Help:Copying FirstGlance Scenes into Proteopedia
FirstGlance in Jmol makes it easy to obtain certain molecular scenes -- easier than generating those scenes in Proteopedia's Scene Authoring Tools. This page explains how to move those scenes into Proteopedia, attaching them to a green link.
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1. If you are already looking at the molecule in FirstGlance in Jmol, click New Session. If not, simply go to 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.
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. Open Jmol's Console: Click on the word Jmol at the lower right corner below the molecule. On the menu that opens, click Console. A new small white window will appear. It is the Jmol Script Console.
6. Write the state script: Enter "write state myscene.spt" (without the quotes) into the lower box of the Jmol Script Console. ("myscene" can be any filename. The word state must be included.) A dialog will appear in which you can choose the location on your computer's disk to save the file. This file contains a script of Jmol commands that will produce your scene.
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Mac Users: Often the state script is longer than the 10,000 characters allowed in the Java Console. In this case, perhaps the best workaround is to do this project on a Windows computer, where the Java Console is not required.
6. Edit the page in Proteopedia where you want to install the scene from FirstGlance in Jmol. Show the Scene Authoring Tool.
7. Load your molecule: Use the load molecule tab to load your PDB code into the Jmol in the Scene Authoring Tool.
8. Click the select all button below Jmol.
9. Open the representations tab and click the hide selection button. This hides the molecule -- there will be nothing in Jmol.
10. Click Jmol at the lower right of Jmol, to open Jmol's menu. Click Console to open the console.
11. Drag your blocked state script and drop it into the bottom box of Jmol's Script Console, but DO NOT press Enter or click Run yet. Also available: more detailed instructions.
12. Comment out the load command. Before you Run the state script, you must insert # before the word "load" in the command at the end of the 3rd block of commands. 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";
}
13. Run the pasted state script by clicking the Run button in Jmol's Script Console. Your FirstGlance scene should appear in the Scene Authoring Tool's Jmol. If it does not, save your state script into a text document, and attach it to an email to User:Eric Martz.
14. Use the save scene tab to save the copied scene. Follow the instructions there to insert a green link into the page to show your scene.
See the similar procedure How to Insert a ConSurf Result Into a Proteopedia Green Link.
Tweaking the Scene from FirstGlanceTweaking the Scene from FirstGlance
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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, selecting boldface, and changing the offsets to 1 and 0 (without entering any label text or clicking the set label button). Finally, .