Which is better for viewing ConSurf results,
FirstGlance in Jmol or Protein Explorer?
FirstGlance in Jmol (FGiJ) is better for most people, in most cases:

- FGiJ is easier to use.
- You don't need to install anything.
- FGiJ works in the most popular browsers on Windows, Mac OS X, and linux.
- You can present your results with static snapshots of your ConSurf results pasted into Powerpoint slides.
- FGiJ easily colors salt bridges and cation-pi orbital interactions by conservation (possible but not easy in Protein Explorer).

Protein Explorer (PE):

- Use PE when you want to make MolSlides that show rotating molecular views to present your ConSurf results. (What are MolSlides? Example of ConSurf Results presented in MolSlides using Jmol.)
- PE works only in MS Windows (including MS Windows inside OS X on an Intel Macintosh).
- PE requires that you download and install the free MDL Chime plugin.
- Making MolSlides works best in the Mozilla Firefox browser.
- In PE, you can customize the molecular view more easily than in FGiJ.
- PE shows the protein sequence, colored by conservation. (FGiJ does not.)

Both FirstGlance in Jmol and Protein Explorer

- Are easy to use, and have lots of help built-in.
- Have essentially the same control panel specialized for viewing ConSurf results.
- Enable you to find, in the 3D view, the locations of residues with specified sequence numbers or ranges.
  - In FGiJ: go to the FirstGlance control panel, and use Find...
  - In PE: click on Clickable ConSurf-Colored Sequence 3D.
- Enable you to display the close contacts (non-covalently bonded atoms) for any moiety you select, colored by conservation.
  - In FGiJ: go to the FirstGlance control panel, and use Contacts...
  - In PE: go to QuickViews. Use the SELECT menu to select something. Open the DISPAY menu and select Contacts. Use the Decorated Surface option. Be sure to check Keep present colors (to keep the ConSurf colors).
- Enable you to download your results as a ConSurf-modified PDB file, containing the ConSurf coloring scheme (as a command script inserted into the header). Thus, you can save your results for later viewing (after they are removed from the ConSurf server), without having to set up and re-run your job.
- Can display the ConSurf Job Information including the submitted job parameters and a summary of the results.

Feedback to Eric Martz.