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About RasMol.
Alongside all the course material, you are provided with a collection of PDB files which are a way to present molecules using RasMol. RasMol displays molecules interactively in 3D. V2.6 Molecular Visualisation Program . RasMol2 is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and the generation of publication quality images. RasMol runs on Microsoft Windows, Apple Macintosh, UNIX and VMS systems.
How to obtain RasMol
RasMol is freely available. You can download it from several source, including the RasMol Homepage where you will find a detailed tutorial of the software.
Download RasMol: from Home site.
A copy of RasMol (Win 32 version for Win 95)is also provided on the CD Rom of "The Molecular Biology Notebook".
Installation in Windows 95.
- Right-click on Start and select Open. The Start Menu window opens.
- double click on the "Programs" folder to open it (or wherever you want RasMol to be).
- Now, right click on start and select explore to open the Windows explorer.
- Use Windows Explorer to find the RasWin program file you downloaded (RW32B2A.EXE).
- Click the right mouse button on the RasWin program file, and select Create Shortcut. A new file will appear.
- Drag it into the Programs window (or wherever you want it).
- Close all windows. Now,
the Start, Programs menu will have RasWin on its list.
Once you installed RasMol, set it up as a Helper application for your browser.
- Internet Explorer: You shouldn't have to do anything
- Netscape 3 and Communicator. If you click on a link to a PDB file you will be asked to pick an application or save the file the first time you want to see one of these files. Choose "pick an application", and browse to the directory where you installed RasMol. Select the RasMol executable file. That's it. Now each time you will click on a link to a PDB file, either in the MBNO or in any other location, RasMol will launch with the selected molecule in it.
Basic RasMol Tutorial
- Description of the package
When RasMol is launched, two windows are opened. A main window contains the graphical interface where you can see the molecule and move it. It also has a menu which offers a shortcut to some of the basic commands. The other window is a command line interface where you can enter some more complex commands, and where are displayed some information taken from the molecule you have loaded.
- Loading a molecule
If you launched RasMol from your Browser, there should be already a molecule in it. If not, click on Open, and navigate to the folder in your machine where all the molecules are.
- Basis mouse functions
- If you click on the molecule and move the mouse, the molecule will rotate in 3 dimensions on your screen
- If you right click and move the mouse, the molecule will move without rotating (translation).
- If you press the Shift key while holding the left mouse button, and move the mouse, RasMol will zoom in or out of the molecule.
- Basic Menu function
The menu functions alter the display of the molecule and also can help you save a particular image in different formats.
Introduction to menu driven commands
It is convenient to set up your screen so that you can see both the RasMol main window, and the RasMol Command window. Note than when the RasMol main window is on focus, it is still possible to type commands in the RasMol command window. This can be very useful.
Example of useful commands: Load the protein hemoglobin as an example:
An advanced tutorial is available at the RasMol site.Name of the command Simple description Try this Backbone Show the backbone of a protein backbone on;
backbone 20;
backbone 100
backbone offColor change the colour of an element to the selected colour. Colours can be designated by their names or by the triplet of their RGB value [nnn,nnn,nnn]. color backbone red;
color backbone [000,255,255]Dots Show the Clouds of electrons as dots around the nucleus dots
dots offRestrict Will restrict the display of the molecule to the area mentioned: affect wireframe and backbone. restrict 1-100:c
Select select a group of amino acids. Most of the commands typed after that will only affect that part select heme
color red
select all
backbone
color backbone purple
backbone 200 select 1-40:a
color red
select 50-150:b
color blue
Spacefill Display a spacefill representation of the molecule. Note you can obtain the same effect whith the command Wireframe 50 spacefill
spacefill offWireframe Show the wireframe of the molecule wireframe on
wireframe 20
wireframe 50
wireframe off
Zap Close the molecule zap
A note on Scripts: It is possible to build a movie that RasMol can display. Please refer to the Homepage of RasMol to download some of these.
- Description of the package
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Rasmol on Wikipedia
Rasmol at Answers. com
Related Links
-Protein ExplorerProtein Explorer is free software for visualizing the three-dimensional structures of protein, DNA,
-Rasmol
V2.6 Molecular Visualisation Program . RasMol2 is a molecular graphics program intended for
-Rasmol QuickStart
The main purpose of RasMol Quick Start is to guide you through the large number of pages at the RasM