User:Wayne Decatur/Sandbox TestCompareinScriptAuthoring

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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' />
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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:
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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:
Result of test:<br>
Result of test:<br>
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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:
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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>
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ABOVE FAILS?!?!
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Compare runs but page locks up in Firefox and Chrome. Cannot rotate aligned structures or do anything.
<br>
<br>
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But it actually should work in Jmol.<br>
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The code is below: <br>
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To verify that, you can even see it work in a pop-up Proteoepdia generates. <br>
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To see for yourself:<br>
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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".
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The code is below: (Unortunately it runs off to the right so make sure you grab it all.<br>
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<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>
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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.
 

Revision as of 02:00, 22 March 2012

test compare

Drag the structure with the mouse to rotate

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:
It reported the rmsd and superimposed. However, the the page locked up and I couldn't save the scene.
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; compare {1.1} {1.2} ROTATE TRANSLATE;




Testing compare running dynamically in Proteopedia with new Jmol version


Compare runs but page locks up in Firefox and Chrome. Cannot rotate aligned structures or do anything.
The code is below: 

define domain1model1 94-139:a and model=1.1;
define domain1model2 100-143:a and model=1.2;
define domain2model1 236-273:a and model=1.1;
define domain2model2 354-388:a and model=1.2;
define domain3model1 324-342:a and model=1.1;
define domain3model2 438-470:a and model=1.2;
define domain5model1 432-438:a and model=1.1;
define domain5model2 634-641:a and model=1.2;
origcoord = {1.1}.xyz.all;
compare {1.1} {1.2} ATOMS {domain1model1}{domain1model2},{domain2model1}{domain2model2},{domain3model1}{domain3model2},{domain5model1}{domain5model2} ROTATE TRANSLATE -2.5;

 
You can even paste in the code below to see the two models go back apart smoothly:

rotate COMPARE {1.1} @origcoord -2.5;

Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur

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