1 / 15

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.

jeslyn
Download Presentation

Structure Visualization

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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”

More Related