These instructions
are designed to give an introduction to the powerful command line instructions
that are found with the RasMol program.
Though several important commands will be covered, a comprehensive listing
is provided under the help section of RasMol (simply click “help” => “user
manual” => “Command Reference”).
Throughout this introduction the bolded type denotes the actual typing
that is done within the command line.
What if you do not
see the command line?
Often the command line will not be displayed immediately. For Windows users it is usually minimized as
an icon, and must be mouse clicked to be visible on the screen.
Mouse
Usage : Manipulating the molecule
through the use of a mouse.
1. 3D Rotation (x,y axis): Click, hold
down and move mouse to rotate the molecule in three dimensional space.
2. Zooming In/Out: Shift and click hold
down each, move up to zoom in and down to zoom out.
3.
Amino Acid Identification: Click on the molecule to find to find the
atom and aa of interest.
Select
Command: This is the most powerful
command and is usually the starting point for further commands and
manipulations. Prior to making additional
commands you must first select what the command will act upon, some of the most
common selections are as follows:
1.
Single Amino Acid: select aa
type #, use the three letter aa abreviation (example select lue27 or select glu121)
2.
Amino Acid Type: select aa type, use the three letter aa
abbreviation (example select asp)
2.
Entire Molecule: select *
3.
Chain: select *chain letter (example select *D)
4.
DNA: select DNA, also select not DNA, to select everything
but DNA
5.
Protein: select protein, also select not protein, to
select everything but protein.
Color Command: After selecting the region of
interest (see Select Command), it is often useful to color that region
1. The command line entry is simple, color
desired color (example color black)
2.
Color commands recognizable by RasMol include; black, white, blue, green, red,
orange, yellow, brown, purple, pink and violet.
3.
Color the molecule to distinguish feature or to give it a little character.
Show Command: Allows you to gain valuable
information on the molecule
1.
Information: show information, gives essential information such
as molecule name, classification and structural determination technique.
2.
Selected: show selected, will display information on the makeup
of a selected portion (see Select Command)
3.
Sequence: show sequence, displays the sequence of the molecule in
question
Slab Command: Allows you to look at internal
regions of the molecule, by slicing on the z axis
1. Zero is define as behind the molecule and
100 is defined as in front of the molecule
2. slab 0-100, example slab 50
cuts at approximately the midline of the molecule.
Stereo Command: Provides side by side display of
the molecule.
1. Make sure entire molecule is selected
2. stereo