Copying and pasting scripts - Revision history

AngelHerraez: clarify: block = highlight

2012-10-05T13:57:05Z

clarify: block = highlight

EricMartz: /* Obtaining the State Script */

2011-10-01T20:07:26Z

‎Obtaining the State Script

EricMartz at 19:39, 29 September 2011

2011-09-29T19:39:19Z

EricMartz at 19:37, 29 September 2011

2011-09-29T19:37:58Z

EricMartz: /* MS Windows */

2011-09-29T18:59:16Z

‎MS Windows

EricMartz: /* Executing the State Script */

2011-09-29T17:58:33Z

‎Executing the State Script

EricMartz: /* Obtaining the State Script */

2011-09-29T17:56:27Z

‎Obtaining the State Script

EricMartz: /* Obtaining the State Script */

2011-09-29T17:55:57Z

‎Obtaining the State Script

EricMartz: /* Obtaining the State Script */

2011-09-29T17:54:34Z

‎Obtaining the State Script

EricMartz: /* Obtaining the State Script */

2011-09-29T17:49:24Z

‎Obtaining the State Script

@@ Line 12: / Line 12: @@
 The following methods have been tested in Leopard OS 10.5.8 (Java 1.5.0_30) and Lion OS 10.7 (Java 1.6.0_26).
-;Summary: Block the state script in the Java Console, then drag and drop it into the Jmol Script Console.
+;Summary: Block (highlight) the state script in the Java Console, then drag and drop it into the Jmol Script Console.
 ====Obtaining the State Script====
 <font color="red">Caution: this procedure often fails: see the red paragraph below.</font>
@@ Line 24: / Line 24: @@
 <b>Display the desired molecular scene</b>, with both the Java and Jmol Consoles open. Click the "Clear" button in the Java Console. Enter the command <i>'''show state'''</i> in the bottom box of the Jmol Console. This will display a long state script in both Consoles.
-'''Block the state script in the Java Console''', starting with the line <i># Jmol state ...</i> (omit lines before that one!), and ending with the line <i>_setState;</i>.  You cannot paste the state script into the destination Jmol Script Console -- you must drag and drop it there. It is possible to drag directly from the Java Console but you need to have the recipient Jmol Script Console ready. So, to facilitate the drag-and-drop operation, we recommend that you copy the state script (Cmd-C) from the Java Console, and then paste it into a plain text document file for safekeeping. Plain text editors are TextEdit (bundled with your Mac OS X system, in Applications), or the free TextWrangler from [http://barebonessoftware.com BareBonesSoftware.Com].
+'''Block (highlight) the state script in the Java Console''', starting with the line <i># Jmol state ...</i> (omit lines before that one!), and ending with the line <i>_setState;</i>.  You cannot paste the state script into the destination Jmol Script Console -- you must drag and drop it there. It is possible to drag directly from the Java Console but you need to have the recipient Jmol Script Console ready. So, to facilitate the drag-and-drop operation, we recommend that you copy the state script (Cmd-C) from the Java Console, and then paste it into a plain text document file for safekeeping. Plain text editors are TextEdit (bundled with your Mac OS X system, in Applications), or the free TextWrangler from [http://barebonessoftware.com BareBonesSoftware.Com].
 <font color="red">Unfortunately, the state script is often longer than the 10,000 bytes allowed in the Java Console. If this happens, perhaps the best workaround is to do the entire project on a Windows computer, where the Java Console is unnecessary (see below).</font>
@@ Line 31: / Line 31: @@
 To execute (run) the state script, you first need to open the Jmol Script Console (see above) in the web page where you want to generate the desired molecular scene.
-In all cases, you need to '''drag''' the blocked state script, and '''drop''' it into the bottom box (command/script entry box) of the Jmol Script Console that belongs to the target applet. You cannot paste it!
+In all cases, you need to '''drag''' the blocked (highlighted) state script, and '''drop''' it into the bottom box (command/script entry box) of the Jmol Script Console that belongs to the target applet. You cannot paste it!
 In simple cases (where the source scene and target scene are on the same server) you may be able to run the state script unmodified.
@@ Line 40: / Line 40: @@
 The following methods have been tested in Windows XP with Java 1.6.0_26, in both Firefox and Internet Explorer.
-;Summary: Block the state script in the Jmol Script Console, and drag/drop it into a temporary text file, or into the Jmol Script Console belonging to the target Jmol applet.
+;Summary: Block (highlight) the state script in the Jmol Script Console, and drag/drop it into a temporary text file, or into the Jmol Script Console belonging to the target Jmol applet.
 ====Obtaining the State Script====
@@ Line 49: / Line 49: @@
 In the Jmol Script Console, click the button at the bottom ''Clear Output''. Now type '''show state''' in the bottom box, and press Enter.
-Click in the top box of the Jmol Script Console, and Ctrl-A to '''block the entire state script'''.
+Click in the top box of the Jmol Script Console, and Ctrl-A to '''block (highlight) the entire state script'''.
-If the target Jmol applet's Jmol Script Console is available, you can now drag the blocked state script into the bottom box. (It is sometimes possible to copy (Ctrl-C) the state script and paste it (Ctrl-V) into the bottom box of the target Jmol Script Console, but this may not always work.)
+If the target Jmol applet's Jmol Script Console is available, you can now drag the blocked (highlighted) state script into the bottom box. (It is sometimes possible to copy (Ctrl-C) the state script and paste it (Ctrl-V) into the bottom box of the target Jmol Script Console, but this may not always work.)
-To avoid frustration, we recommend that you '''save the state script in a plain text file'''. Drag the blocked state script into a [http://www.proteopedia.org/wiki/index.php/Help:Plain_text_editors plain text editor], or paste it, and save it in a plain text file for safekeeping. Later, you can open this file and either copy or drag the blocked script into the target Jmol Script Console.
+To avoid frustration, we recommend that you '''save the state script in a plain text file'''. Drag the blocked (highlighted) state script into a [http://www.proteopedia.org/wiki/index.php/Help:Plain_text_editors plain text editor], or paste it, and save it in a plain text file for safekeeping. Later, you can open this file and either copy or drag the blocked (highlighted) script into the target Jmol Script Console.
 ====Executing the State Script====
 To execute (run) the state script, you first need to open the Jmol Script Console (see above) in the web page where you want to generate the desired molecular scene.
-In all cases, you need to '''drag''' the blocked state script, and '''drop''' it into the bottom box (command/script entry box) of the Jmol Script Console that belongs to the target applet. Alternatively, you may be able to copy and paste the state script, but this has not always worked.
+In all cases, you need to '''drag''' the blocked (highlighted) state script, and '''drop''' it into the bottom box (command/script entry box) of the Jmol Script Console that belongs to the target applet. Alternatively, you may be able to copy and paste the state script, but this has not always worked.
 In simple cases (where the source scene and target scene are on the same server) you may be able to run the state script unmodified.

