Use picking to find residues 64 and 72. You may need to manipulate the model to bring these residues into view. Notice that residues 64 through 72 constitute an alpha helix. Now you will examine the helix more closely.
Rasmol > restrict 64-72 < return > The restrict command selects all atoms specified, and removes all others. It does not alter the display of the selected atoms. Subsequent commands will affect only the selected atoms.
Display: Sticks
Colours: CPK
RasMol draws residues 64 through 72 as a stick model. Try
rotating the model so that all main chain carbonyls point upward. You
will find that the rotation behavior is strange, because RasMol is
still rotating about the center of the whole molecule. Fix this as
follows:
RasMol > set picking center < return
>
Now find the lysine residue at one end of the helix. Click on its
alpha carbon. The command line should read
Rotating about lys72.ca (578)
If some other atom is listed, search again for the alpha carbon of lysine 72 and click on it to get this message. RasMol will now rotate the model around this atom.
RasMol > set picking ident < return
>
This resets picking to identify picked atoms without changing the
centering of rotation. After issuing a command, always check the
command line to see if RasMol gives back a message. If there is no
message, it means that RasMol recognized the command. RasMol reports
syntax errors in commands if it cannot recognize them.
Now you will reduce the display further to just one residue.
RasMol > restrict 72 < return
>
Now only the lysine residue is shown. Bring the residue to the center
of the display. Click on the atoms of this one residue, starting with
the alpha nitrogen (blue, near the red oxygen), then the alpha carbon
attached to it, the carbonyl carbon, and the carbonyl oxygen (red).
Note their atom names on the command line. In the same order, they
are N, CA, C, and O. In the PDB file, these are the names of the
main chain atoms of each residue. Now find the atoms of the
side chain and click on them, noting their names on the command line.
Starting next to the alpha carbon, they are the beta carbon (CB),
gamma carbon (CG), and so forth, out to the zeta atom, which is
nitrogen (NZ). PDB files contain lists of all atoms in a protein,
named in the same way as this residue, along with the data needed to
display them as a graphics model.
In addition to display data, a PDB file contains other useful information. This is a good time for you to take a break and look at PDB File Contents.
Now you will bring the entire alpha helix back into the display, and center the rotation about the alpha carbon of the central residue, arginine 68.
RasMol > select 64-72 < return
>
Display: Sticks
RasMol > center arg68.ca < return >
The last command is another way to change the center of rotation.
Notice the syntax of the atom expression that follows the word
center. An atom expression describes a particular atom
or set of atoms. This expression for a single atom consists of the
abbreviation of the residue (arg), followed -- without a space
between -- by the residue number (68), a period, and the atom name
(ca for alpha carbon). An atom name is always preceded by a period.
The previous command also contained an atom expression: 64-72.
RasMol is pretty picky about the syntax of these expressions, so take
careful note when you encounter them. You can use these expressions
in select and restrict commands as well.
For more information about expressions, type help expressions, help primitives, and help examples. Although atom expressions may seem daunting to you now, you will see many examples before you complete the tutorial.
Arrange the helix so that it takes up most of the screen, with carbonyl carbons pointing upward. Press the cursor-up key next to the keypad and watch the command line. Each time you press cursor-up, RasMol reprints your previous command. Keep pressing until you bring your restrict 64-72 command back to the command line. If you go past it, use cursor-down to retrieve more recent commands. When the command is on the command line, add and mainchain to the command, and press return. In other words,
RasMol > restrict 64-72 and mainchain
< return >
The side chains disappear, giving you a clear view of the main chain
conformation in an alpha helix. You have restricted the
selected atoms to residues 64 through 72, and to the mainchain
atoms of the protein. Mainchain is one of many "sets" that you
can specify in RasMol commands. The mainchain set
includes only atoms N, CA, C, and O from each residue. For a listing
of the names of other sets, type help sets return. For
a listing of residues in each set, see the RasMol
Manual.
RasMol > hbonds < return >
RasMol draws dotted lines for all the main-chain hydrogen bonds of
currently selected residues. Now use picking to confirm that
most hydrogen bonds in an alpha helix are from the carbonyl
oxygen of residue n to the N-H of residue n + 4. Note
that hydrogen atoms are not present in this file. In the x-ray
crystallographic image of proteins, it is usually not possible to
resolve the hydrogen atoms, but we deduce their locations from
principles of structural chemistry (we assume that, at each central
atom, they are just like small organic molecules)
RasMol only looks for hydrogen bonds between mainchain atoms, such as those in helix and sheet. What is more, it "finds" the bonds by simple criteria of geometry and distance, criteria that are sometimes met more than once by the same atom (for instance, notice the two hydrogen bonds drawn to the nitrogen of lysine 72). In this case, the "real" bonding situation is unclear.