What can you learn about a protein/DNA molecule with RasMol?
by Eric Martz, 6/97 (revised 8/6/97, 9/14/97, 2/27/98, 4/3/98, 4/27/98, 10/26/98)
If you are reading a paper version of this document, it is
also available at
Beginners should first read RasMol
Quick Start at
. There you can get RasMol and the 1d66.pdb atomic coordinate file
needed for the first chapter below.
- For background, get the short, excellent and readable
Introduction to Protein Structure by Carl Branden and John Tooze,
Garland Publishing, 1991
- This document has two chapters. In the first, you apply specific
commands to a specific molecule, 1d66.pdb, a protein:DNA complex.
In the second, general instructions are listed which are applicable
to any molecule of your choice.
- Other tutorials on RasMol are at
The RasMol Reference Manual, answers to Frequently Asked Questions
(FAQ), and other helpful documents are at
Commands below preceded by M are best done from the
pull-down Menus. Commands not preceded by M must be typed
in the white command-line window.
(RasMol has two windows, one black and one white. On Windows, the
white command-line window starts minimized. Look for it on the
taskbar. On Macintosh it starts behind the black window. Move the
white window below the black window, but keep the bottom line in view.)
Commands listed below separated by semicolons should
be typed on separate lines into the white window,
pressing Enter after each command.
Comments are italics -- these are not commands.
- Run RasMol, and do M(enu) File -> Open. Select 1d66.pdb
(gal4 transcriptional regulator complexed to DNA)
(If you don't see 1d66.pdb, detailed troubleshooting is
- After a select command, subsequent commands affect only the
selected atoms. The display representations of unselected atoms
will remain unchanged. A restrict command is like a select command
except that it hides all unselected atoms.
Questions & Answers about 1d66.pdb
- How many chains are there?
reset; rotate z 90; zoom 150; rotate y 40
Type each semicolon-separated command
on a separate line, pressing Enter after each one.
This sequence positions the molecule nicely.
M(enu) Display -> Backbone, M Colours -> Chain
Now each chain is a different color.
Click on each chain to report its ID letter code (last item in the report).
- Is there anything else in this PDB file besides the protein/DNA chains?
select hetero; M Display -> Spacefill
Now you see oxygens from water in the
M Colours -> CPK
CPK is the Corey-Pauling-Koltun color scheme.
Click on an atom to find out what element its color signifies.
restrict not water
This hides water; click on what remains to find
out what it is.
The older PDB standard and files
have some ambiguities; CD could mean either carbon delta
or cadmium -- here it is the latter.
The physiologic metal for gal4 is zinc; cadmium was
substituted in the crystallized protein.
For a general introduction to how to select or restrict (hide)
atoms, residues, chains,
ligands, groups of residues (such as hydrophobic or charged) and
nearest neighbors, see
Select Commands in
Chime and RasMol
|Mouse Click and Drag Summary
- Where are the hydrophobic amino acids?
select hydrophobic; color magenta; wireframe 0.4
Note amphipathicity of alpha helices.
select not water; M Display -> Spacefill; M Options -> Slab mode
Slice thru the molecule to look at distribution of
hydrophobic and hydrophilic residues.
Move the slab plane with the mouse.
- What holds the Cd ions in place?
M Options -> Slab mode
Toggle the slab mode off.
M Edit -> Select All
M Display -> Backbone; M Colours -> Chain
select cd; M Display -> Spacefill; M Colours -> CPK
select within(2.6, cd)
This selects all atoms within 2.6 Angstroms of the Cd++ ions.
M Display -> Spacefill; M Colours -> CPK
Click to discover the identity of the caging atoms.
How do we save this view?
save script myview1.spt; M File -> Close
How do we restore the view later?
RasMol-saved views (scripts) can be played back smoothly in the
correct order from a master script. See
Preparing RasMol-Saved Scripts for Teaching (complete
with troubleshooting) at
Your RasMol-saved scripts
can easily be installed in web pages for delivery via Chime
(no programming needed!). See Presenting RasMol-Saved Scripts in Chime
where you can download the template at
Where are the alpha helices and beta strands?
