Rasmol is a molecular visualization software that allows users to view and rotate 3D protein structures. It reads .pdb files, which describe the locations of atoms in a molecule using X, Y, Z coordinates. To use Rasmol, users need the Rasmol software installed on their computer and a .pdb file of the molecule they want to view. Rasmol allows users to manipulate the molecular view using commands or the mouse to zoom, rotate, select atoms, and change colors and display styles to better understand the 3D structure of proteins and other molecules.

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.

18. Color types
Zoom 200
Menu(Display->Spacefill)
Menu(Colors->CPK)
Menu(Display->ribbons)
Menu(Colors->Group/chain/Structure/)

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