Advanced Downloading & Customization of ConSurf Job Results
    Saving all ConSurf output:

  1. Create a folder for the files belonging to this job, such as "my_molecules/pipes/1xxx_a_consurf", where "1xxx" is the PDB identification code, and "a" is the chain specifed in the ConSurf job.

  2. Go to the (If it is no longer present on the server, you'll have to re-run the job).

  3. Use your browser's File menu to Save the Job Status page into the job folder you have created for it.

  4. Now, display each of the text-file results in turn, saving each into the job folder. (Use the links at the bottom of the Job Status page to "Amino Acid Conservation Scores", "PSI-BLAST Output", "The Homologues found by PSI-BLAST (in FASTA format)", "Multiple Sequence Alignment (in Clustal format)", "Phylogenetic Tree", etc.)

  5. Open your saved copy of "output.html" in your browser. You may want to bookmark it, or add a link to it in the file "my_molecules/pipes/mypipes.htm" (see creating mypipes.htm) using an HTML editor.

  6. The links in the Job Status page to the various text output files should now work off-line, displaying your saved copies.

  7. The link "View ConSurf Results with Protein Explorer" will not work. To make it work:

    1. Copy or move your job output pdb file into the job folder. (This is the file with a name in the format 1xxx_consurf0000000000_pipe.pdb.)

    2. Use a text editor to modify the file output.html as follows.

    3. Paste the following two lines just above the line "</head>". Note that the relative filepaths in the following examples assume that you saved your files in the path indicated in step #1 above.
      <script src="../template/pe_path.js"></script>
      <script src="../template/pstart.js"></script>

    4. Change the "href" for the link to Protein Explorer to this:
      <A HREF="javascript: start_pe('1xxx_consurf0000000000_pipe.pdb');">
      where the filename matches the actual PDB filename.

  8. If you got this far, and your saved results page is not working properly, please contact me at the feedback link (bottom of this document) with details, and I'll try to help.

    Organizing your saved ConSurf results with a page of links.

  9. 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. How you do this depends on whether you have saved only the PDB files, or all the job output files (see above).

    For PDB files only:

    1. These instructions assume you have collected the ConSurf PDB files in the folder my_molecules/pipes/my_consurfs.
    2. Copy the file my_molecules/pipes/consurf/index.htm into my_consurfs.
    3. If you have not already done so, create the file mypipes.htm in the folder my_molecules/pipes. Here are instructions.
    4. Use an HTML editor program or a plain text editor program, as you prefer, to add a link to my_consurfs/index.htm in the file my_molecules/pipes/mypipes.htm.
    5. Use your editor to change the links in my_consurfs/index.htm to go to your downloaded ConSurf PDB files. Delete what isn't applicable, add notes about your ConSurf results, etc. as you wish.
    6. Now you can access your downloaded ConSurf PDB files from the PE FrontDoor by clicking on Presentations in PE, then Examples, then My PiPEs, then the link you made there.

    For all job results:

    1. These instructions assume you followed the above instructions and put your job results files into a folder with a name of the format 1xxx_a_consurf, inside the folder my_molecules/pipes. Substitute the real name(s) of your folder(s) below.
    2. If you have not already done so, create the file mypipes.htm in the folder my_molecules/pipes. Here are instructions.
    3. You could put the links to your saved jobs in mypipes.htm. Alternatively, especially if you plan to save lots of ConSurf jobs, or create PiPEs that are not simply ConSurf results, you can create a separate HTML file just for ConSurf jobs.
        If you prefer the latter, copy the file mypipes.htm to myconsurfs.htm. Then, using an HTML editor program, make a link in mypipes.htm to myconsurfs.htm.
    4. Using an HTML editor program, make link(s) in mypipes.htm (or myconsurfs.htm) to the index.htm file(s) in your 1xxx_a_consurf folder(s).
    5. Optionally you can annotate your consurf results in mypipes.htm (or myconsurfs.htm).
    6. To access your saved ConSurf results, at PE's FrontDoor, click on Presentations in PE (right hand gray box), then Examples, then My PiPEs (and if you made a separate file myconsurfs.htm, on the link you made to that file).

    Changing the conservation color scheme.

  10. To get a clear idea what this is about, take a look at the example with an alternate color scheme on the ConSurf PiPE Examples page.

  11. In order to change the conservation color scheme, you must first download the result of the ConSurf Job (see

  12. In your downloaded ConSurf PDB file, using a plain text editor program, find the block of color definitions below. Change the hexadecimal RGB values to a color value of your choice. (The values shown below are from the alternate color scheme example above.)

  13. When displayed in PE, your ConSurf PDB file should now use the new colors in the molecular view, and also in the ConSurf-colored sequence window (ConSurf Seq3D).

  14. Optionally, you can create a color key to match your new color scheme. The easiest way to do this is to use a graphics program to change the color values in one of the color key GIF files below. Keeping the dimensions exactly the same avoids having to change the pixel values in the HTML <MAP ...> image map block.
    Standard color key (protexpl/consurf/colorkey.gif, isd.gif)

    Alternate color key (protexl/consurf/altkey.gif, altisd.gif)

    If you create a customized color key, you tell PE to use it by adding these two lines in the PiPE block of the PDB file header. Add the lines below just after the line
    !! Specify the custom consurf control panel:

    Customizing the ConSurf control panel.

  15. This can be done only in a downloaded ConSurf PDB file. Copy the file protexpl/consurf/consurf.htm to a file named altcp1.htm. Edit the HTML and javascript in altcp1.htm as you wish. Then inform PE to use the new control panel by changing the filename specified in this line in the PiPE block of the PDB file header:

Feedback to Eric Martz.