What FirstGlance in Jmol can reveal in a
result.

Contents What are FirstGlance in Jmol and Pepitope? Changing from the Pepitope to the FirstGlance control panel -- and back. Hiding and Finding portions of the molecule. Salt Bridges and Cation-Pi Orbital interactions. Epitopes vs. contacts (non-covalent bonds) to any selected moiety. Elsewhere: Making presentations that show Pepitope results. Downloading Pepitope results to save them for later display.

What are FirstGlance in Jmol and Pepitope?
- FirstGlance in Jmol (first available Fall, 2005) is a simple tool for visualizing 3D macromolecular structure. It works on-line, in a web browser. Nothing specific needs to be installed to use it. It is free, and an open-source project. Several scientific journals and structural bioinformatics websites provide links to FirstGlance in Jmol to make it easy for their users to see protein and nucleic acid structures. Snapshots.. Interactive Gallery.. More..
  Beginning with version 1.3 (January, 2007), FirstGlance in Jmol can display Pepitope results. (Earlier, in August 2006, FirstGlance in Jmol was adapted to display results from the ConSurf Server.)
- Pepitope (first available Fall, 2006) is a free server that predicts antibody binding epitopes on the surface of the native 3D structure of a protein antigen, given one or more peptides that bind well to the antibody.
  The remainder of this document concerns the use of FirstGlance in Jmol for viewing Pepitope results.
  Changing from the Pepitope to the FirstGlance control panel -- and back.
- When you view a Pepitope result in FirstGlance in Jmol, you start at a special control panel designed to show the Pepitope result. At the bottom left is a link (Explore Further in FirstGlance in Jmol) that enables you to change to the main control panel of FirstGlance in Jmol -- the only control panel available when looking at a protein molecule that has not been processed by Pepitope.
  Once you enter the main FirstGlance in Jmol control panel, there is always a link (Pepitope Controls) near the middle of the left side that takes you back. Thus, you can move freely back and forth between the two control panels.
  FirstGlance offers you views of the molecule (unrelated to epitopes) that will help you understand the molecular structure in greater detail.
  Some of the views in FirstGlance can use the Pepitope colors, as an alternative to their usual colors. You can control which color scheme is used with the checkbox (Pepitope Colors) near the left middle.
  Hiding and finding portions of the molecule.
- In complicated molecules with many chains, it may be useful to hide some chains to simplify examination of the predicted epitopes in the chain(s) of interest.
  A Hide.. dialog is available in the FirstGlance control panel. Here, you can hide portions of the molecule by clicking on them. The hidden portions remain hidden in all other views, including views obtained at the Pepitope control panel, until you re-enter the Hide.. dialog and explicitly re-display them (or click Reset in the FirstGlance control panel).
- A Find.. dialog is available in the FirstGlance control panel. Here, you can enter sequence numbers or other designations for specific parts of the molecule, and those parts will be highlighted with gold halos. You can see the Pepitope colors clearly inside the halos. These halos persist in all other views, including views obtained at the Pepitope control panel, until you re-enter the Find.. dialog and clear the designated parts.
  Salt Bridges and Cation-Pi Orbital interactions.
- Under the Tools Tab is an option to show all salt bridges and cation-pi orbital interactions in the molecule. With a Pepitope result, these can be colored by predicted epitope. This will reveal any salt bridges or cation-pi interactions that involve residues in the predicted epitope(s).

  Portions of predicted epitopes (red and blue) in the dark gray chain are in contact with the light gray chain.

  Epitopes vs. the contacts (non-covalent bonds) to any selected moiety.
- Contacts (non-covalent bonds) to any selected moiety can easily be visualized, using the Contacts.. dialog in the FirstGlance control panel. While you select the moiety of interest (by clicking on it), the color scheme will temporarily be changed to simply color each chain differently. After you display the contacts to the selected moiety, the color scheme will automatically return to the Pepitope colors.
  A special checkbox is provided, Color Target Gray. This may make it easier to visualize the Pepitope colors in the atoms contacting the target.

Feedback to Eric Martz.