Using RASMOL
updated 18/10/02

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Use the RasMol program to construct three dimensional models of molecules

Go to the Rasmol Home Page Page and answer the following questions:

Create your answers in a word processor and save the file in Word document format. Wordpad, which comes bundled with Windows is one of many processors that can save  in *.doc format.

Submit your saved document  to the Assignment Data base.

Read the history of the Visualization of Molecules

Download  RasMol on your computer The rasmol program is available from two locations: From the Rasmol download page ,you can also download a copy from this page   During busy times of the day it may be difficult to log onto the Rasmol Website. Therefore, an abbreviated  Tutorial on how to use Rasmol is included to get you started. The Rasmol Reference Manual provides online help and a  user manual  is included in the software download package for offline help.

Install RaMol on your computer. The program that you have just downloaded eg Raswin95.exe) is in fact a bundle of several programs that must be installed. Just double click on the file name and the three files will be extracted and installed on your computer.

Download a data file containing the  spatial molecular coordinates of a molecule either from  the Brookhaven Protein Database of 3D protein structures PDB database or from Molecules: a collection of database files for molecules that are described in Kuby's immunology

 Run Rasmol from your computer 

Take a look at the Protein Morpher and the Protein Explorer developed by Eric Martz

Installation of RASMOL for Windows 95,98, XP
File Name Download Description
Raswin95.exe   A collection of three files that are used to run RasMol
Installation of RASMOL for Windows 3.1
File Name Download Description
raswinsx.exe 16-bit RasWin for computers without floating point hardware (first available November 20, 1996). This is what you need for an 80286 or any SX computer (such as a 386SX) which lacks a floating point math coprocessor (lacks 80287 or 80387). If you try to run one of the versions below and you get a floating point error message, try this version. It will be very slow.
raswin16.exe 16-bit RasWin for computers with floating point hardware (made available with stereo September 4, 1996, some bugs fixed November 20, 1996). This is 3- to 4-fold slower than 32-bit RasWin on computers which can run both versions.
raswin32.exe REQUIRES THE EXTRA FILE PW1118.EXE

To run 32-bit RasWin (some bugs were fixed November 20, 1996) under Windows 3.1x, you must have

  • (i) an 80386 or better CPU,
  • (ii) floating point hardware (this is built into 80486DX and Pentiums) and
  • (iii) a free accessory provided by MicroSoft called Win32S/Ole installed with your Windows 3.1x.
PW1118.EXE NEEDED for RASWIN32.EXE PW1118.EXE. is a bit over 2 megabytes in size.
Under DOS, put this file in a temporary DOS directory (for example, C:\INSTALL) and run it. It will create INSTALL.BAT; run this.
Then run Windows, File, Run, and select C:\INSTALL\DISK1\SETUP.EXE. When you have finished, you can delete all contents of C:\INSTALL (all files in all subdirectories under it). For more detailed and technical installation instructions, consult Microsoft's documentation.

Installation. RasWin (either 16- or 32-bit) is installed as follows under Windows 3.1x. Create a new directory (for example,
C:\RASWIN) and put the file you downloaded (RASWINSX.EXE, RW16B2A.EXE, or RW32B2A.EXE) there along with
the two essential help files rasmol.hlp and raswin.hlp. (Get rashelp.exe, run it under DOS in your raswin directory, and it will
self-unpack into these two files. These on-line help files are only up to date with version 2.5.)

Now, in Windows, select File, New (Program Item), Browse, and select C:\RASWIN\RASWIN.EXE (or RASWIN32.EXE),
OK. In the Description field, put RasWin followed by the version you are installing (for example RasWin32 2.6 Beta2). In the
Working Directory field, put C:\RASWIN or wherever you plan to keep your scripts and PDB (atomic coordinate) data files.

 

Rasmol is an excellent viewer for those protein structures found in the Protein Data Bank.

If the appropriate version of Rasmol is not already installed you will have to download and install the software to your own computer by clicking on the window below

Rasmol Home Page Its home page contains different versions of Rasmol for Windows 3.1, Windows 95 Unix, Macs etc. ,instructions, tips, updates etc

Acess the Rasmol Home Page by clicking on the underlined title and follow the tutorial that will teach you how to use the Rasmol program to build molecules that have been downloaded from the Brookhaven Database in the PDB format

Rasmol is an excellent viewer for those protein structures found in the Brookhaven Protein Database, Its home page contains different versions of Rasmol for Windows 3.1, Windows 95 Unix, Macs etc. ,instructions, tips, updates etc

During busy times of the day it may be difficult to log onto the Rasmol Website. Therefore, an abbreviated tutorial is included here to get you started. Spend some time with the rasmol user manual that is included in the software download package.

RESOURCES:

Protein Database : database for 3D protein structures

Rasmol Home Page : excellent viewer for those protein structures found in the Brookhaven Protein Database, contains different versions of Rasmol for Windows 3.1, Windows 95 Unix, Macs etc. instructions tips updates etc

Swiss Protein Sequence Database :database for protein sequencesGo to the resources section of the course website and download Protein Database files for B cell receptors and epitopes

Molecules: a collection of database files for molecules that are described in Kuby's immunology