OCA:3VMM

loadScript /oca-docs/jsmol/j2s/core/package.js

loadScript /oca-docs/jsmol/j2s/core/corejmol.z.js

loadScript /oca-docs/jsmol/j2s/J/translation/PO.js

loadScript /oca-docs/jsmol/j2s/core/corescript.z.js

JSmol exec jmolApplet0 start applet null

Jmol JavaScript applet jmolApplet0__8415082882879856__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__8415082882879856__)

vwrOptions:

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setting document base to "https://oca.weizmann.ac.il/oca-bin/ccpeek?id=3VMM"

Jmol Version: 16.2.17 2024-06-07 15:31

java.vendor: Java2Script (HTML5)

java.version: 2022-06-24 05:54:49 (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:jmolApplet0 (signed)

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor #FFFFFF

backgroundColor = "#FFFFFF"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

StatusManager APPLETREADYcallback set f=Jmol._readyCallback

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 null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue MODELKITCallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SELECTCallback null

Jmol getValue SERVICECallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue SYNCCallback null

Jmol getValue doTranslate null

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Jmol getValue popupMenu null

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Jmol getValue load null

Jmol applet jmolApplet0__8415082882879856__ ready

script 1 started

loadScript /oca-docs/jsmol/j2s/core/coretext.z.js

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antialiasDisplay = false

FileManager.getAtomSetCollectionFromFile(https://oca.weizmann.ac.il/oca-bin/sendStructure?id=3vmm)

FileManager opening url https://oca.weizmann.ac.il/oca-bin/sendStructure?id=3vmm

The Resolver thinks MMCif

loadScript /oca-docs/jsmol/j2s/J/adapter/readers/cif/MMCifReader.js

loadScript /oca-docs/jsmol/j2s/J/adapter/readers/cif/CifReader.js

loadScript /oca-docs/jsmol/j2s/JU/CifDataParser.js

loadScript /oca-docs/jsmol/j2s/core/corebio.z.js

TITLE: Structural and enzymatic characterization of BacD, an l-amino acid dipeptide ligase from Bacillus subtilis

ADP = ADENOSINE-5'-DIPHOSPHATE

HOH = WATER

MG = MAGNESIUM ION

P0D = (2S)-3-[(S)-[(1R)-1-aminoethyl](phosphonooxy)phosphoryl]-2-benzylpropanoic acid

Setting space group name to HM:P 65 2 2

biomolecule 1 operators 1 ASYM_IDs A,B,C,D,E,F

found biomolecule 1: A,B,C,D,E,F

3VMM

12 bonds added

loadScript /oca-docs/jsmol/j2s/core/coresym.z.js

SpaceGroup - 0 settings generated

Precision set to 4; packing set to 0.02

Time for openFile(https://oca.weizmann.ac.il/oca-bin/sendStructure?id=3vmm): 3453 ms

reading 3873 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

3873 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 111 ms

TITLE: Structural and enzymatic characterization of BacD, an l-amino acid dipeptide ligase from Bacillus subtilis

ADP = ADENOSINE-5'-DIPHOSPHATE

HOH = WATER

MG = MAGNESIUM ION

P0D = (2S)-3-[(S)-[(1R)-1-aminoethyl](phosphonooxy)phosphoryl]-2-benzylpropanoic acid

found biomolecule 1: A,B,C,D,E,F

3VMM

12 bonds added

Precision set to 4; packing set to 0.02

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loadScript /oca-docs/jsmol/j2s/J/thread/SpinThread.js

Script completed

Jmol script terminated