RasMol Tutorial

Double click on the RasMol icon on your desktop.

RasMol is called Rasmac on Macintoshes and Raswin on PCs running Windows. When you click on the icon, the program should start and two windows should appear: the display window (black) and the command window. On computers running Windows, the command window will be in the command bar that appears when the mouse is placed at the bottom of the terminal. Double click on the RasMol command line icon to activate this window. Once both windows are open, it's best to resize and arrange them, together with this tutorial, as shown at left. When you use RasMol without a tutorial, it's still a good idea to have a similar arrangement for the RasMol windows: Many scripts are designed so that the text they use to discuss examples is contained on about 6 lines of the command line window, so at least this many lines should be visible.

Type help in the command line window

The help file gives brief explanations of most RasMol commands. If the help file is not found by RasMol, make sure the file (called rasmol.hlp) is in the same folder as the executable.

More thorough documentation can be found in: Online RasMol documentation. If you download the online RasMol documentation and save it on your own computer, be warned that the venn diagram and several images (including two illustrations showing colors) don't download.

Open PDB file 1lmb.pdb using the pulldown menu at the top of the display window.

If there was a file loaded already, select Close from the pull-down menu first to remove it.

If you followed the directions above, the PDB file depicting the lambda repressor:DNA complex should be in your RasMol folder. The protein should appear in the display window as a wireframe model. On Windows computers, if your file does not appear in the selection window, type * for filename and return. All files in the directory will now be listed. If you have difficulty opening a file, make sure the file is ASCII (plain text) and that the folder name is all one word (e.g. RasMol, not Ras Mol). Files can be checked with an editor. If you save the file from a program like Word, make sure you save it as text with line breaks.

Rotate, Translate, and Magnify using the mouse.


(note that the ways to do these movements differ for the Mac and the PC)

The first operation to learn is manipulating the image with the mouse. You can rotate it, translate it, or zoom the image. The ways to do all but the first differ for the Mac and PC.

Mac:

Click in the display window to make it the active window:

• To rotate, hold the mouse button down and move the mouse back-and-forth and up-and-down.
• To translate, hold the apple key down, and move the mouse in the window. You don't have to hold the mouse key down.
• To zoom, hold the shift key and the mouse button down, and move the mouse in the window.
• To rotate about the Z axis, hold down the shift key, apple key, and mouse button, and move the mouse horizontally.

Practice these operations until you feel comfortable with them.

PC:

Click in the display window to make it the active window:

• To rotate, hold the left mouse button down and move the mouse.
• To translate, hold the right mouse button down and move the mouse.
• To zoom, hold the shift key and left mouse button down, and move the mouse in the window.
• To rotate about the Z axis, hold down the shift key, and right mouse button, and move the mouse.

Practice these operations until you feel comfortable with them.

Change the display style using the 'Display' and 'Colours' pulldown menus.

The next operation is to use these pulldown menus to change the appearance of the molecule(s). Experiment with the settings in the two menus.

In "Display", the "ribbons" option displays secondary structure for proteins; an alpha helix looks like a spiral, and a beta strand (not present in this protein) looks like a relatively flat ribbon lying next to one or more other ribbons.

'CPK' colors each atom according to type (nitrogen is blue, carbon is gray, oxygen is red). 'Structure' colors each residue according to the type of secondary structure the residue is in.

Note that each selection affects the whole structure. Next we'll see how to change selected portions of the structure.

Display/Cartoons

Finally, in preparation for the next part, use the pulldown menu to simplify display the molecule as indicated.

Now we need to begin using the command window to change the image in ways that aren't available from the pulldown menu. Commands are entered at the "prompt" in the command window; a blinking rectangle ("cursor") lies to the right of this prompt, which looks like

RasMol>

The commands below are entered at this prompt, followed by hitting the Enter (Return) key.

The difficult part about learning these commands is learning to phrase the commands in the proper form. Some are simple; "color red" means color the selected atoms red. Others are less obvious, but if you don't enter them correctly (according to what computer types call the "syntax") they won't do what you want them to do. There is some help available; if you know the command, for example "background", you can enter "help background" and some rather terse help is provided. In Windows, there is a help button which provides more help. Two other sources are the On-line Documentation and a reference that helps with the Select commands. Unfortunately, there is a learning curve; I hope the benefits of learning the program outweigh the effort to get to that point.