M Edit -> Select all; M Display -> Backbone; M Colours -> Structure
This colors alpha helices purple, and beta strands yellow (there aren't
any beta strands in 1d66.pdb).
structure; M Colours -> Structure.
This forces RasMol to make its own determination.
Notice the appearance of blue "turns".
How do I find the distance between two atoms?
M Display -> Spacefill; set picking distance
Now click on two atoms, and watch the report in the command line window.
If you want label the two atoms with the distance, try this:
set picking monitor
Now click on two atoms near the edge of the molecule.
(This will work best if there is black background between the two atoms.)
Watch what these do:
color monitor white; set monitor off; monitor off
set picking ident
The above restores the normal clicking function of identifying the atom.
RasMol can also report angles and torsion angles. See
How do I find the bonds between protein and DNA?
- reset; M Display -> Backbone;
color green; backbone 0; rotate z 91; translate y -17; zoom 200
select dna; color white; spacefill; center selected
select dna and backbone; color yellow
- Now you can see the DNA, with backbone and base pairs in different
colors, and you can see the backbone of the protein as a thin green line.
- select within(3.1, dna) and not dna
- If you left out "and not dna", you'd select the DNA also!
The above command should select 35 atoms.
- Now press the "up arrow" key until you see the "within" command, and
add to the end of it and not water. Press Enter, and
19 atoms should be selected.
- spacefill 0.6;
- Now the putatively bonded protein atoms are small solid spheres within
dot-spheres, while the hydrogen-bonded water oxygens are hollow red dot-spheres.
- select within(3.1, protein) and dna; color cpk
- Now you can zoom in and click on prospective donor and
acceptor atoms to identify the residue to which they belong and
evaluate the liklihood that a given pair is in fact hydrogen-bonded
(or otherwise bonded).
How do I see the inside of a molecule?
- Don't rotate the molecule with the mouse at any time during this sequence.
- reset; M Edit -> Select All;
M Display -> Spacefill; M Colour -> Chain.
rotate x 83; zoom 200
M Options -> Hetero Atoms (Toggle off waters)
select dna; color cpk;
M Options -> Slab Mode (Toggle on slab mode)
- The front half of the molecule has been cut away. You see
the cut face, and everything behind it.
- set slabmode section;
- Now only the cut face is show. Everything in front of and behind
the cut plane is hidden. Only the atoms hit by the "knife" are shown.
- slab 76
- Now you see a GC base pair, cut through the plane where the three
Watson-Crick hydrogen bonds are. (This won't work if you moved the molecule
with the mouse anytime since the reset.)
- slab 68
- What is this? Use the mouse to move the slab plane
(Hold down Ctrl, then click and drag up and down). Can you find a base pair
which is completely out of Watson-Crick position? (Answer is at the end of
Controlling RasMol's Display
How do I keep the DNA from rotating off screen?
- reset; restrict dna; rotate z 90; zoom 200
Try rotating around the axis of the DNA helix (move the mouse up
Notice how the DNA rises and falls as it rotates around the center
of mass, which includes the invisible protein.
Now try again and notice the difference.
How do I get multiple representations of the same atoms?
- restrict :d; M Colours -> CPK
:d means all atoms in chain D.
M Display -> Backbone, M Display -> Ball & Stick
Notice how you get one or the other but not both when you use the Display menu.
This is because each representation on the Display Menu turns off all other
representations for the selected atoms. In contrast, when representations are applied
from the command line, they do not turn off other representations.
Be sure to include the decimal point after the one, which makes
RasMol interpret it as Angstroms.
When you type display commands, existing representations are not
turned off (unlike with the display menu).
"Sticks" are wireframe with a nonzero radius. Balls are spacefill
with a uniform radius. Watch these:
spacefill off; wireframe 0.5; wireframe 0.1; spacefill 0.3; backbone 0.1; zoom 500
How do I label an atom?
- set picking label
Now click on a few atoms.
color labels white; label off; set picking ident
Click on an atom and notice its atom ID number (3rd word in the report).
