This part is to specify what
will be displayed from the whole molecule.
specify if you want or not to represent the backbone (should also work soon for nucleic acids).
specify if you want or not to represent
the side chains (should also correspond soon to the bases of the
(all that is not amino-acid
or nucleic acid). A distinction is possible between solvent (water,
some ions) and the other groups such as Hemes, lipids, etc. This fields
permit also, by specifing "Ligands", to define the representation for
the chemical compound in the case of a
specify if you want or not a
representation of the molecular surface. The "interface" facility is
display the part of the surface located at the interface of two protein
Hence there is no interface for single chain entries. This "interface" feature is still experimental.
Also, nucleic acid chains are not considered currently. The
opacity of the surface can be adjusted to allow the remaining of
the structure to be seen by
transparency. Notice that if you use transparent surface with the povray rendering engine,
this lead to a high augmentation of the computation duration.
More details on
the conventions used for the display and colouring patterns here
For each of this topics, you can choose a specific rendering mode, and
coloring pattern. I hope their names are rather self explicit. Play with
the above menu to look at differents exemples of displays representations:
Note: For each of the backbone,
side-chains, ... surface sections, you can choose None, in order to
adjust the representation use the supplementary
Charge: Presently, colouring is by residue type, no accurate
electrostatic potential calculatiuon is performed.
Hydrophobicity: TRP,ILE,MET,VAL,TYR,LEU,PHE are considered as
hydrophobic. PRO and GLY are colored according to their amino-acid
colors. Other residues are coloured as hydrophylic.
Class: Residue classes are: basic (ARG,LYS), acidic (ASP,GLU),
polar(SER,THR,TYR,HIS,CYS,ASN,GLN), aromatic (PHE,TYR,HIS,TRP),
T factor: Colouring is a funciton of the values of the
temperature factors of the PDB file. Two zones are defined: low values
and large values. For each a color gradient is established. A
supplementary color gradient is established between the colors defining
respectively the end and the beginning ot the two zones. (See the advanced parameters section).
BallnStick: Atoms are displayed using small spheres, covalent
bonds are represented by cylinders joining the atoms
Spheres: Atoms are displayed as spheres using as radius the Van
der Waals radii of the atomic types.
Trace: Only the alpha-carbons are represented. Cylinders join the
Cartoon: A high level representation of the structure, involving
splines and information about the secondary structure. Beta strand
orientation is symbolized by arrows pointing towards the C-terminus.
Lines: covalent bonds are represented by small cylinders joining
Spline: The drawing followas a beta-spline passing through the
None: No display is performed.
Atom: Each atom is coloured depending on its type (carbon,
nitrogen, oxygen, sulfur, etc).
Residue Type: The atoms of each residues are coloured depending
on the type of amino-acid (or base).
Secondary structure: Parts of the structure that correspond to
alpha-helix, beta-strand or none of these are coloured
T factor: The colours are assigned depending on the temperature
factor values specified in the PDB file. See the PDB
documentation for more explainations.
Charge: Charges are assigned on the basis of negative charges for
ASP and GLU, positive charges for LYS and ARG. A more accurate
representation based on more realistic charges can be obtained using PCE-pot.
Hydrophobicity: two classes of residues are coloured differently:
hydrophobic ("ALA,VAL,PHE,PRO,MET,ILE,LEU,TRP) and not hydrophobic
(remaining residues). In addition, PRO and GLY are coloured using the
colour of their residue types.
Class: different colors are applied for the classes of residues:
basic (ARG,LYS), acidic (ASP,GLU), polar (SER,THR,TYR,HIS,CYS,ASN,GLN),
aromatic (PHE,TYR,HIS,TRP), aliphatic (ALA,GLY,ILE,LEU,MET,PRO,VAL).
Chain: If the file contains several chains, each if coloured
Named color: A unique colour is applied.
The colours associated with each of these patterns can be modified in
the advanced parameters section.