SELECT atoms to change display characteristics. The SELECT command causes additional commands to apply only to the selected atoms. Type the following commands in the command line window and note what happens. *** In the following, individual command lines are separated by a space. Some commands may wrap around in this table due to the size of the table cell, but you should type them on a single line. ***.

select dna

wireframe

cartoons off

color blue

It's too simplified; change the DNA back to wireframe. First select the DNA, then make it wireframe. Notice a difference from using the menus; the "cartoons" rendition doesn't go away, whereas the menus are either/or.

select protein

color red

Now color the protein.

select *:4

color orange

Color one subunit orange. Note: the * is a "wild-card" meaning "all the atoms"; the :4 means chain 4 (a chain is a single molecule); so *:4 means all the atoms in chain 4. In this structure, each DNA strand is a chain, as is each protein monomer.

reset

rotate y -80

rotate x -25

rotate z 5

Now let's rotate the molecule to see it a bit better. Note that you can control the rotation with commands. The "reset" command restores the initial orientation so that the subsequent commands will give the desired image. For looking at molecules, this isn't necessary. For tutorials like this, though, it ensures that the viewer sees the desired image. It's also useful in writing scripts (files that make an image to show someone else).

Note the syntax of the rotate command:

rotate (dimension) (angle)

In this case, both a dimension and an angle must be specified.

select protein and 44-51

color yellow

This selects a group of residues in the protein. Note the syntax of this expression. Only those atoms are selected that fulfill two criteria: they are in the protein, and their residues are numbered 44 to 51. In this case, it is necessary to specify protein because, although the DNA doesn't have residue numbers in this range, there are water molecules that do. (For water molecules, only certain representations, like spacefill, display them.)

This particular part of lambda repressor is called the "recognition helix", because many of the amino acids that contact the DNA are in it. Note how it lies in the major groove of DNA.

See note at right before entering:

select protein and 44-51 and sidechain

wireframe

color white

wireframe 50

Note: as a shortcut in typing commands, you can hit the up arrow to get the previous commands. Try this here. Hit the up-arrow twice; it should display "select protein and 44-51"; then type "and sidechain" at the end of the command to give the first line at left.

Now we can see the sidechains of these helices. They are rather thin, so the last command sets the thickness. Note that this can't be done from the pulldown menus. If you like, experiment with different values, then make it 50 before going on.

select protein and 44-51 and sidechain

wireframe off

Now the sidechains are off.

select protein and (44,45) and sidechain

wireframe 50

spacefill 250

Here is a more complicated expression. Click here for an explanation of the logic.

The parentheses are important; if you left them out, you would select all of residue 44.

Now the sidechains of Gln44 and Ser45 are visible.

"Spacefill" gives an alternative representation.

select atomno=1841

color violet

select *45.og

color white

Finally, let's look at some ways of selecting particular atoms. One way is to describe the atom by its atom number in the PDB file. You can learn this by clicking on the atom.

The -OH oxygen of Ser45 should be colored violet. This atom makes a hydrogen bond with a base in the DNA.

Alternatively, the same atom can be described by its chemical nature, in this case a gamma oxygen in Ser. You can learn how atoms in proteins or DNA are described by clicking on many of them and seeing the result.

In this case, the atoms in Ser45 residues of both subunits are selected. Look at the other one to see. How would you select only the one in the subunit you've been looking at?

select protein

spacefill

select protein and hydrophobic

color green

select basic

color blue

select at and not backbone

color white

(when you are finished with this, simplify the display):

select *:4

color orange

select *:3

color red

RasMol has a number of "predefined sets" of atoms or groups. We've already seen one--sidechain. Here are a few more examples.

This set of commands turns the hydrophobic residues green.

"Basic" means lysines and arginines.

This turns the bases of the A-T base pairs white.

The list of predefined atoms, such as hydrophobic and sidechain, can be obtained by typing 'help sets' in the command window.

Further help is available in the Online RasMol documentation.

