Cartoon
This representation is a general overview of the molecule and highlights the important aspects of secondary structure. The helices, sheets and loops are all assigned a cartoon representation and are colored; helices in red, sheets in yellow and loops in cyan. If DNA and/or RNA are present in the molecule, they are colored green. Any ligands present are set to display as spheres and are colored according to the CPK system.
Color by Chain
PDB files include information regarding the different chains found in the structure. In this preset, the chain information is utilized in a way such that each chain is assigned a different color, allowing them to stand out to the user.
Ball and Stick
This preset shows a classic ball and stick view similar to those used in high school chemistry classes. DNA and RNA are colored with the CPK color palette and are represented with ball and sticks on a ribbon.
Surface
This shows a solvent accessible surface placed over the molecule, colored according to the CPK scheme.
Hetero Atoms
The purpose of this preset is to clearly display the presence of hetero atoms, also known as “ligands”, in the molecule. T hese atoms are shown in a sphere representation. T he interaction between the hetero atoms and the molecule are displayed by showing sticks in the surrounding regions. T he remainder of the molecule is made transparent, so the ligands and surrounding sticks can be visualized better.
Polarity
This view is similar to the surface view. Colors are applied to differentiate hydrophilic residues from hydrophobic residues, using red for hydrophobic and blue for hydrophilic. DNA and RNA, if present in the molecule, are displayed as a ribbon. The ligands will also be shown as spheres and colored green.
Aromatics
The protein is viewed as a transparent cartoon, and aromatic residues are colored red and shown as sticks.
Putty View
The name “Putty” refers to the type of cartoon representation being used. Aside from the different cartoon type and lacking ligands, this view is identical to the default.
DNA and RNA
This shows the protein as a grey colored cartoon, and colors all nucleic acid according to a certain scheme. The nucleic acid coloring key pops up in a window and stays in the forefront while the protein can be manipulate. Each base has a distinct bright color, corresponding with the standard coloring scheme, and stands out from the grey protein around it.
Chain Contact
Chain contact shows the protein as a mesh and then colors the regions of interaction between the chains in the CPK coloring scheme.
Show Charged
Shows the protein as a gray cartoon and shows the charged amino acids as sticks. The negative amino acids are colored red and the positive amino acids are colored blue.
Surface Cartoon
The protein is shown as a cartoon, over which a transparent surface is shown.
Surface on Sticks
The protein is shown as a sticks, over which a transparent surface is shown.
Surface on Spheres
The protein is shown as a spheres, over which a transparent surface is shown.
Mesh on Sticks
The protein is shown as sticks, over which a blue mesh surface is shown.
Dots on Lines
The protein is shown as lines, over which a dot surface is shown.
Lines on Cartoon
Shows the protein as a cartoon, over which lines for the individual amino acids are shown.
CPK
Shows the protein as spheres in their Van der Waals radii and colored in the CPK coloring scheme.