First time at Proteopedia? Click on the green links: they change the 3D image. Click and drag the molecules. Proteopedia is a 3D, interactive encyclopedia of proteins, RNA, DNA and other molecules. With a free user account, you can edit pages in Proteopedia. Visit the Main Page to learn more.

From Proteopedia

Please see Conservation, Evolutionary for an introduction and overview to this topic.

Examples

Articles in Proteopedia that contain a ConSurf scene include:

• Avian Influenza Neuraminidase, Tamiflu and Relenza
• Lac repressor
• Mechanosensitive channels: opening and closing
• Molecular Playground/Hexameric ClpX
• Nitrogenase
• Structure of E. coli DnaC helicase loader
• Triose Phosphate Isomerase

Procedure

The procedure below assumes that you have obtained a ConSurf result that you wish to display from a green link in an article in Proteopedia.

It is possible to create a green-linked scene with a molecule colored by evolutionary conservation simply by using the button "evolutionary conservation" in the "color" tab of the Molecular Scene Authoring Tools. However, as explained in Caveats, this pre-calculated color scheme often obscures important parts of the conservation pattern. (See also ConSurfDB_vs._ConSurf).

More likely, you will want to follow the instructions in ConSurfDB vs. ConSurf in order to limit the conservation analysis to proteins of a single function, thereby revealing all conservation relevant to that function. If you have obtained such a result, here is how to attach it to a green link in Proteopedia.

1. Using either the ConSurf Database or the ConSurf Server, obtain the desired result.
2. At the ConSurf result page, use the link RasMol Coloring Script to display either the script showing or hiding insufficient data. Block and copy the entire script.
3. We assume that you already have an article in Proteopedia, with a Jmol applet in place for displaying your ConSurf result. (If not, see the Video Guides and Help:Editing.)
4. Edit your Proteopedia page, and open the Scene Authoring Tools.
5. Load the desired molecule into Jmol in the Scene Authoring Tools.
6. Click on "Jmol" (at the lower right of Jmol) to open Jmol's menu, and there, click on '"Console'".
7. In the small white Console window, paste your RasMol Coloring Script into the bottom box, and click Execute. On Mac OS X, you may be unable to paste into the Console. In that case, drag the blocked script and drop it into the bottom box of the Console, then click Execute.
8. Make any other changes you wish to this scene, and then save the scene.
9. Copy the wikitext for the green link that will display your scene, and close the Scene Authoring Tool.
10. Paste the green link wikitext into your page, and save the page.

The color key that you see at the very top of this page can be inserted in any page using this wikitext:

{{Template:ColorKey_ConSurf}}

See also Help:Color_Keys for other variations on the color key. If something is not clear, please let us know at .

See Also

• Evolutionary Conservation
• ConSurfDB vs. ConSurf: How the servers work and how to get optimal results from ConSurf.
• Help:Copying FirstGlance Scenes into Proteopedia.