RESTRICT commands: The RESTRICT command is similar to select, but differs in that it will allow only the specified atoms to be displayed. Note what happens with the following commands.

restrict 44-51

Only residues 44-51 should remain on the screen.

restrict 44-51 and sidechain

spacefill off

wireframe 100

Only sidechains remain.

select at

spacefill 250

restrict at

The AT base pairs appear. The bases are still in white because that's how we colored them earlier.

center selected

Use the CENTER command to change the center of rotation. The center of rotation should now be around the DNA chain, since AT base pairs are all along it. Rotate the molecule to see.

select atomno=426

color orange

center selected

This selects an atom near the end of the chain. Rotate the image to see that it is now the center of rotation. As you rotate it, the orange atom doesn't move.

define s45 (*:4 and 45 and not backbone)

select s45

spacefill 250

color purple

define g16 (dna and 16 and not backbone)

select g16

spacefill 250

color purple

select s45,g16

center selected

Use the DEFINE command to define a complicated set of residues. This is very useful if you wish to select these atoms repeatedly. Note that "define s45 *:4 and 45 and not backbone" is all one line. Note that the name "s45" is arbitrary; it is a name that you give to the group in parentheses. It can be anything except a word (such as "protein" or "dna") that is used by RasMol to define a set.

Now the sidechain of Ser45 and the base it contacts are highlighted. Still, it is a little hard to see.

Change it so that only these two groups are shown. Hint: you can do this in one line, since you have defined the two groups.

Once you have just the two groups visible, rotate the image as you like.

Now let's measure the distance between the atoms that are hydrogen-bonded to one another.

set picking distance

select atomno=1841

color yellow

select atomno=322, atomno=319

color orange

monitor 1841 322

monitor 1841 319

color labels red

select atomno=322

label G16 O6

select atomno=1841

label S45 -OH

The command 'SET PICKING DISTANCE' causes the distance between the next two picked atoms to be determined. If you want to turn it off, type "set picking".

With the mouse, click on 1841 (yellow) and 322 (orange); then on 1841 and 319. Are the distances reasonable for hydrogen bonds?

To display the distance, use the "monitors" command; to turn off a particular distance, repeat that command, to turn off all monitors enter "monitors off".

If the numbers aren't readily visible, rotate the image. Often you can rotate it about the z axis and they will be more visible.

You can also color them a different color, as shown; this command affects all the labels in the figure.

Finally, you can label selected atoms (or groups of atoms) as indicated.

The "set picking" command can be used to measure other quantities as well. If Angle is specified instead of Distance, then the angle between the next three picked atoms is determined, and if Torsion is specified, then the torsional (dihedral) angle between the next four atoms is determined. Typing Set Picking by itself turns off measurements.

If you want to turn off the result of a "monitor" command, you can enter the same command a second time (this is especially useful if you make a typing error!).

define reshelix (*:4 and 44-51)

restrict reshelix

spacefill off

monitors off

wireframe 50

hbonds

color hbonds green

hbonds 20

The command 'HBONDS' causes main chain hydrogen bonds to be displayed. Only those atoms that are currently SELECTED are searched for hydrogen bonds. The color of the hydrogen bonds can be changed with the color command, e.g. COLOR HBONDS GREEN.

RasMol searches for hydrogen bonding groups such as oxygen and nitrogen that are within hydrogen bonding distance and draws a dashed line between them. This procedure connects some groups that are not actually hydrogen bonded together, such as oxygens and nitrogens that are close together but whose electron orbitals are improperly aligned for hydrogen bonding.

You should faintly see the H bonds in the alpha helix; "hbonds 20" makes them thicker.

The hbonds can be turned off with the commands SELECT ALL followed by HBONDS OFF.

When you want to make a script for later use, you need to save it using the following command:

write script xxx.scr

[where xxx is your name or initials]

This command will create a script file called xxx.scr that contains the commands for recreating the current view. Such files are quite long because they set the values for every variable in RasMol. However, near the top of the file, the current rotation, translation, magnification, and slab are listed. If you are writing a new script (see below), placing this information in the file will help you display the view of interest. For example, if you run 'intro.scr' to completion, rotate the final image, and type 'write script new.scr', the file new.scr will contain text similar to this:

reset
slab off
rotate z 2
rotate y -9
rotate x -46
translate y -1
zoom 150

Note: there is a small bug in RasMol that causes the view to be slightly off when certain commands are given in conjunction with the translation command.

script xxx.scr

Finally, run your script (again substituting your name or initals for "xxx"). If all went well, the view will be recreated. For a tutorial on making and editing scripts, and on further use of define commands to improve the appearance of your images, follow this link.