User:Wayne Decatur/Sandbox TestCompareinScriptAuthoring - Revision history

Wayne Decatur at 20:33, 10 October 2012

2012-10-10T20:33:09Z

← Older revision		Revision as of 20:33, 10 October 2012
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	compare {1.1} {1.2} ROTATE TRANSLATE;		compare {1.1} {1.2} ROTATE TRANSLATE;

	'''UPDATE: FAKE GREEN SCENE LINK BELOW SEEMS TO NOW WORK WITH NEW JMOL IN PROTEOPEDIA.'''		'''UPDATE: FAKE GREEN SCENE LINK BELOW SEEMS TO NOW WORK WITH NEW JMOL IN PROTEOPEDIA. HOORAY!!!'''

Wayne Decatur at 20:32, 10 October 2012

2012-10-10T20:32:19Z

← Older revision		Revision as of 20:32, 10 October 2012
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	New attempts after new Jmol version AND STARTING WITH CLEAN, NEW MULTI-MODEL SCENE to run compare and save resulting compared version as a Protopedioa scene using Scene Authoring Tools. On LepA page, loaded 'LepA/Lepaefgbothh/1' scene and entered compare command in console:		New attempts after new Jmol version AND STARTING WITH CLEAN, NEW MULTI-MODEL SCENE to run compare and save resulting compared version as a Protopedioa scene using Scene Authoring Tools. On LepA page, loaded 'LepA/Lepaefgbothh/1' scene and entered compare command in console:
	Result of test:<br>		Result of test:<br>
	It reported the rmsd and superimposed. However, the the page locked up and I couldn't save the scene.<br> The same script works great pasted into the console of a popup from the scene authoring window. Scripts tested ~~inclde~~ below and one built into this page, both failed:		It reported the rmsd and superimposed. However, the the page locked up and I couldn't save the scene.<br> The same script works great pasted into the console of a popup from the scene authoring window. Scripts tested include below and one built into this page, both failed:
	model all;		model all;
	compare {1.1} {1.2} ROTATE TRANSLATE;		compare {1.1} {1.2} ROTATE TRANSLATE;

			'''UPDATE: FAKE GREEN SCENE LINK BELOW SEEMS TO NOW WORK WITH NEW JMOL IN PROTEOPEDIA.'''

Wayne Decatur at 17:46, 2 April 2012

2012-04-02T17:46:12Z

← Older revision		Revision as of 17:46, 2 April 2012
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	</jmol>		</jmol>
	<br>		<br>
	Compare runs and doesn't lock up using the development version [http://proteopedia.org/wiki/index.php/User:Wayne_Decatur/Sandbox_TestCompareinScriptAuthoring?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned.jar here]]		Compare runs and doesn't lock up using the development version [http://proteopedia.org/wiki/index.php/User:Wayne_Decatur/Sandbox_TestCompareinScriptAuthoring?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned.jar here]
	<br>		<br>
	The code is below: <br>		The code is below: <br>

Wayne Decatur at 17:45, 2 April 2012

2012-04-02T17:45:36Z

← Older revision		Revision as of 17:45, 2 April 2012
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	</jmol>		</jmol>
	<br>		<br>
	Compare runs and doesn't lock up using the development version ~~at [~~[User:Wayne_Decatur/Sandbox_TestCompareinScriptAuthoring?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned.jar]]		Compare runs and doesn't lock up using the development version [http://proteopedia.org/wiki/index.php/User:Wayne_Decatur/Sandbox_TestCompareinScriptAuthoring?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned.jar here]]
	<br>		<br>
	The code is below: <br>		The code is below: <br>

Wayne Decatur at 17:44, 2 April 2012

2012-04-02T17:44:52Z

← Older revision		Revision as of 17:44, 2 April 2012
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	</jmol>		</jmol>
	<br>		<br>
	Compare runs and doesn't lock up using the development version at [~~http:proteopedia.org/wiki/index.php/~~User:Wayne_Decatur/Sandbox_TestCompareinScriptAuthoring?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned.jar]		Compare runs and doesn't lock up using the development version at [[User:Wayne_Decatur/Sandbox_TestCompareinScriptAuthoring?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned.jar]]
	<br>		<br>
	The code is below: <br>		The code is below: <br>

Wayne Decatur at 17:43, 2 April 2012

2012-04-02T17:43:33Z

← Older revision		Revision as of 17:43, 2 April 2012
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	</jmol>		</jmol>
	<br>		<br>
	Compare runs ~~but page locks~~ up ~~in Firefox and Chrome~~. ~~Cannot rotate aligned structures or do anything~~.		Compare runs and doesn't lock up using the development version at [http:proteopedia.org/wiki/index.php/User:Wayne_Decatur/Sandbox_TestCompareinScriptAuthoring?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned.jar]
	<br>		<br>
	The code is below: <br>		The code is below: <br>