We'll refer to the number as ### in the command below.
select atomno = ###; label "My Favorite Atom"
How do I see the molecule in stereo?
M Options -> Stereo
Now you need to translate to the left to center the image.
By default, you get cross-eyed stereo. To get wall-eyed stereo:
Viewing stereo takes practice, can be hard on the eyes, and is not necessary
for most purposes. Rotation without stereo
gives you an excellent perception of major 3D relationships.
However, if you view molecular graphics frequently, learning how
to view images in stereo will enable you to see complex
spatial relationships more clearly.
Gale Rhodes has provided an excellent introduction to stereo viewing
Exploring the Molecule of Your Choice
- Obtain a PDB file for the molecule of your choice. See
Molecules Galore at
- Look in the PDB file (use a text viewer such as Wordpad or Word)
for references to journal articles. Reading these papers is often essential
to understanding what you are looking at! For example, how much of the
intact molecule is represented in the PDB file? How was it prepared?
- Use RasMol's File, Open menu to display your molecule.
If you don't see your molecule, detailed troubleshooting is
- If a command has no effect, you may have nothing selected to
which it applies. For example, if you select hetero and
later color structure, there are no proteins selected to
which the secondary structure color scheme applies, so nothing
happens. Solution: select all, or select the relevant moieties
and re-issue the command.
- How many chains are there?
- M Display -> Backbone; M Colour -> Chain
- At any time, you can restrict your view to one or a subset
of the chains present. Click to find out the chain letter. Suppose
you want to hide all chains except B and D:
restrict :b or :d . To restore the view to all chains,
M Edit, Select all.
If you want to look at only part of a large PDB file
(greater than 500,000 bytes), it will greatly improve RasMol's
performance if you make a copy of the PDB file from which you delete
all atoms except the series you wish to view. To do this, select
the desired atoms/chains/residues/ligands in RasMol, then
save pdb filename.pdb
Open the new PDB file in RasMol for further work. Be sure you didn't
omit important ligands!
- Are any ligands present?
- select hetero; M Display -> Spacefill; M Colour -> CPK
Click on a ligand to see its 3-letter "residue" code, assigned
in the PDB file. You can select ligands with their 3-letter
Often the PDB file contains remarks about the ligands
(open it in a text viewer, such as Wordpad or Word).
restrict not water .
Often the view is cluttered with water oxygens. (Remember,
hydrogens cannot be resolved by X-ray crystallography.) Protein
crystals are quite "wet" and gelatinous; the structures obtained from
crystals agree well with structures obtained from proteins in solution
by NMR. Most of the water molecules in crystals diffuse randomly,
making them "blurry" and invisible. The rare visible water molecules were
tightly bound and immobilized. To hide the water,
- What is the secondary structure?
- M Display -> Cartoon; M Colour -> Structure
Alpha helices are red, beta strands yellow, turns blue, and everything
else is white. Often the PDB file specifies secondary structure with HELIX
and SHEET records. If it does, RasMol obeys it. If it does not, RasMol
makes its own determination. You can force RasMol to make its own
determination with the command structure.
- Where are the N and C termini?
- M Colour -> Group (Backbone display is best for this.)
Each chain should begin blue, changing color through a rainbow series
(green, yellow, orange) and end in red. If the chain(s) is mostly blue,
M Options -> Hetero atoms (leaving Hetero Atoms unchecked),
then again M Colour -> Group.
Here are mnemonics. Synthesis begins with the old end; new residues
are added to the new end.
- Blue = cold = old (N terminus of proteins, 5' end of nucleic acids)
- Red = hot = new (C terminus of proteins, 3' end of nucleic acids)
- The amino terminus has the blue CPK color of N; the carboxy terminus,
the red CPK color of O. The 3' hydroxy terminus of nucleic acids has the
red CPK color of O.
- Where are the hydrophobic side chains?