@@ Line 14: / Line 14: @@
 ;Summary: Block the state script in the Java Console, then drag and drop it into the Jmol Script Console.
 ====Obtaining the State Script====
 The state script cannot be obtained from the Jmol Script Console, but it can be copied or dragged from the Java Console. So first you need to <b>open the Java Console</b>. Run <i>Java Preferences</i> (in Applications:Utilities). Under the <i>Advanced</i> tab, check <i>Java Console: Hide Console</i>.
@@ Line 23: / Line 25: @@
 '''Block the state script in the Java Console''', starting with the line <i># Jmol state ...</i> (omit lines before that one!), and ending with the line <i>_setState;</i>.  You cannot paste the state script into the destination Jmol Script Console -- you must drag and drop it there. It is possible to drag directly from the Java Console but you need to have the recipient Jmol Script Console ready. So, to facilitate the drag-and-drop operation, we recommend that you copy the state script (Cmd-C) from the Java Console, and then paste it into a plain text document file for safekeeping. Plain text editors are TextEdit (bundled with your Mac OS X system, in Applications), or the free TextWrangler from [http://barebonessoftware.com BareBonesSoftware.Com].
 ====Executing the State Script====

@@ Line 3: / Line 3: @@
 Example 1: Certain molecular scenes are generated much more easily in [http://firstglance.jmol.org FirstGlance in Jmol] than elsewhere (e.g. showing contacts to a ligand). Such a scene can be reproduced in [http://proteopedia.org Proteopedia.Org] by generating the state script in FirstGlance, and executing it in Proteopedia's molecular Scene Authoring Tools (see [http://www.proteopedia.org/wiki/index.php/Help:Copying_FirstGlance_Scenes_into_Proteopedia instructions]).
-Example 2: After you color a protein by evolutionary conservation using [http://consurf.tau.ac.il ConSurf], you may wish to install that color scheme in a Proteopedia page. This is a bit easier than the steps below: see [http://www.proteopedia.org/wiki/index.php/Help:How_to_Insert_a_ConSurf_Result_Into_a_Proteopedia_Green_Link How to insert a ConSurf result into a Proteopedia green link].
+Example 2: After you color a protein by evolutionary conservation using [http://consurf.tau.ac.il ConSurf], you may wish to install that color scheme in a Proteopedia page. This is a bit easier than the steps below because the requisite script can be copied from a web page. (It is not a ''state script''.) Step by step instructions are here: [http://www.proteopedia.org/wiki/index.php/Help:How_to_Insert_a_ConSurf_Result_Into_a_Proteopedia_Green_Link How to insert a ConSurf result into a Proteopedia green link].
 [http://www.proteopedia.org/wiki/index.php/Java Java] presents some technical obstacles to copying and pasting scripts. Below are described known workarounds.

