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

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

Why download results from Pepitope?
- Downloaded Pepitope results (PDB files) can be uploaded to FirstGlance in Jmol (version 1.3 or higher, see below), which will display them exactly as they appeared after the job was completed on the Pepitope Server. This requires an Internet connection.
- 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 color scheme in a downloaded Pepitope 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 Pepitope job.
- This single saved PDB file includes the original PDB file, plus the Pepitope 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. The job parameters can be displayed from the link Pepitope Job Information available when the file is displayed in either FirstGlance in Jmol. (The format of the Pepitope 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 Pepitope job results offered as separate files, such as the lists of which peptides align with each cluster (FirstGlance in Jmol shows only the one most significant alignment for each cluster), the list of all peptides submitted, and all alignments found for each peptide. These pages can be saved separately if you wish (using your browser's File, Save (Page) As).

How to download this Pepitope result:
1. Decide where, on your computer, you want to put your downloaded Pepitope results, and create a folder (directory) for them.
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 Pepitope Job Status & Results page has a link (near the bottom) for downloading the The PDB file with Pepitope results in its Header, for FirstGlance in Jmol. 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_pepsurf0000000000_pipe.pdb, where "1xxx" is the PDB identification code, "0000000000" is the Pepitope job number, and the ending "_pipe.pdb" signifies the format of the modifications to the PDB file. 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 Pepitope Job Status Page nor the several text files linked to it (see details above).
   Using your downloaded Pepitope results.
4. Simply go to firstglance.jmol.org, and click on Upload your own PDB file. Use the Browse button to find your saved Pepitope PDB file, and then click View in FirstGlance.
5. Optionally, you can make an HTML ("web browser") page with links to your saved Pepitope 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 color scheme in your downloaded Pepitope results
- You are not limited to the colors used by Pepitope to indicate predicted epitopes. Changing this color scheme in your downloaded PDB file is relatively simple.
- In order to change the conservation color scheme, you must first download the result of the Pepitope Job (see details above).
- In your downloaded Pepitope PDB file, using a plain text editor program, find the block of color definitions below. Change the hexadecimal RGB values to color values of your choice. The carbon and phosphorus colors are used to color the backbone traces of chains that lack clusters. The "color_chain" values are applied to chains that include clusters.

      !color color_carbon C8C8C8
      !color color_sulfur FFC832
      !color color_phosphorus FFA500
      !
      !! Pepitope Cluster Colors Follow
      !!
      !color color_cluster1 FF6060 # pale red
      !color color_cluster2 8080FF # pale blue
      !color color_cluster3 FF40FF # pale magenta
      !color color_chain1 808080
      !color color_chain2 B0B0B0
      !color color_chain3 E0E0E0

- When displayed in PE, your Pepitope PDB file should now use the new colors in the molecular view.
  Presenting Pepitope-colored molecular views.
- The easiest way to present a Pepitope result is to bookmark the job result page. However, your job will remain on the Pepitope server for a limited time. At the top of this document is explained how to save the Pepitope results on your computer.
- You can also incorporate Pepitope-colored molecular views into presentations.

Feedback to Eric Martz.