Help:Copying FirstGlance Scenes into Proteopedia: Difference between revisions
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<applet load='1gpk' size='350' frame='true' align='right' caption='Selected contacts between an anti-Alzheimer's drug analog and acetylcholinesterase.' /> | <applet load='1gpk' size='350' frame='true' align='right' caption='Selected contacts between an anti-Alzheimer\'s drug analog and acetylcholinesterase.' /> | ||
1. 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. | 1. 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. | ||
Revision as of 22:09, 6 February 2010
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1. 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.
2. 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 Console.
3. Display the state script: Click the console buttons Clear Output, then State. A long Jmol command script will appear in the top box of the Console. This script describes the current state or scene in Jmol. (If you are using this as a guide to help copy scenes from other Jmol-based sources, you should note that for later versions of Jmol, such as 11.8.9, you show the state by selecting Show and then Current state from the Jmol menu that comes up under the Jmol frank. Counter-intuitively (and counter earlier versions), hittting the State button in the console presently does not show the state script.)
4. Copy the state script: Click in the top box of the Console, then Ctrl-A (Windows) or Cmd-A (Apple) to select the long script. Ctrl-C (Windows) or Cmd-C (Apple) to copy the script to the clipboard.
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 into the Jmol in the Scene Authoring Tool.
7. Open the selections tab and click the select all button.
8. Open the representations tab and click the hide selection button. This hides the molecule -- there will be nothing in Jmol.
9. Click Jmol at the lower right of Jmol, to open Jmol's menu. Click Console to open the console.
10. Paste your state script (from the clipboard) into the bottom box of Jmol's Console, and click the Execute button. Your FirstGlance scene should appear in the Scene Authoring Tool's Jmol. 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, the click Execute.
11. 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.
(An example will be provided here later.)
See the similar procedure How to Insert a ConSurf Result Into a Proteopedia Green Link.