← Older revision		Revision as of 19:37, 29 September 2011
Line 1:		Line 1:
−	Jmol [[Scripting\|scripts]] are groups of Jmol [http://chemapps.stolaf.edu/jmol/docs/ commands] that, when executed in Jmol, produce a desired molecular scene. Sometimes it is useful to obtain a script from one place, and run it in Jmol somewhere else. ~~For example, certain~~ molecular scenes are generated much more easily in [http://firstglance.jmol.org FirstGlance in Jmol] than elsewhere (e.g. showing contacts to a ligand). Such a scene can be reproduced in [http://proteopedia.org Proteopedia.Org] by generating the state script in FirstGlance, and executing it in Proteopedia's molecular Scene Authoring Tools (see [http://www.proteopedia.org/wiki/index.php/Help:Copying_FirstGlance_Scenes_into_Proteopedia instructions]).	+	Jmol [[Scripting\|scripts]] are groups of Jmol [http://chemapps.stolaf.edu/jmol/docs/ commands] that, when executed in Jmol, produce a desired molecular scene. Sometimes it is useful to obtain a script from one place, and run it in Jmol somewhere else.
		+
		+	Example 1: Certain molecular scenes are generated much more easily in [http://firstglance.jmol.org FirstGlance in Jmol] than elsewhere (e.g. showing contacts to a ligand). Such a scene can be reproduced in [http://proteopedia.org Proteopedia.Org] by generating the state script in FirstGlance, and executing it in Proteopedia's molecular Scene Authoring Tools (see [http://www.proteopedia.org/wiki/index.php/Help:Copying_FirstGlance_Scenes_into_Proteopedia instructions]).
		+
		+	Example 2: After you color a protein by evolutionary conservation using [http://consurf.tau.ac.il ConSurf], you may wish to install that color scheme in a Proteopedia page. This is a bit easier than the steps below: see [http://www.proteopedia.org/wiki/index.php/Help:How_to_Insert_a_ConSurf_Result_Into_a_Proteopedia_Green_Link How to insert a ConSurf result into a Proteopedia green link].

	[http://www.proteopedia.org/wiki/index.php/Java Java] presents some technical obstacles to copying and pasting scripts. Below are described known workarounds.		[http://www.proteopedia.org/wiki/index.php/Java Java] presents some technical obstacles to copying and pasting scripts. Below are described known workarounds.

@@ Line 30: / Line 30: @@
 ===MS Windows===
-The following methods have been tested in Windows XP with Java 1.6.0_26.
+The following methods have been tested in Windows XP with Java 1.6.0_26, in both Firefox and Internet Explorer.
 ;Summary: Block the state script in the Jmol Script Console, and drag/drop it into a temporary text file, or into the Jmol Script Console belonging to the target Jmol applet.

@@ Line 48: / Line 48: @@
 ====Executing the State Script====
 ==Application==
 (please provide details here)

@@ Line 43: / Line 43: @@
 Click in the top box of the Jmol Script Console, and Ctrl-A to '''block the entire state script'''.
-If the target Jmol applet's Jmol Script Console is available, you can now drag the blocked state script into the bottom box. It is also possible to copy (Ctrl-C) the state script and paste it (Ctrl-V) into the bottom box of the target Jmol Script Console.
+If the target Jmol applet's Jmol Script Console is available, you can now drag the blocked state script into the bottom box. (It is sometimes possible to copy (Ctrl-C) the state script and paste it (Ctrl-V) into the bottom box of the target Jmol Script Console, but this may not always work.)
 To avoid frustration, we recommend that you save the state script in a plain text file. Drag the blocked state script into a [http://www.proteopedia.org/wiki/index.php/Help:Plain_text_editors plain text editor], or paste it, and save it in a plain text file for safekeeping. Later, you can open this file and either copy or drag the blocked script into the target Jmol Script Console.