-
How many chains are there?
-
Commands:
-
Backbone
color 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,
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?
-
Commands:
-
select hetero
spacefill
color 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 codes. Often the PDB
file contains remarks about the ligands (open it in a text viewer, such
as Wordpad or Word).
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,
restrict not water .
-
What is the secondary structure?
-
Commands:
-
cartoon
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?
-
Commands:
-
color 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,
set hetero off (leaving Hetero Atoms
unchecked), then again type
color 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?
-
Commands:
-
select all
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?
-
Commands:
-
wireframe;
ssbonds 0.8
-
The disulfide bonds should now be visible as rods 0.8 Angstroms in radius.
It may help to
color ssbond(s) 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:
Select All
and repeat the above commands.
Backbone
color 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 ssbond(s) backbone.
-
Where are the hydrogen bonds?
-
Commands
-
select All
backbone
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).
