Help:Copying FirstGlance Scenes into Proteopedia
This procedure applies to any situation where a website provides tools for obtaining a desired molecular scene in the Jmol applet, that you wish to transfer into Proteopedia.
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1. Mac users only: Open the Java Console. This is different from the Jmol Scripting Console. For instructions, please see these instructions. (Not necessary for Windows users.)
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. 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.
4. Display the state script: Click the console button Clear Output. Now type into the lower box of the Jmol Script Console the command show state, and press Enter. (The State button does not work as intended in some versions of Jmol.) A long Jmol command script will appear in the top box of the Console. This script describes the current state or scene in Jmol. This may also work: select Show and then Current state from the Jmol menu that comes up under the Jmol frank.
5. Obtain the state script: Instructions differ between Windows and Macs. Follow the details explained in Copying and pasting scripts.
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. Paste your state script (from the clipboard) into the bottom box of Jmol's Console, but DO NOT press Enter or click Run yet. On Mac OS X, paste with Ctrl-V instead of Cmd-V, but DO NOT press Enter of click Run yet.
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, which is required. 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 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, .