Downloading Results of ConSurf Jobs.
Using and Customizing the Downloaded Files.
Making Presentations Showing ConSurf Results.

    How to download this ConSurf result:

  1. Decide where, on your computer, you want to put your downloaded ConSurf results, and create a folder (directory) for them. We recommend that this folder be named consurf/pdb_only. If you use a different folder name, substitute that name wherever consurf/pdb_only is mentioned below.
  2. Click on MDL at the lower right of the molecular image at the top of this page. On the menu that opens, select File, Save Molecule As. Save the PDB file into consurf/pdb_only.

  3. The previous step saves only the visualization result, but not the ConSurf Job Status Page nor the several text files linked to it, including "Amino Acid Conservation Scores", "PSI-BLAST Output", "The Homologues found by PSI-BLAST (in FASTA format)", "Multiple Sequence Alignment (in Clustal format)", and "Phylogenetic Tree". If you want to save these, please see

    Using your downloaded ConSurf results.

  4. The simplest way to use your downloaded ConSurf result files is to start Empty Protein Explorer (PE). You will need to use Protein Explorer version 2.78 or higher, and either a downloaded copy of PE, or Netscape 4.8 with PE on-line. (See * below for why.) Look for the Empty Explorer link on PE's FrontDoor (middle gray box). After PE has started, you will see the "Load Molecule" control panel. Use the Browse button there to select your downloaded ConSurf PDB file, then click Load.

  5. Optionally, you can make an HTML ("web browser") page with links to your saved ConSurf results. This enables you to add some description to each result, and to order the results as you wish. An example of such a page is the saved ConSurf Examples included with Protein Explorer. Please see

    Changing the conservation color scheme in your downloaded ConSurf results

    ConSurf's Color Scheme

    Color Scheme Inspired by MSA3D
  6. ConSurf uses a series of nine colors from turquoise through white through burgandy to represent conservation grades from variable through conserved, respectively. Changing this color scheme in your downloaded PDB file is relatively simple. At right is shown an alternative color scheme inspired by PE's MSA3D (in which grades 4, 5, and 6 use the same color). Please see

Presenting ConSurf-colored molecular views.

The easiest way to present a ConSurf result is to bookmark the job result page. However, your job will remain on the ConSurf server for a limited time. Below are methods for saving the results on your computer, and using them in presentations.

Changing the PE control panel used by your saved ConSurf results

Technically-savvy users will be interested to know that it is also possible to customize the control panel PE uses for ConSurf. Please see

Feedback to Eric Martz.