Help:Copying FirstGlance Scenes into Proteopedia

Procedure

This procedure was improved in July, 2024.

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.
• If you want to color the protein by evolutionary conservation, there are two methods:
  • 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 may obscure important parts of the conservation pattern. This is explained at Diversity in the MSA and with an example under Average Pairwise Distance.
  • You can use custom settings at the ConSurf Server to limit the MSA largely to proteins of a single function. Some examples are explained at Interpreting ConSurf Results, and the basic ConSurf Server procedure is at the ConSurf Quick Analysis Procedure.

2. 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.

3. Right-click (Mac: Ctrl-click) on or near the molecule to open JSmol'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 JSmol commands that will produce your scene.

4. Delete the load command. Edit the state script file with a plain text editor. Before you use the state script, you must the entire command at the end of the 3rd block of commands, and then save the file with that change. Delete everything shown below in red: the entire command beginning with "load", deleting everything up until the closing bracket "}" (keeping that closing bracket!). The load command may be long, wrapping onto several lines in your plain text editor.

function _setFileState() {

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

}

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

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

7. Exit load molecule mode by clicking on, for example, the selections tab. Additional options will appear below the molecule.

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

9. 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, .