Help:Copying FirstGlance Scenes into Proteopedia

Procedure

1. View the molecule in FirstGlance.

• If the molecule has a PDB code, search for the page titled with that PDB code in Proteopedia. At that page, click on the link to FirstGlance beneath the molecule, in the Resources block.
• Or, simply go to firstglance.jmol.org and enter the PDB code.
• If the model does not have a PDB code (e.g. a homology model), upload the PDB file at firstglance.jmol.org.

2. Use the small link at the bottom "Advanced Options", and on that page check Use the signed Jmol applet. Using the signed applet is essential.

3. Load the appropriate molecule into FirstGlance, giving the signed applet permission to operate. To the lower right of the molecule, instead of seeing Jmol, you should see Jmol_S, confirming that the signed applet is being used.

4. Obtain the desired scene in FirstGlance in Jmol. Turn off spinning (even if you want it to spin in Proteopedia), and orient and zoom the molecule as you want it to appear initially.

5. Click on Jmol_S to open Jmol's menu. Select File, Save script with state. A dialog will appear in which you can choose the location on your computer's disk to save the file. Take note of the name of the file and where you are putting it. This file contains a state script of Jmol commands that will produce your scene.

6. Comment out the load command. Edit the state script file with a plain text editor. Before you use the state script, you must insert # before the word "load" in the command at the end of the 3rd block of commands, and then save the file with that change. This disables the command -- disabling it is crucial. It should look something like this:

function _setFileState() {

  set allowEmbeddedScripts false;
  ... blah blah blah ...
  set smartAromatic true;
  #load /*file*/"http://www.rcsb.org/pdb/cgi/export.cgi/1GPK.pdb.gz";

}

7. Edit the page in Proteopedia where you want to install the scene from FirstGlance in Jmol. Show the Scene Authoring Tool.

8. Load your molecule: Use the load molecule tab to load your PDB code (or uploaded molecule) into the signed Jmol in the Scene Authoring Tool.

9. Drag the edited state script file and drop it into Jmol (where the molecule is displayed). Your scene should appear in a few seconds.

10. Use the save scene tab to save your scene. Follow the instructions there to insert a green link into the page to show your scene.

Tweaking the Scene from FirstGlance

1gpk was displayed in FirstGlance in Jmol. were visualized in FirstGlance in Jmol using the Contacts.. and Hide.. dialogs, simply by clicking on controls. The scene was transferred into Proteopedia using the above procedure.

Then, in Proteopedia's SAT, the by clicking select all, then in the labels dialog, reducing the size to 12^[1], changing the color to orange, and changing the offsets to 1 and 1 (all without entering any label text or clicking the set label button). Finally, .