User:Angel Herraez/Sandbox Advanced Scenes

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(importing external states into a scene)
Current revision (16:34, 16 June 2016) (edit) (undo)
 
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If you have prepared a complex visualisation in the Jmol application (or copied it from some webpage, with permission from its author) and want to incorporate it in a Proteopediia scene, this is the way:
If you have prepared a complex visualisation in the Jmol application (or copied it from some webpage, with permission from its author) and want to incorporate it in a Proteopediia scene, this is the way:
-
# Make a note of the PDB ID involved
+
# Make a note of the PDB ID involved.
-
# Prepare the model with the rendering you like
+
# Prepare the model with the rendering you like.
-
# From Jmol pup-up menu, choose <code>File > Save > Save script with state</code> --or in the console, type <code>show state</code> and copy all the output.
+
# From Jmol pop-up menu, choose <code>File > Save > Save script with state</code> --or in the console, type <code>show state</code> and copy all the output.
-
# In your Proteopedia page, open the SAT and create a new scene
+
# Edit that output (content of the state script file), find the line that starts <code>load /*file*/ </code> and delete it --or comment it out by prepending two slashes or a hash sign:
-
# Load the file by its PDB ID (this will load it from the copy at Proteopedia and prevents subsequent errors in properly handling the scene)
+
// load /*file*/
-
# Open the Jmol Script Console (via the pop-up menu in the JSmol within the SAT)
+
# load /*file*/
-
# Paste the full state script that you obtained in step #3
+
# In your Proteopedia page, open the SAT and create a new scene.
-
# Save your scene, paste its code into the page as usual, then close the SAT and test the green link in your page
+
# Load the file by its PDB ID (this will load it from the copy at Proteopedia and prevents subsequent errors in properly handling the scene).
 +
# Open the Jmol Script Console (via the pop-up menu in the JSmol within the SAT).
 +
# Paste the full state script that you obtained in step #4.
 +
# Fix any problems that you may see in the rendering (if ti does not look exactly like you intended).
 +
# Save your scene, paste its code into the page as usual, then close the SAT and test the green link in your page.

Current revision

How to import Jmol renderings prepared outside Proteopedia into a scene

(For advanced users that are proficient in Jmol scripting out of Proteopedia)

If you have prepared a complex visualisation in the Jmol application (or copied it from some webpage, with permission from its author) and want to incorporate it in a Proteopediia scene, this is the way:

  1. Make a note of the PDB ID involved.
  2. Prepare the model with the rendering you like.
  3. From Jmol pop-up menu, choose File > Save > Save script with state --or in the console, type show state and copy all the output.
  4. Edit that output (content of the state script file), find the line that starts load /*file*/ and delete it --or comment it out by prepending two slashes or a hash sign: 
// load /*file*/ 
#  load /*file*/
  1. In your Proteopedia page, open the SAT and create a new scene.
  2. Load the file by its PDB ID (this will load it from the copy at Proteopedia and prevents subsequent errors in properly handling the scene).
  3. Open the Jmol Script Console (via the pop-up menu in the JSmol within the SAT).
  4. Paste the full state script that you obtained in step #4.
  5. Fix any problems that you may see in the rendering (if ti does not look exactly like you intended).
  6. Save your scene, paste its code into the page as usual, then close the SAT and test the green link in your page.

Proteopedia Page Contributors and Editors (what is this?)

Angel Herraez

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