Part 3. Chain rendering settings
Using the set of options described in this section, one can define how
each chain is to be represented. Chains can be specified
individually or in groups. Several options can be set for
the same chain, if combined rendering is needed. For
example, sticks can be overlaid with the cartoon representation.
Individual chains settings
For each chain of a macromolecular structure it is possible to specify
its rendering style and coloring scheme. In particular, a
protein chain can be shown as:
secondary structure elements formed by a chain backbone.
Wireframe when all bonds
including side chains are represented by sticks.
representing atoms as spheres of different radii
depending on an atom type.
Balls and sticks showing atoms and
chemical bonds as spheres and sticks, respectively.
surface, which is
available with the PyMol rendering program only, whereas
the use of RasMol with this setting will make chain rendered in
spherical representation (CPK).
And finally, a chain can be set to be
example if it is not of interest in context of the image.
To specify a chain to be customized, one needs to enter its label
(single character) in the corresponding text field. In the
case of unlabelled chains, a space or dash (minus) sign
should be used. Row(s) with per-chain settings will be
ignored by the server if no chain label is specified.
NOTE: use the
button to see available chain labels for a given input.
A number of coloring schemes are available for showing chains under
different perspectives. They include simple profiles, such
as hydrophobicity or temperature factors, and more complex
annotations that involve additional analysis,
e.g. evolutionary conservation profiles or mapping
interacting residues from homologous proteins to the query
Currently, the following coloring schemes are available:
By custom color − allows one
to pick a color from the color grid, and to apply it to
the corresponding chain. In addition, the selected color
is also shown in HTML format for reference.
By atom type − can be used to
color the atoms of the backbone and side chains
according to their properties.
By B-factor − shows
temperature factors optionally included in PDB files to
estimate the extent of thermal fluctuations and identify
rigid, as well as relatively flexible regions of the
structure. Note that each rendering program has its own
coloring scheme for representing temperature
factors. Moreover, many programs or web-servers use
B-factor field to encode some other information, e.g.,
conservation scores or class assignments. POLYVIEW-3D
accepts prediction results in such a way from two
(see legends below).
By conservation − invokes a
PsiBLAST run to derive multiple sequence
alignment against nr database and to
calculate the corresponding position specific
conservation scores, as defined in the
Residue highlighting settings
section. All residues within the chain are colored
according to their conservation, see the color scale below.
By interaction − performs
an automatic search for close sequence homologs of the
query chain deposited in PDB, and involved in different
types of interactions. Interacting residues with
interchain contacts are identified and mapped to the
corresponding residues of the query chain. Interacting
sites are colored according to the type of interaction
(see legend below), whereas the rest of the chain is
white. Note, that due to mapping from multiple
complexes, the same residue may be found to interact
with another protein chain or a DNA molecule, depending
on the complex.
By hydrophilicity − colors
residues by the hydrophobicity, polarity, charge and
combination of these properties, see amino acid
By acidity − discriminates
basic and acidic residues, other amino acids are colored
in white, see assignments below.
By spectrum − renders a chain
using rainbow colors with blue for N-terminus and red
By secondary structure −
colors amino acid residues according to protein
secondary structure they are in a given protein as
defined using the DSSP program. Helices are colored red,
beta-sheets are green, and coils are blue. Note that
secondary structures defined by DSSP may differ from
definitions and thus structure representations by
rendering programs (PyMol and RasMol).
To add or delete rows of per-chain settings, use the corresponding
− buttons on the
right hand side of the option text fields.
Images below demonstrate several alternative ways of rendering protein
chains along with different color schemes applied. As an
example, a high affinity protein complex between human
placental RNase inhibitor (hRI) and vessel-inducing human
angiogenin (Ang) is shown under various perspectives (PDB
id 1a4y). Panel in the middle might help
explaining the high binding affinity due to extended
|Rendering: cartoon (hRI), wireframe and CPK (Ang)
||Surface rendering (hRI) and coloring by hydrophilicity (hRI) and acidity (Ang)
||Coloring by conservation (hRI) and known interactions (Ang)
Click on respective image to see options used for its rendering.
Other chains settings
All chains not specified in individual
chain settings fall into the group called
rest chains. And the same
rendering settings, as well as coloring schemes, defined in
previous section can be applied to them as a group with a
few differences. Analog of
By custom color option is
All in same color
and allows one to shade the remaining chains down from
those of special interest using the same color. In the
case of structures with multiple chains, it is convenient
to select coloring scheme
By chain that makes
rendering programs automatically assign different colors
to each chain. NOTE:
apply their own conventions on colors when performing this
Caution should be exerted when applying coloring schemes
By conservation and
to the group
rest chains. In the case
of multichain structures, it may require a considerably
long period of time to fully process this kind of request.
Last modified: Thu Feb 9 14:02:01 EST 2012