Use of Rasmol and study of proteins
- 1. Rasmol Dr. Kamal Modi Resident doctor, Biochemistry,GMCS.
- 2. Rasmol What is Rasmol? Rasmol is most popular 3D molecular graphics viewer. It is particularly good at viewing and rotating protein molecules, although it also works perfectly with smaller molecules.
- 3. Rasmol is a molecular visualization software raster display of molecules Raster=display of pixels on monitor pixel=one dot on monitor Protein Explorer, Chime, Jmol, pymol are other similar softwares used
- 4. To use Rasmol, your computer need Rasmol software and PDB data file Rasmol Software is available for Windows and Linux. PDB files for various molecules are available on Internet
- 5. Getting and installing Rasmol Google “Rasmol” And get installation file for windows/Linux www.umass.edu/microbio/rasmol/ For linux Run command “apt-get install rasmol” Or search and install from Linux Synaptic manager
- 6. What is a .pdb file? pdb=Protein Data Bank It is a text file describing location of various atoms of a molecule in X,Y,Z axis It can be read in notepad (Windows), gEdit(Linux) .pdb files are read by Rasmol to display a molecule
- 7. How does .pdb file look like? COMPND ASPIRIN ATOM 1 C ASP 1 -1.888 -0.992 -1.576 ATOM 2 C ASP 1 -1.364 -2.148 -0.992 ATOM 3 C ASP 1 -0.076 -2.148 -0.468 ATOM 4 C ASP 1 0.708 -0.988 -0.524 ATOM 5 C ASP 1 0.208 0.156 -1.196 ATOM 6 C ASP 1 -1.104 0.160 -1.652 ATOM 7 C2 ASP 1 2.084 -1.032 0.100 ATOM 8 O2 ASP 1 2.532 -2.036 0.636 ATOM 9 O3 ASP 1 2.880 0.024 0.108 ATOM 10 O3 ASP 1 0.752 1.332 -1.084 ATOM 11 C2 ASP 1 0.668 2.020 0.032 ATOM 12 O2 ASP 1 1.300 3.060 0.152 ATOM 13 C3 ASP 1 -0.240 1.572 1.140 ATOM 14 H ASP 1 -2.876 -0.964 -1.984 ATOM 15 H ASP 1 -1.984 -3.036 -0.956 ATOM 16 H ASP 1 0.300 -3.064 -0.008 ATOM 17 H ASP 1 -1.484 1.080 -2.056 ATOM 18 H ASP 1 2.568 0.780 -0.328 ATOM 19 H ASP 1 -0.756 0.632 0.932 ATOM 20 H ASP 1 -1.004 2.344 1.288 ATOM 21 H ASP 1 0.348 1.432 2.056 TER 22 ASP 1 CONECT 7 8 8 CONECT 11 12 12 CONECT 1 2 2 CONECT 3 4 4 CONECT 5 6 6
- 8. How to find .pdb files? Example: Google “Hemoglobin PDB” Most .pdb files are stored at Research Collaboratory for Structural Bioinformatics (RCSB) website. http://www.rcsb.org
- 9. How to learn Rasmol? Open any PDB in Rasmol and experiment. In this lecture 2HHB.pdb is used to understand rasmol
- 10. Open 2HHB.pdb Double click 2HHB.pdb Or Start RASMOL go to Menu(File->Open->2HHB.pdb)
- 11. Look from every angle before you fall in love with Hb Press left mouse button and move the mouse. Try Left<->Right Try Up<->Down Try northeast<->southwest Etc... Go to Menu(View->command prompt) Write command: reset It moves molecule to its default position defined by author
- 12. Moving a molecule in Rasmol (Panning) Press RIGHT mouse button and move the mouse.
- 13. Mouse/Menu/Command Prompt Some actions can be done from menu. Some actions can be done using mouse. Some actions can be done only with command prompt. All actions can be done using command prompt
- 14. Zoom At command prompt write: Zoom 200 And press enter Exercise: zoom to 50 and 200 When zoomed to 200, Pan all area
- 15. Display types Wireframe Spacefill Ball and stick Backbone Ribbon Strands Cartoon
- 16. To change the color of the background: Command: background white To close a PDB file, type “zap” at the prompt. Command: zap
- 17. CPK colors of atoms Zoom 400 Menu(Display->spacefill) Click gray, blue,red,yellow atoms see command prompt region Identify atom. carbon is gray, hydrogen is white, oxygen is red, nitrogen is blue. This is the standard color code. CPK molecular models designed by chemists Robert Corey and Linus Pauling, and improved by Walter Koltun.
- 19. Display and Color selected atoms Changing display and colors of selected atoms helps in understanding molecular structures
- 20. Select Vs Restrict Menu: Display Wireframe Color CPK Commands: Select Protein(=globulin) Color blue Commands: Select not Protein(=heme) spacefill
- 21. Study globin: Command:Restrict protein Menu: Display Ribbon Menu: Color chain Selecting a chain and color specifically Command: Select :a Command: color green Command: restrict :a (Count number of alpha helix,do group from colour for easy count)
- 22. hydrophobic amino acids: Command:select hydrophobic Command:color yellow Command:select his Command:color magenta
- 23. Thank you