ConSurf Results Download

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:

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?
Using your downloaded ConSurf results.
Presenting ConSurf-colored molecular views.
Changing the conservation color scheme in your downloaded ConSurf results.

Why download results from ConSurf?

Downloaded ConSurf results (PDB files) can be uploaded to FirstGlance in Jmol, which will display them exactly as they appeared after the job was completed on the ConSurf Server.
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.
Re-running the job may give slightly different results depending on the time elapsed between runs, due to growth of the sequence databases, and improvements in the ConSurf Server.
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. The job parameters can be displayed from the link ConSurf Job Information available when the file is displayed in either FirstGlance in Jmol. (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 using the button Download all files at the original results page on the ConSurf Server.

Using your downloaded ConSurf results.
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.

Presenting ConSurf-colored molecular views.
FirstGlance makes it easy to save animations or high-resolution static images of any view, including views of ConSurf results, in files ready to drop into your slides (GIF files for animations, PNG files for static images). Instructions.
Alternatively, you can simply bookmark the ConSurf job result page to display in a browser during your presentation. 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.

Changing the conservation color scheme in your downloaded ConSurf results

ConSurf's Color Scheme

Color Scheme Inspired by MSA3D
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 (no longer available) MSA3D in Protein Explorer (in which grades 4, 5, and 6 use the same color).

At the ConSurf Server, you can also download a FirstGlance-compatible PDB file with an alternative color scheme that is color-blind friendly.

The color scheme is specified in the PDB file downloaded from ConSurf using RGB (red green blue) color codes. Each code has three, 2-digit hexadecimal values. Examples: red is FF0000, white is FFFFFF, black is 000000, blue is 0000FF, magenta is FF00FF, and a middle-gray is 808080. Below is ConSurf's standard color scheme as it is encoded in the PDB file downloaded from ConSurf. You can change the color scheme by editing the RGB values in the PDB file with a plain text editor. Then upload the edited PDB file to FirstGlance.
```
!! Ten ConSurf color grades follow:
!!
!color color_grade0 FFFF96 insufficient data yellow
!color color_grade1 10C8D1 turquoise variable
!color color_grade2 8CFFFF
!color color_grade3 D7FFFF
!color color_grade4 EAFFFF
!color color_grade5 FFFFFF white average
!color color_grade6 FCEDF4
!color color_grade7 FAC9DE
!color color_grade8 F07DAB
!color color_grade9 A02560 burgundy conserved
```

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