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' /> | ||
| - | + | 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 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; | ||
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| + | '''UPDATE: FAKE GREEN SCENE LINK BELOW SEEMS TO NOW WORK WITH NEW JMOL IN PROTEOPEDIA. HOORAY!!!''' | ||
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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] | |
<br> | <br> | ||
| - | + | The code is below: <br> | |
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| - | + | ||
| - | The code is below: | + | |
<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. | ||
Current revision
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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:
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 include below and one built into this page, both failed:
model all;
compare {1.1} {1.2} ROTATE TRANSLATE;
UPDATE: FAKE GREEN SCENE LINK BELOW SEEMS TO NOW WORK WITH NEW JMOL IN PROTEOPEDIA. HOORAY!!!
Testing compare running dynamically in Proteopedia with new Jmol version
Compare runs and doesn't lock up using the development version here
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;
