• Start Rasmol and open the file you wish to display (use "File", "Open" from the menubar)

• Click the box in the Task Bar labeled "Rasmol Command Line; it will open up and give you a window with a "Rasmol>" prompt; adjust the two windows so you can see them both

  Rasmol Windows (command window below)

• Place the cursor within the Rasmol command window and type "background cyan";if you make a typo, nothing will happen, otherwise the background color will change to a bright blue (other color selections are noted below; white is usually a safe choice)

• Now rotate (left click, drag) and zoom (left click, shift-drag) to place the molecule in the middle of the window at a reasonable size

Place the cursor in the command window:

• Type "select protein"

• From "Display" on the menubar, choose your presentation for the protein: Ribbons, Cartoon, etc. (You can also type "cartoon" in the command window)

• To color the protein a single solid color, type "color colorname"; the "Colours" selection on the menubar has some choices that allow coloring by structure

• Type "select hetero" or "select ligand" (In pdb files, "hetero" refers to things that are not part of the protein; "ligand" refers to bound substrates, cofactors, etc.)

• From the Display menu, select a display type different from that you are using for the protein (or type "display typename"). The ligand will appear in the chosen display mode.

• To change the color of your selected object, type "color colorname" in the window, or make a selection from the "Colours" menu.

If you know which amino acids are in the binding site for your ligand, your can now repeat the selection process for each in turn. Type, for example, "select Tyr100", then change the display mode and color, and repeat for each identified residue.

If you are not sure about the groups around your ligand, you can use the "within" modified to the select command:

In this command, "distance" is a distance in Angstroms, corresponding to the radius of a bubble around the target. Anything within this distance is selected.

For example

selects all atoms within 4.0 A of the calcium ion a protein

You can then manipulate the display as above to visualize the residues. To identify the species now displayed, use the label command:

The "%n" calls for the residue name, and the "%r" gives the residue number. Alternatively, click on the species in the display window, and the command window will identify it. Label colors can be changed by using "color label colorname".

If the portion of the molecule you wiant to examine is somewhat buried, the "slab" command may be helpful.

• Type "slab on". This divides the volume occupied by the molecule displayed into 100 slices of equal thickness, numbered from 0 at the rear to 100 at the front.

• Typing "slab 85", for example, now deletes from the display all portions of the molecule from slab 86 to slab 100. "Slab 0" would erase the display entirely.

• Changes are not permanent; follow "slab 0" with "slab 100" and the molecule will reappear. "Slab off" will turn off slabbing.

Rasmol keeps track of the commands you issue, and will write them to a file, called a script, that you can use to reproduce any display. When you are satisfied with the display you have created, type:

where 'filename' is the name you choose for the script file. To load the structure display again, just type:

The script will run, and the display will appear.

Finally, if you wish to save a graphic containing your display, choose 'Export', and select either the 'bmp' or 'gif' format. Then enter a filename on the form that will appear. The .gif format will provide more detail, but either can be pasted into a word processor document and printed.

If you have the Adobe Acrobat Reader on your computer, you can download here a Quick Reference Card that summarizes Rasmol commands. If you don't have Acrobat, click the icon below to download a FREE copy.

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