Displaying the Structure


RasMol is the tool to view structure provided as a PDB (Protein Data Bank) file. RasMol is aveilable on various platform such as Macintosh, Microsoft Windows, Linux etc.
For more detailed information, see http://rasmol.org/.

Installation of RasMol

Download and Installation

RasMol can be downloaded at the following site.
http://rasmol.org/
Download and uncompress compressed binary file and help file. Help file must be the same directory as executable.
There is also the help file for Windows help.

Start and loading a structure

Start RasMol with double-clicking the executable and there will be two windows; Graphics and Command-line windows. To load PDB file, choose the menu "File -> Open... " at Graphics window and select the PDB file.

Mouse Usage

In Graphicus window, manipulation of the molecule and operation via menubar are available.

Windows
Macintosh
rotaition
left button
mouse button
translation
right button
command + button
Z rotation
Shift + right button
Shift-Command+button
zoom
Shift + left button
Shift + button
slab
Ctrl + left button
Ctrl + button
RasMol Window
Graphics window: Molecular graphics is displayed.

RasMol Help

RasMol Command Window
Command-line window: Help and various commands are available.

Help

On-line help is available in Command-line window if help file is installed.

RasMol> help commands
Available commands are listed.

RasMol> help (command)
The help of the commands is displayed.

RasMol> help explessions
How to specify the atoms is shown.

Windows Help can be with RasWin (Windows version of RasMol).

Hints

To view around sepcified atoms

Select the menu "Settings -> Pick Centre" and pick the atom then the atom is centered. Z-clipping by selection of the menu "Option -> Slab On" is useful to display around the center atom.

To change the style of specified atoms

Type "select" command into Command-line window to select atoms. Then change of the style and colour by "Display" and "Colours" menus are appliedn in selected atoms.
example 1:display alanine residues in Ball-and-Stick style
RasMol> select 10-20
Display -> Ball & Stick
The selection can used in conjunction with other Command-line commands.
example 2:change the color of the residues 10-20 into cyan
RasMol> select 10-20
RasMol> colour cyan

For other commands, use on-line help.
Setting Menu




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Gifu International Institute of Biotechnology