Guide to Understanding PDB Data
Introduction
PDB Overview
Protein Hierarchical Structure
Beginner’s Guide to PDBx/mmCIF
Missing Coordinates and Biological Assemblies
Dealing with Coordinates
Primary Sequences
Biological Assemblies
Computed Structure Models
Small Molecule Ligands
Exploring Carbohydrates
Methods for Determining Structure
Crystallographic Structure Factors and Electron Density, Resolution, and R-value
Molecular Graphics Programs
Introduction to RCSB PDB APIs

Molecular Graphics Programs

Biomolecular structures are complex, consisting of hundreds or thousands of atoms. Over the years, researchers have developed a variety of molecular graphics methods to display protein structures to make it easier to study and explore their properties. These molecular graphics programs allow you to upload a PDB file, display the structure on your computer, and create custom pictures of it. In addition, they often include analysis tools that allow you to measure distances and bond angles, and identify interesting structural features.

Several molecular graphics programs are available directly from the Structure Summary page for each PDB entry. These programs give slightly different options, and allow different levels of control. Spend a few minutes and try each one to find which one fills your needs the best. Mol* was used to create the pictures shown here.

There are also many advanced molecular graphics programs that use sophisticated methods to create high-quality images and images of complex molecular properties like electrostatics and dynamics. Take a look at this list of Molecular Graphics Software for ideas.

What does a protein or nucleic acid look like?

Proteins and nucleic acids are composed of a collection of atoms bonded together in specific arrangements. Since they are far too small to see with light, we need to devise artificial ways of representing them. Researchers have developed several ways to do this, each way highlighting different aspects of the structure.

Three main types of pictures are shown:

  1. Ball and Stick Diagrams (shown at the left in the figure). For these images, a stick represents each of the covalent bonds formed between the atoms and small balls are used to represent the atoms. Atoms are generally colored by type: carbon in green, oxygen in red, and nitrogen in blue.
  2. Spacefilling Diagrams (shown in the middle). For these images, a sphere is drawn around each atom, showing the relative size of the atom. Here, atoms are colored as they are in the ball-and-stick image.
  3. Backbone and Ribbon Diagrams (shown on the right). These images highlight the way a protein chain folds. The simplest ones draw a tube that connects the positions of each amino acid. Ribbon diagrams add two special representations: a spring-shaped ribbon for alpha helices and a flat arrow that shows beta strands. The familiar ladder diagram is used for nucleic acids, with a smooth ribbon for the backbone and rungs for the bases.

Different representations are good for different uses, and when you are looking at a structure, such as the phosphoglycerate kinase structure shown here (PDB entry pdb_00003pgk), it is often good to try several different representations and find the best one for a given task. Wireframe and ball-and-stick diagrams are great if you want to look at the details of a protein structure, such as the way an active site works or the way metal ions are coordinated. Spacefilling diagrams are good if you are interested in seeing how different proteins interact with one another--they show the overall shape and size of a protein. For instance, all three of these images have been created at the same magnification--notice how the bond and ribbon diagrams might lead you to underestimate the size of the protein. Ribbon and backbone diagrams are useful when you are thinking about protein folding, and comparing the similarities in folding between different proteins.

Selection and Coloring

Since proteins are so complicated, molecular graphics programs often give you lots of options to select and color portions of a molecule, so you can customize your picture. In this way, you can display and highlight the parts that interest you, and ignore all the rest. Here are a few techniques that are useful:

To get an overall view of a protein, its fold, and its ligands, display the protein as a ribbon and the ligands as balls and sticks. For example, this image shows hemoglobin (PDB entry pdb_00002hhb), which is composed of four protein chains, each with a heme group. Notice that each protein chain is colored differently to highlight the different portions of the molecule and allow exploration of the quaternary structure of the entry. The heme groups are shown as balls and sticks. You can see water molecules shown as balls as well. This is the default representation used by Mol*.
To highlight the folding of the chain the protein can be colored by Sequence ID. Here the backbone atoms of the polymer are colored by the order in which they appears in the polymer sequence from the N-terminal end (red) to the C-terminal end (blue/violet). The residues in between are colored according to the colors of the rainbow.
To explore the interaction of a ligand with the protein you can zoom to see exactly what is happening. In this picture, the heme group (pink) is interacting with a histidine (red) of one of the hemoglobin chains through coordination with the iron (gray sphere) atom. Notice that the iron atom is pulled towards the histidine out of the plane of the heme.