Help:Copying FirstGlance Scenes into Proteopedia: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Wayne Decatur, Eran Hodis

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 . '''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''.
-. '''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.
+. '''Write the state script into a file:''' Enter "write state myscene.txt" (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.
-.
+. '''Comment out the load command.''' Edit myscene.txt with a [[Help:Plain text editors|plain text editor]]. Before you use the state script, you must insert # before the word "load" in the command at the end of the 3rd block of commands, and then save the file with that change. This disables the command -- disabling it is crucial. It should look something like this:
-<font color="red">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.</font>
-. Edit the page in Proteopedia where you want to install the scene from FirstGlance in Jmol. Show the '''Scene Authoring Tool'''.
-. '''Load your molecule:'''
-Use the '''load molecule''' tab to load your PDB code into the Jmol in the ''Scene Authoring Tool''.
-. Click the '''select all''' button below Jmol.
-. Open the '''representations''' tab and click the '''hide selection''' button. This hides the molecule -- there will be nothing in Jmol.
-. Click '''Jmol''' at the lower right of Jmol, to open Jmol's menu. Click '''Console''' to open the console.
-. '''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: [http://wiki.jmol.org/index.php/Copying_and_pasting_scripts more detailed instructions].
-. '''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:
 <blockquote>
 function _setFileState() {
@@ Line 45: / Line 28: @@
 }</blockquote>
-. '''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]].
+. Edit the page in Proteopedia where you want to install the scene from FirstGlance in Jmol. Show the '''Scene Authoring Tool'''.
+. '''Load your molecule:'''
+Use the '''load molecule''' tab to load your PDB code (or uploaded molecule) into the signed Jmol in the ''Scene Authoring Tool''.
+. '''Drag''' the edited file myscene.txt and '''drop''' it into Jmol (where the molecule is displayed). Your scene should appear in a few seconds.
-. 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.
+. 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.
-See the similar procedure [[Help:How_to_Insert_a_ConSurf_Result_Into_a_Proteopedia_Green_Link|How to Insert a ConSurf Result Into a Proteopedia Green Link]].
+See the similar procedure .
 ==Tweaking the Scene from FirstGlance==
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 ==See Also==
-[[Copying and pasting scripts]]
+*[[Help:How_to_Insert_a_ConSurf_Result_Into_a_Proteopedia_Green_Link]]
+*[ Copying and pasting scripts]