How To Use The ConSurf Server
with FirstGlance in Jmol, July, 2026.

In July, 2026, for use with FirstGlance in Jmol, we recommend using ConSurf Colab instead of ConSurf Server. The Colab puts job parameters and additional results into its output PDB file, in a form displayed by FirstGlance. Also, Colab output uses a newer, streamlined interface in FirstGlance that lets you choose one of three color schemes (including one for color blindness).

ConSurf Server also works very well. Below are instructions on how to obtain and analyze its results in FirstGlance.

Overview:

Step By Step:
  1. Familiarize yourself with the protein structure of interest by exploring it in FirstGlance in Jmol. In particular, note the single character ID of the protein chain whose evolutionary conservation you wish to visualize. (If more than one chain of different sequences, you will need to run a separate ConSurf job for each.)

  2. At the ConSurf Server, enter a PDB ID code, or upload a .pdb or .cif file (such as an AlphaFold model). (Version 4.7 of FirstGlance can process AlphaFold .cif files, but NOT .cif files from the wwPDB.)

  3. Fill in the Job Name and your email address.

  4. Click Submit with default parameters.

  5. Bookmark or copy the URL of your job so that you can easily find your job results later.

  6. When your job finishes, click the button near the top Go To The Results

  7. Scroll down to the bottom, and click + High Resolution Figures and PDB files. Click Download ConSurf PDB File for FirstGlance in Jmol. This file can be dragged and dropped into the Front Door of FirstGlance.

  8. Insufficient Data:
    ConSurf is uniquely powerful in indicating when the multiple protein sequence alignment does not have sufficient information to calculate a meaningful conservation value for a given amino acid. When the confidence interval for the conservation score is excessive, the calculated conservation score for that residue is meaningless, and it is given conservation grade 10: insufficient data. This is obviously important to know. The only acceptable reason for hiding which amino acids have insufficient information would be if they are few, and not relevant to the point being made. "Hiding" means that the meaningless conservation grades for those amino acids will be shown. This can be accomplished by downloading a separate ConSurf result PDB or CIF file that omits insufficient data grades. When hidden, that fact must be disclosed.

    Conservation grades assigned by ConSurf are integers from 1 (highly variable) to 9 (highly conserved), with 10 (or 0) indicating insufficient data. The original ConSurf color scheme is below. Two alternative color schemes are also offered by FirstGlance when viewing ConSurf Colab results.


  9. Visualization of Conservation: Drag your downloaded ConSurf-Colab PDB file and drop it onto the Front Door to FirstGlance in Jmol. The protein chain processed by ConSurf will be automatically colored with the above scheme. You can color by evolutionary conservation all salt bridges, non-covalent contacts to any ligand or moiety that you specify, amino acids covalently linked to sugar glycosides, cysteines in disulfide bonds, amino acids forming crosslinks between chains, etc. Instructions and demonstrations:
  10. Examples:
    The following links display ConSurf Colab-processed PDB files in FirstGlance:

Feedback to