is a powerful and free option. Dr. Guo has an excellent tutorial on PyMOL @ http://cciweb.uncc.edu/%7Ejguo4/BINF8202_11/itsc8202lec8.pdf

  7. RasMol • Modified from Wikipedia: RasMolis a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures. • It was originally developed by Roger Sayle in the early 90s. • Historically, it was an important tool for molecular biologists since the extremely optimized program allowed the software to run on (then) modestly powerful personal computers. • Before RasMol, visualization software ran on graphics workstations that, due to their expense, were less accessible to scholars. • RasMolhas become an important educational tool as well as continuing to be an important tool for research in structural biology. • Does not typically produce journal-quality images. • Many tutorials available online.

  8. RasMol

  9. RasMol

  10. RasMol Help Manual: http://www.rasmol.org/software/RasMol_2.7.5_Manual.html

  11. RasMol Help Manual: http://www.rasmol.org/software/RasMol_2.7.5_Manual.html

  12. RasMol scripts execute RasMol commands (file.ras)

  13. RasMol scripts execute RasMol commands (file.ras) load 3ZR9.pdb background white wireframe off Ribbons # co-rigid select 50-64,76-92,95-112,195-203,224-237,257-266 spacefill color blue pause # co-flexible select 65-75 color red select 210-223 color orange pause # active site metals select cd spacefill color green select zn spacefill 1.5 color purple pause  Makes ‘animating’ rasmol scripts possible # 'isostatic' domain select 115-190,238-255 color yellow

  14. RasMol scripts (file.ras)

  15. Color ‘temperature’ All atoms “Slab 50”

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