This scheme is adopted for almost all images generated with RasMol, InsightII, WebLab
and MolScript. There are, however, a few MolMol, Setor
and Sybyl images, where carbon is colored gray and phosphorus
is not colored magenta
.
ATP-gammaS spacefill representation with MolMol. Moving the mouse pointer over the molecule switches between the two coloring schemes.
Residue Coloring Scheme
Residues are color-coded according to the scheme originally used by the
program SETOR written by Stephen Evans.
Residue coloring scheme. When moving the mouse pointer over the figure a part of a nucleic acid structure with an AT and a GC base pair is shown.
Secondary Structure Elements Coloring and Drawing
Alpha-helices are either drawn as cylinders or as ribbons. The
preferred color used in most cases is red (RasMol, InsightII, WebLab). MolScript
and MolMol draw helices as ribbons with a different outside
(red) and inside (yellow) coloring. Beta-strands are colored
blue (RasMol, InsightII, WebLab) or cyan (MolScript, MolMol). A
few graphics programs color turns in yellow (MolScript, RasMol, InsightII).
The MHC class I binding groove, built by alpha-helices and a beta-sheet
on the bottom, is shown complexed with a stretched peptide (MolMol
image from part of the MHC structure, PDB code: 1A1N). Moving the mouse pointer over the figure shows a secondary structure representation of the same structure generated with MolScript and with turns colored in yellow.
Secondary Structure Determination
Secondary
structure information is often but not always included with the
coordinate files from the NDB and PDB. RasMol, MolMol, InsightII, Midas
and Setor use the PDB secondary structure information if there
is any.If
there are no secondary structure information records provided with the
coordinate file, then the secondary structure assignment is calculated
according to the Kabsch and Sander DSSP algorithm. MolScript
and WebLab do not use the PDB secondary structure information
at all, but calculate this information in all cases. Moreover, some
programs cannot display very short helices (3 amino acids).
Warning:This may lead to slightly different secondary
structure representations for one and the same structure.
Different secondary structure determination (MolMol and MolScript
images of plastocyanin, PDB code: 1PLC)
Active Sites and Disulfide Bonds
Sites as defined in the coordinate file are displayed as ball and
sticks by MolScript or sticks only by RasMol and MolMol.
Disulfide bonds are displayed if there are SS bond records in the
coordinate file. They are shown as lines by MolScript, RasMol
or MolMol. However, older MolMol representations do not
display SS bonds. SS bonds are often not shown in InsightII, Midas
and WebLab images. Setor and Prepi adopt a
cartoon-like representation of SS bonds.
The trypsin catalytic site amino acids His57
, Asp102 and Ser195 are
shown as thick sticks, the thin lines are disulfide bonds (image
generated with MolMol, PDB code: 1SGT). Moving the mouse pointer over the figure shows a secondary structure representation of the same structure generated with MolScript with ball and stick representation of the active site.
Ligands, Modified Residues, Ions
The heterogen section of the PDB file header defines 'non-standard'
residues, such as modified amino acids or nucleotides, prosthetic
groups, inhibitors, metal ions and solvent components. Non-standard
residues are shown as spacefill representation in RasMol, MolScript
and MolMol images . For more detailed information see
the PDB Contents Guide (PDF format). The nucleotide I (inosine) and the modified nucleotides
+C, +G, +A, +T, +U, +I are considered as standard residues according to
the PDB definition. They are, however, treated in a different way by RasMol
and MolScript. RasMol displays these nucleotides as
sticks and in MolScript images the base plates are drawn in the
same color as the "mother" nucleotide but contrary to C, G,
A, T, U, I the lines are colored in an atom-specific manner.
Atom Coloring Scheme