Wayne Decatur: closer now

2012-03-22T02:00:54Z

closer now

← Older revision		Revision as of 02:00, 22 March 2012
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	<Structure load='3cb4' size='600' frame='true' align='right' caption='test compare' scene='LepA/Lepaefgbothh/1' />		<Structure load='3cb4' size='600' frame='true' align='right' caption='test compare' scene='LepA/Lepaefgbothh/1' />
	~~First~~ attempts to run compare and save resulting compared version as a Protopedioa scene using Scene Authoring Tools. ~~From 3cb4~~, loaded '~~nextto~~ scene~~, version8'~~ and entered compare command in console:		New attempts after new Jmol version AND STARTING WITH CLEAN, NEW MULTI-MODEL SCENE to run compare and save resulting compared version as a Protopedioa scene using Scene Authoring Tools. On LepA page, loaded 'LepA/Lepaefgbothh/1' scene and entered compare command in console:
	Result of test:<br>		Result of test:<br>
	~~IT NEVER ROTATED AND TRANSLATED IN SCENE AUTHORING TOOL WINDOW, although it~~ reported the rmsd. <br> The same script works great pasted into the console of a popup from the scene authoring window. ~~Script~~ tested:		It reported the rmsd and superimposed. However, the the page locked up and I couldn't save the scene.<br> The same script works great pasted into the console of a popup from the scene authoring window. Scripts tested inclde below and one built into this page, both failed:
	model all;		model all;
	compare {1.1} {1.2} ROTATE TRANSLATE;		compare {1.1} {1.2} ROTATE TRANSLATE;




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	</jmol>		</jmol>
	<br>		<br>
	~~ABOVE FAILS?!?!~~		Compare runs but page locks up in Firefox and Chrome. Cannot rotate aligned structures or do anything.
	<br>		<br>
	~~But it actually should work in Jmol.<br>~~		The code is below: <br>
	~~To verify that, you can even see it work in a pop-up Proteoepdia generates. <br>~~
	~~To see for yourself:<br>~~
	Click on the pop-up below the Jmol window to open the two models in a pop-up window, and thn paste the code used for the script that the button (green text) should trigger into the Jmol Console and it works moving the models to superimpose and reports "RMSD 3.64 --> 3.54 Angstroms".
	The code is below: ~~(Unortunately it runs off to the right so make sure you grab it all.~~<br>
	<pre>		<pre>
	define domain1model1 94-139:a and model=1.1;		define domain1model1 94-139:a and model=1.1;
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	rotate COMPARE {1.1} @origcoord -2.5;		rotate COMPARE {1.1} @origcoord -2.5;
	</pre>		</pre>

	It looks fairly good for a structural alignment that was done quickly eyeballing parts that would be expected to match. So I did it quick to have something to test, there is probably room for improvement of the actual correspondences.

Wayne Decatur at 01:53, 22 March 2012

2012-03-22T01:53:44Z

← Older revision		Revision as of 01:53, 22 March 2012
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	<Structure load='3cb4' size='600' frame='true' align='right' caption='test compare' scene='~~3cb4~~/~~Nextto~~/8' />		<Structure load='3cb4' size='600' frame='true' align='right' caption='test compare' scene='LepA/Lepaefgbothh/1' />
	First attempts to run compare and save resulting compared version as a Protopedioa scene using Scene Authoring Tools. From 3cb4, loaded 'nextto scene, version8' and entered compare command in console:		First attempts to run compare and save resulting compared version as a Protopedioa scene using Scene Authoring Tools. From 3cb4, loaded 'nextto scene, version8' and entered compare command in console:
	Result of test:<br>		Result of test:<br>

Wayne Decatur at 02:39, 21 March 2012

2012-03-21T02:39:57Z

← Older revision		Revision as of 02:39, 21 March 2012
Line 51:		Line 51:
	rotate COMPARE {1.1} @origcoord -2.5;		rotate COMPARE {1.1} @origcoord -2.5;
	</pre>		</pre>

			It looks fairly good for a structural alignment that was done quickly eyeballing parts that would be expected to match. So I did it quick to have something to test, there is probably room for improvement of the actual correspondences.

Wayne Decatur at 02:34, 21 March 2012

2012-03-21T02:34:18Z

← Older revision		Revision as of 02:34, 21 March 2012
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	</pre>		</pre>
	<br>		<br>
	You can even paste in the code below to see it go back:<br>		You can even paste in the code below to see the two models go back apart smoothly:<br>
	<pre>		<pre>
	rotate COMPARE {1.1} @origcoord -2.5;		rotate COMPARE {1.1} @origcoord -2.5;
	</pre>		</pre>