User:Wayne Decatur/Sandbox TestCompareinScriptAuthoring: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
Wayne Decatur (talk | contribs)
Editor, widgeteditor
7,824 edits
mNo edit summary
Wayne Decatur (talk | contribs)
Editor, widgeteditor
7,824 edits
mNo edit summary
 
(14 intermediate revisions by the same user not shown)
Line 1: Line 1:
<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 ran compare and saved compared version of nextto scene, version8:
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:
Result of test:<br>
IT NEVER ROTATED AN TRANSLATED IN SCENE AUTHORING TOOL WINDOW, but same script works great in a popup:
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. HOORAY!!!'''
<br>
==Testing compare running dynamically in Proteopedia with new Jmol version==
<jmol>
<jmolLink>
  <script>
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;
</script>
  <text>Compare LepA and Ef-G</text>
</jmolLink>
</jmol>
<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>
The code is below:  <br>
<pre>
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;
</pre>
&nbsp;<br>
You can even paste in the code below to see the two models go back apart smoothly:<br>
<pre>
rotate COMPARE {1.1} @origcoord -2.5;
</pre>
Retrieved from "https://proteopedia.org/User:Wayne_Decatur/Sandbox_TestCompareinScriptAuthoring"