Downloading Results of ConSurf Jobs
for display in FirstGlance in Jmol,
and for
Using and Customizing the Downloaded Files.
Making Presentations Showing ConSurf Results.

Download the PDB File here for this ConSurf Job: Windows: Right-Click, Save Target/Link As. Results must be downloaded before they are removed from the server. | Contents Why download results from ConSurf? What is included in the downloaded PDB file? How to download this ConSurf result. Using your downloaded ConSurf results. Changing the conservation color scheme in your downloaded ConSurf results. Presenting ConSurf-colored molecular views.

Why download results from ConSurf?
- Downloaded ConSurf results (PDB files) can be uploaded to FirstGlance in Jmol (version 0.995 or higher, see below), which will display them exactly as they appeared after the job was completed on the ConSurf Server. This requires an Internet connection.
  - ConSurf results downloaded before FirstGlance in Jmol was installed at the ConSurf server can also be displayed by uploading them to FirstGlance in Jmol, because no change in the results file contents was needed for FirstGlance in Jmol.
- Saving your results will keep them available after they have been removed from the server. You can re-run the job, of course, but saving the results avoids the time required to set-up and re-run the job. This may be especially desirable when you wish to show the results to an audience in a presentation.
- It is relatively easy to change the conservation color scheme in a downloaded ConSurf PDB file.
  What is included in the downloaded PDB file?
- The above download link enables you to save the customized (PDB file) created in each ConSurf job.
- This single saved PDB file includes the original PDB file, plus the ConSurf job parameters and command scripts for coloring the molecule. The latter are inserted near the top of the PDB file, into its "header", in a format understood by FirstGlance in Jmol or Protein Explorer. The job parameters can be displayed from the link ConSurf Job Information available when the file is displayed in either FirstGlance in Jmol or Protein Explorer. (The format of the ConSurf results, inserted into the PDB file header, was developed for the now-obsolete Presentations in Protein Explorer (PiPEs).)
- The saved PDB file does not include ConSurf job results offered as separate files, such as "Amino Acid Conservation Scores", "Multiple Sequence Alignment", "Phylogenetic Tree", etc. which can be saved separately if you wish (using your browser's File, Save (Page) As).

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. Download from one of these two places:
   1. Follow the instructions at the top left of this page, where you will find a link for downloading.
   2. The ConSurf Job Status & Results page has a link (near the bottom) for downloading the The PDB file with ConSurf results in its Header, for FirstGlance in Jmol or Protein Explorer. In MS Windows, right click on this link, and select Save Target/Link As.
      We strongly recommend that you keep the original filename, of the form 1xxx_consurf0000000000_pipe.pdb, where "1xxx" is the PDB identification code, "0000000000" is the ConSurf job number, and the ending "_pipe.pdb" is required by Protein Explorer. These names alphabetize by PDB code, and within jobs for the same PDB code, by job number.
      Using either link listed above to save the PDB file ensures that the filename will be correct. (If you save the file directly from Jmol's menu, the filename may not be correct.)
3. The previous step saves only the visualization result and job parameters, 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". These pages can be saved separately if you wish (using your browser's File, Save (Page) As).
   Using your downloaded ConSurf results.
4. Simply go to firstglance.jmol.org, and click on Upload your own PDB file. Use the Browse button to find your saved ConSurf PDB file, and then click View in FirstGlance.
   Displaying ConSurf results requires FirstGlance in Jmol version 0.995 or higher. The version number is at the lower right, just below Jmol (the molecule). It is also shown near the bottom of the main page, in the link All About Firstglance in Jmol version X.XX.
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. Examples of such links are in the Gallery and Technical Gallery, available at FirstGlance's main page. This requires that you have an account on an HTTP server, and that you know how to use an HTML editor to make hyperlinks in an HTML document. FirstGlance includes instructions on how to format these links to specify your saved PDB files. The saved PDB files must be on an HTTP server along with your HTML page containing the links, in order to work with FirstGlance.
   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 the earlier (now obsolete) ProteinExplorer's MSA3D (in which grades 4, 5, and 6 use the same color).

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. At the top of this document is explained how to save the ConSurf results on your computer.
- You can also incorporate ConSurf-colored molecular views into presentations.

Feedback to Eric Martz.