RasMol Tutorial for Viewing Proteins
What is RolMol? What can it do?
RasMol is a program that view PDB files. PDB is a file format used for large molecules such as protein or DNA
These files can be found on the web in Brookhaven protein data bank or created using other programs, such as Spartan. RasMol can be used to rotate the molecule, change mold type it is viewed in, and color the molecule. Specific residues can be identified, as well as different structures. RasMol can only look at one PDB file at a time. RasMol images can be saved in different picture formats for display on the web or within a word document. RasMol is "freeware", which means you can install in anywhere for free.
RasMol Resources
RasMol Home Page
http://www.umass.edu/microbio/rasmol/index.html
RasMol Manual
http://www.umass.edu/microbio/rasmol/distrib/rasman.htm
RasMol on your desktop
See the attached instructions, How to use RasMol from any Mac... or How to get RasMol on PC..., if RasMol is not already on your computer.
Getting a Structure
Open up Netscape and go to http://www.pdb.bnl.gov/
Select 3D Browser (half way down the page)
Fill in parts of the search form by typing myoglobin under Keyword.
Click on Search
Click on Keep Working.
The window will renew its self and under the seat criteria will be the results of your search.
High light the compound you want to look at. (There is only for this case.)
Click on the "Retrieve Data" box
A text will come up that shows the author, journal source, and references. The amino acid sequence also usually give.
Click on the RasMol "asymmetric unit" link to download the PDB.
Click on Pick app
Open up the RasMol folder on the desk top and select RasMol
Click on Open
You will only have to select the application the first time you open it.
Using RasMol
RasMol is capable of displaying the protein in many different configurations and colors.
RasMol has two windows: one is the main window that displays the image and the other is the command line window.
The command line window allows the user to enter commands. Many of the commands can also be accessed in a user
friendly manner by using the menu options at the top of the screen. However, there are commands that can only
be done by typing in the command. This next section will show you a few of each type of commands.
RasMol will open the protein you have chosen in wireframe
Notice the two different windows
The front window is the Main Window the molecule is shown
The other window behind the Main Window is the Command Line Window
Under the Display Menu select Ribbon
Notice the heme is not visible. This is because ribbon viewing only shows the backbone of the protein.
To view heme
Click on the Command Line window
At the RasMol prompt type: select hem
At next prompt type: color red
At the next prompt type: wireframe
You can also go to the view menu and select different ways of viewing the heme.
Those that show only the backbone, like strands, will not show the heme.
View and Color
The commands you chose from the view menu will work only one the selected item, if you want to change the whole protein select all under the edit menu and then the view mode you want.
Play around with the different viewing and color styles by going under the View Menu and randomly selecting of the options. Do the same thing under the Color Menu.
Background color
Sometimes another background color is desirable, especially when printing.
In the Command Line Window
Type background white or what ever color you want
The rest of the pictures will have white backgrounds to save ink when printed out.
Selecting Amino Acid Side Chains
In the Command Line Window
(Start in ribbon view and monochrome color.)
Type "select his" at the prompt
Type "color yellow" at the prompt
This shows you all the histidines in the protein
If you click on one of the in the Main window, the number of the histidine will be printed in the Command Line Window.
NOTE: Sometimes it is hard to click on the histidine and not accidentally on another residue.
Hydrogen Bonds
In the command line window and with whole selected.
Type hbonds on
Some times the hydrogen bonds are hard to see depending on the background and the color of the protein.
To get ride of them type hbonds off.
(Again the whole protein must be selected when you perform this command.)
Restricting
Select the whole protein and put it in the wireframe display.
In the Command Line Window:
Type "restrict 3-16, hem" This will also show you the heme with the first helix (amino acids 3-16).
To get rid of restrict: select all and choose wireframe.
Zoom
In the command window
Type zoom 200
The protein should appear bigger than original
Type zoom 50
The protein should appear smaller than original
Type zoom 100
The protein should be back to original size.
Slab
In the command window
Type slab 50
This shows what it looks like if you sliced the protein in half.
When you rotate the molecule the slab will change.
To get rid of slab type "slab 100"
Rotate
Type "rotate x 100" in the command line.
This will rotate the image on the x axis 100 degrees
Set Axes
Type "set axes on" in the command line.
This will show axes
"color axes green" will change axes color.
Printing from RasMol
Under File, select Print
Click on OK
Exporting image as gif, pict, ..
Under Export, select the image type you desire.
Give the file a name and select the desired folder. Click on OK.
Summary of Commands
> select "number of residue or structure type"
> select 64
> select hem
> color "color name"
> color yellow
These commands will color what is currently selected
> background "color"
> background white
These commands will make background different color
> hbonds on
> hbonds off
The will show the hydrogen bonds
> restrict 3-16
This command will only show residues 3 through 16
> zoom 200
This will make structure twice as big
> slab 50
This command will show have of molecule
http://www.mtholyoke.edu/~emlaughl/mmlab/rasmol/raspro.htm
written by: Elsa Laughlin 2/12/98