This part is to specify what will be displayed from the whole molecule.

backbone: specify if you want or not to represent the backbone (should also work soon for nucleic acids).

side-chains: specify if you want or not to represent the side chains (should also correspond soon to the bases of the nucleic acids).

heteros (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 receptor-drug animation.

surface: specify if you want or not a representation of the molecular surface. The "interface" facility is intended to display the part of the surface located at the interface of two protein chains. 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:
Display Representation :

Note: For each of the backbone, side-chains, ... surface sections, you can choose None, in order to adjust the representation use the supplementary representations.

Coloring pattern notes:

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), aliphatic (ALA,GLY,ILE,LEU,MET,PRO,VAL).
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).

Drawing modes:

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 consecutive alpha-carbons.
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 the atoms.
Spline: The drawing followas a beta-spline passing through the alpha-carbons.
None: No display is performed.

Colouring patterns:

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 differently.
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 differently.
Named color: A unique colour is applied.
The colours associated with each of these patterns can be modified in the advanced parameters section.