User:Wayne Decatur/Sandbox TestCompareinScriptAuthoring

From Proteopedia

Jmol._Canvas2D (Jmol) "jmolApplet1"[x] loadScript /wiki/extensions/jsmol/j2s/core/package.js loadScript /wiki/extensions/jsmol/j2s/core/corejmol.z.js loadScript /wiki/extensions/jsmol/j2s/J/translation/PO.js loadScript /wiki/extensions/jsmol/j2s/core/corescript.z.js JSmol exec jmolApplet1 start applet null Jmol JavaScript applet jmolApplet1__616733279978076__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(jmolApplet1__616733279978076__) vwrOptions: { "name":"jmolApplet1","applet":true,"documentBase":"https://proteopedia.org/wiki/index.php?JMOLJAR=http%3A%2F%2Fchemapps.stolaf.edu%2Fjmol%2Fdocs%2Fexamples-12%2FJmolAppletSigned.jar&printable=yes&title=User%3AWayne_Decatur%2FSandbox_TestCompareinScriptAuthoring","platform":"J.awtjs2d.Platform","fullName":"jmolApplet1__616733279978076__","codePath":"https:/wiki/extensions/jsmol/j2s/","display":"jmolApplet1_canvas2d","loadStructCallback":"manageLoadStructCallback","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"616733279978076","messageCallback":"msgCb","bgcolor":"white" } setting document base to "https://proteopedia.org/wiki/index.php?JMOLJAR=http%3A%2F%2Fchemapps.stolaf.edu%2Fjmol%2Fdocs%2Fexamples-12%2FJmolAppletSigned.jar&printable=yes&title=User%3AWayne_Decatur%2FSandbox_TestCompareinScriptAuthoring" (C) 2015 Jmol Development Jmol Version: 14.31.8 2020-09-26 10:04 java.vendor: Java2Script (HTML5) java.version: 2019-06-08 00:17:46 (JSmol/j2s) os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com) Access: ALL memory: 0.0/0.0 processors available: 1 useCommandThread: false appletId:jmolApplet1 (signed) Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor white backgroundColor = "white" Jmol getValue ANIMFRAMECallback null Jmol getValue APPLETREADYCallback Jmol._readyCallback APPLETREADYCallback = "Jmol._readyCallback" StatusManager callback set for APPLETREADYCallback f=Jmol._readyCallback cb=APPLETREADY Jmol getValue ATOMMOVEDCallback null Jmol getValue AUDIOCallback null Jmol getValue CLICKCallback null Jmol getValue DRAGDROPCallback null Jmol getValue ECHOCallback null Jmol getValue ERRORCallback null Jmol getValue EVALCallback null Jmol getValue HOVERCallback null Jmol getValue IMAGECallback null Jmol getValue LOADSTRUCTCallback manageLoadStructCallback LOADSTRUCTCallback = "manageLoadStructCallback" StatusManager callback set for LOADSTRUCTCallback f=manageLoadStructCallback cb=LOADSTRUCT Jmol getValue MEASURECallback null Jmol getValue MESSAGECallback msgCb MESSAGECallback = "msgCb" StatusManager callback set for MESSAGECallback f=msgCb cb=MESSAGE Jmol getValue MINIMIZATIONCallback null Jmol getValue SERVICECallback null Jmol getValue PICKCallback null Jmol getValue RESIZECallback null Jmol getValue SCRIPTCallback null Jmol getValue SYNCCallback null Jmol getValue STRUCTUREMODIFIEDCallback null Jmol getValue doTranslate null language=en_US Jmol getValue doTranslate null Note -- Presence of message callback disables disable translation; to enable message translation use jmolSetTranslation(true) prior to jmolApplet() Note -- language translation disabled Jmol getValue popupMenu null Jmol getValue script null Jmol getValue loadInline null Jmol getValue load null Jmol applet jmolApplet1__616733279978076__ ready script 1 started pdbGetHeader = true FileManager opening url https://proteopedia.org/wiki/extensions/Proteopedia/spt/functions.spt?1733933141 loadScript /wiki/extensions/jsmol/j2s/core/coretext.z.js Loading, please wait ... platformSpeed = 8 FileManager opening url https://proteopedia.org/wiki/scripts/LepA/Lepaefgbothh/1.spt loadScript /wiki/extensions/jsmol/j2s/J/thread/MoveToThread.js spinqualitylabelsall models test compare Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

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 LepA and Ef-G
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;