Structure Home Graphics Intro PDB Database SpdbV Manual
1: Get PDB 2: Look at it 3: Make dimer 4: Display 5: View maps

Bioc585 - Graphics Example

The purpose of this exercise of viewing a protein structure is to acquaint you with one scheme at obtaining structural information for your possible research questions. We will be using a free graphics program, Swiss PDB Viewer, available for Win/Tel, Mac, and Unix platforms, but there are numerous other graphics programs available. Differing programs have differing functions and specializations. So, you may want to acquaint yourself with a few of the software packages available.

The example consists of these steps:

  1. Retrieving the structural information from either a structural biologist collaborator, or a structural database.
  2. Looking at the contents (text) of the structure file.
  3. Creating the biologically relevant molecule.
  4. Displaying the structural information graphically and addressing some typical beginning questions.
  5. Viewing electron density for the model; one step closer to the experimental data.

To begin this local example, click on either the first word of any step, or use the navigation bar at the top of the page. The discussions of the steps are for non-specific platforms; in other words, the exact menu item and steps may be a bit different depending on if you are using a NT box, a Mac, or an Unix box. If you encounter difficulty ask Bryan for help.