Help:Copying FirstGlance Scenes into Proteopedia: Difference between revisions
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1. Be sure to start | 1. Be sure to start [[FirstGlance in Jmol]] from the''' link beneath the molecule in Proteopedia'''. This link goes to a version of FirstGlance in Jmol that uses a Jmol version matched to the version of Jmol in Proteopedia. If you go to firstglance.jmol.org, you will get an older version that will not work for copying scenes in to Proteopedia. If you upload a custom PDB file, even from the older version of ''FirstGlance in Jmol'', the uploaded model will automatically be displayed in the newer Proteopedia-compatible version of ''FirstGlance in Jmol'' (version 1.39 or higher). | ||
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. | 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. | ||
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(An example will be provided here later.) | (An example will be provided here later.) | ||
See the similar procedure [[Conservation%2C_Evolutionary#How_to_Insert_a_ConSurf_Result_Into_a_Proteopedia_Green_Link|How to Insert a ConSurf Result Into a Proteopedia Green Link]]. | |||
Revision as of 09:15, 4 June 2009
1. Be sure to start FirstGlance in Jmol from the link beneath the molecule in Proteopedia. This link goes to a version of FirstGlance in Jmol that uses a Jmol version matched to the version of Jmol in Proteopedia. If you go to firstglance.jmol.org, you will get an older version that will not work for copying scenes in to Proteopedia. If you upload a custom PDB file, even from the older version of FirstGlance in Jmol, the uploaded model will automatically be displayed in the newer Proteopedia-compatible version of FirstGlance in Jmol (version 1.39 or higher).
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 Console.
4. 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.
5. 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.
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. Open the selections tab and click the select all button.
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, 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.
12. 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.