Use of Rasmol and study of proteins

Rasmol

Dr. Kamal Modi

Resident doctor,

Biochemistry,GMCS.

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

Open 2HHB.pdb

Double click 2HHB.pdb

Or

Start RASMOL go to Menu(File->Open->2HHB.pdb)

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

Moving a molecule in Rasmol (Panning)

Press RIGHT mouse button and move the mouse.

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

Display types

WireframeSpacefillBall and stickBackboneRibbonStrandsCartoon

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

Thank you