Use of Rasmol and study of proteins
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Transcript of Use of Rasmol and study of proteins
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.
Rasmol is a molecular visualization software
raster display of moleculesRaster=display of pixels on monitor
pixel=one dot on monitor
Protein Explorer, Chime, Jmol, pymol are other similar softwares used
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
Getting and installing Rasmol
Google “Rasmol”And get installation file for windows/Linux
www.umass.edu/microbio/rasmol/
For linuxRun command “apt-get install rasmol”
Or search and install from Linux Synaptic manager
What is a .pdb file?
pdb=Protein Data BankIt 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
How does .pdb file look like?COMPND ASPIRINATOM 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 8CONECT 11 12 12CONECT 1 2 2CONECT 3 4 4CONECT 5 6 6
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
How to learn Rasmol?
Open any PDB in Rasmol and experiment.
In this lecture 2HHB.pdb is used to understand rasmol
Look from every angle before you fall in love with Hb
Press left mouse button and move the mouse.Try Left<->RightTry Up<->Down
Try northeast<->southwestEtc...
Go to Menu(View->command prompt)Write command: reset
It moves molecule to its default position defined by author
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
Zoom
At command prompt write: Zoom 200
And press enterExercise: zoom to 50 and 200When zoomed to 200, Pan all area
To change the color of the background:
Command: background white
To close a PDB file, type “zap” at the prompt.
Command: zap
CPK colors of atoms
Zoom 400Menu(Display->spacefill)
Click gray, blue,red,yellow atoms see command prompt regionIdentify 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.
Color typesZoom 200
Menu(Display->Spacefill)Menu(Colors->CPK)
Menu(Display->ribbons)Menu(Colors->Group/chain/Structure/)
Display and Color selected atoms
Changing display and colors of selected atoms helps in understanding molecular structures
Select Vs Restrict
Menu:Display WireframeColor CPK
Commands:Select Protein(=globulin)Color blue
Commands:Select not Protein(=heme)spacefill
Study globin:
Command:Restrict proteinMenu: Display RibbonMenu: Color chain
Selecting a chain and color specificallyCommand: Select :aCommand: color green
Command: restrict :a (Count number of alpha helix,do group from colour for easy count)
hydrophobic amino acids:
Command:select hydrophobic
Command:color yellow
Command:select his
Command:color magenta