- M Edit -> Select All; M Display -> Spacefill
- select protein; color [180,180,180]
- select protein and backbone; color [100,0,100]
- select protein and not (backbone or hydrophobic); color magenta
- Optionally select not protein; color greenblue
- The hydrogen bonding requirements of backbone atoms are
generally satisfied within the backbone. Hence backbone atoms are not
usually extensively hydrogen bonded to nonbackbone atoms. Backbone
atoms are assigned a dark (magenta) color, indicating they are weakly
hydrophilic. Hydrophobic side chains are gray to indicate their high
carbon content. Polar or charged sidechains are bright magenta to
indicate their strongly hydrophilic nature. Magenta is used to
represent a mixture of equal parts of red and blue (red for O=positive and
blue for N=negative charges or partial charges).
Large patches of hydrophobic sidechains on the surface of the protein
suggest that these regions contact something hydrophobic, rather than water.
Examples could be proteins that form multimers with each other, or proteins
that surround themselves with or bind to lipids.
- Where are the disulfide bonds?
- M Display -> Wireframe; ssbonds 0.8
- The disulfide bonds should now be visible as rods 0.8
Angstroms in radius. It may help to color ssbonds yellow.
The first ssbonds command reports the count as "Number of bridges";
if the count is zero, your molecule doesn't have any!
If you got a nonzero count, but don't see any ssbonds, you probably didn't
have the cystine-containing protein selected. Solution: M
Edit -> Select All and repeat the above commands.
- M Display -> Backbone; M Colour -> Chain
- Now only the alpha carbon positions are shown. None of the other
atoms in the cystines are shown. Since the ssbonds connect sulfur atoms
on the sidechains of cystines (not shown), the ssbonds appear to "float
in space". You can render the ssbonds as connecting the alpha carbons
of the cystines with set ssbonds backbone.
- Where are the hydrogen bonds?
- M Edit -> Select All; M Display -> Backbone;
M Colour -> Structure
- restrict helix; backbone 0; hbonds 0.5; color hbonds white
- RasMol shows only the backbone hbonds. It is not
capable of displaying hbonds between sidechains, beween chains,
between ligands and their binding sites, etc.
As with the ssbonds, the hbonds appear to be "floating in space" since
the atoms which they bond are not shown in a backbone display. The hbonds
can be schematized as linking backbone alpha carbons with:
set hbonds backbone
- Now hbonds off, and repeat the above sequence but
instead of restrict helix, substitute
restrict sheet. And again, substituting
restrict not (helix or sheet).
- Where are the interchain bonds? The ligand:protein bonds?
- As explained under hydrogen bonds, the hbonds command in
RasMol is not capable of displaying interchain hbonds. To find bonds
of all sorts between moieties, you must use the within
command, customizing the example in the section above on 1d66.pdb to your
molecule. A standard hydrogen bond has a length of 3.0 Angstroms
between the donor and acceptor atoms (for example, N and O). This is
made up of a 1.0 Angstrom covalent bond between the hydrogen and its
covalently bonded atom, plus a 2.0 Angstrom hydrogen bond between the
hydrogen and the hbonded atom. Therefore, a distance of 3.0 or generously,
3.2 Angstroms is appropriate for the within command.
Hydrophobic bonds tend to be longer (carbon to carbon), up to 4.0 Angstroms.
There is no ideal way to "paint in" an arbitrary hydrogen bond.
The best way to indicate such a bond is with the set picking
monitor command (see section above entitled "How do I find the
distance between two atoms?"). This draws a dotted line between the
atoms, optionally labeled with the distance in Angstroms. The
limitation is that you cannot make the monitor line thick (as in a
stick representation of a bond).
The above methods using the within command are
quite laborius. Therefore an automated interface has been
developed called the Noncovalent Bond Finder at
Answer to base pair question in item 10: slab 53. Inquiry from the
author of the paper (Ronen Marmorstein) revealed that the position of
cytosine 28 is in error. There is no reason to believe that this base
would be pulled out of Watson-Crick position by some unusual
interactions with neighboring moieties. The lesson is: don't believe
everything in a PDB file. Just because every atom is assigned a precise
position doesn't mean the positions are correct!