GLmol, 3Dmol, and JSmol multiple

Last updated

Jun 3, 2019
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- JSmol Orbitals
- Examples (all three systems) 1

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$\newcommand{\range}{\mathrm{range}\,}$

$\newcommand{\RealPart}{\mathrm{Re}}$

$\newcommand{\ImaginaryPart}{\mathrm{Im}}$

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$\newcommand{\norm}[1]{\| #1 \|}$

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$\newcommand{\Span}{\mathrm{span}}$ $\newcommand{\AA}{\unicode[.8,0]{x212B}}$

$\newcommand{\vectorA}[1]{\vec{#1}} % arrow$

$\newcommand{\vectorAt}[1]{\vec{\text{#1}}} % arrow$

$\newcommand{\vectorB}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}} }$

$\newcommand{\vectorC}[1]{\textbf{#1}}$

$\newcommand{\vectorD}[1]{\overrightarrow{#1}}$

$\newcommand{\vectorDt}[1]{\overrightarrow{\text{#1}}}$

$\newcommand{\vectE}[1]{\overset{-\!-\!\rightharpoonup}{\vphantom{a}\smash{\mathbf {#1}}}}$

$\newcommand{\vecs}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}} }$

$\newcommand{\vecd}[1]{\overset{-\!-\!\rightharpoonup}{\vphantom{a}\smash {#1}}}$

$\newcommand{\avec}{\mathbf a}$

$\newcommand{\bvec}{\mathbf b}$

$\newcommand{\cvec}{\mathbf c}$

$\newcommand{\dvec}{\mathbf d}$

$\newcommand{\dtil}{\widetilde{\mathbf d}}$

$\newcommand{\evec}{\mathbf e}$

$\newcommand{\fvec}{\mathbf f}$

$\newcommand{\nvec}{\mathbf n}$

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$\newcommand{\qvec}{\mathbf q}$

$\newcommand{\svec}{\mathbf s}$

$\newcommand{\tvec}{\mathbf t}$

$\newcommand{\uvec}{\mathbf u}$

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$\newcommand{\wvec}{\mathbf w}$

$\newcommand{\xvec}{\mathbf x}$

$\newcommand{\yvec}{\mathbf y}$

$\newcommand{\zvec}{\mathbf z}$

$\newcommand{\rvec}{\mathbf r}$

$\newcommand{\mvec}{\mathbf m}$

$\newcommand{\zerovec}{\mathbf 0}$

$\newcommand{\onevec}{\mathbf 1}$

$\newcommand{\real}{\mathbb R}$

$\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}$

$\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}$

$\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}$

$\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}$

$\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}$

$\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}$

$\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}$

$\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}$

$\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}$

$\newcommand{\laspan}[1]{\text{Span}\{#1\}}$

$\newcommand{\bcal}{\cal B}$

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$\newcommand{\scal}{\cal S}$

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$\newcommand{\ecal}{\cal E}$

$\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}$

$\newcommand{\gray}[1]{\color{gray}{#1}}$

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$\newcommand{\rank}{\operatorname{rank}}$

$\newcommand{\row}{\text{Row}}$

$\newcommand{\col}{\text{Col}}$

$\renewcommand{\row}{\text{Row}}$

$\newcommand{\nul}{\text{Nul}}$

$\newcommand{\var}{\text{Var}}$

$\newcommand{\corr}{\text{corr}}$

$\newcommand{\len}[1]{\left|#1\right|}$

$\newcommand{\bbar}{\overline{\bvec}}$

$\newcommand{\bhat}{\widehat{\bvec}}$

$\newcommand{\bperp}{\bvec^\perp}$

$\newcommand{\xhat}{\widehat{\xvec}}$

$\newcommand{\vhat}{\widehat{\vvec}}$

$\newcommand{\uhat}{\widehat{\uvec}}$

$\newcommand{\what}{\widehat{\wvec}}$

$\newcommand{\Sighat}{\widehat{\Sigma}}$

$\newcommand{\lt}{<}$

$\newcommand{\gt}{>}$

$\newcommand{\amp}{&}$

$\definecolor{fillinmathshade}{gray}{0.9}$

https://awesomefiles.libretexts.org

script 1 started

zoomLarge = false

antialiasDisplay = true

callback set for errorCallback myCallback ERROR

errorCallback = "myCallback"

Jmol JavaScript applet jmolApplet51751__400852418685617__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet51751__400852418685617__)

vwrOptions:

{ "name":"jmolApplet51751","applet":true,"documentBase":"https://chem.libretexts.org/Ancillary_Materials/Interactive_Applications/Molecular_and_Protein_Interactive_Figures/GLmol_3Dmol_and_JSmol_multiple","platform":"J.awtjs2d.Platform","fullName":"jmolApplet51751__400852418685617__","codePath":"https://awesomefiles.libretexts.org/Molecules/JSmol/j2s/","display":"jmolApplet51751_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"400852418685617","bgcolor":"white" }

setting document base to "https://chem.libretexts.org/Ancillary_Materials/Interactive_Applications/Molecular_and_Protein_Interactive_Figures/GLmol_3Dmol_and_JSmol_multiple"

Jmol Version: 14.29.3 2018-02-03 09:25

java.vendor: Java2Script (HTML5)

java.version: 2018-01-28 23:38:52 (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:jmolApplet51751 (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"

callback set for APPLETREADYCallback Jmol._readyCallback 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 null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

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 popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet51751__400852418685617__ ready

Jmol JavaScript applet jmolApplet99904__400852418685617__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet99904__400852418685617__)

vwrOptions:

{ "name":"jmolApplet99904","applet":true,"documentBase":"https://chem.libretexts.org/Ancillary_Materials/Interactive_Applications/Molecular_and_Protein_Interactive_Figures/GLmol_3Dmol_and_JSmol_multiple","platform":"J.awtjs2d.Platform","fullName":"jmolApplet99904__400852418685617__","codePath":"https://awesomefiles.libretexts.org/Molecules/JSmol/j2s/","display":"jmolApplet99904_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"400852418685617","bgcolor":"white" }

setting document base to "https://chem.libretexts.org/Ancillary_Materials/Interactive_Applications/Molecular_and_Protein_Interactive_Figures/GLmol_3Dmol_and_JSmol_multiple"

Jmol Version: 14.29.3 2018-02-03 09:25

java.vendor: Java2Script (HTML5)

java.version: 2018-01-28 23:38:52 (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:jmolApplet99904 (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"

callback set for APPLETREADYCallback Jmol._readyCallback 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 null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

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 popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet99904__400852418685617__ ready

script 1 started

zoomLarge = false

antialiasDisplay = true

callback set for errorCallback myCallback ERROR

errorCallback = "myCallback"

GLmol

Jmol JavaScript applet jmolApplet1513__400852418685617__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet1513__400852418685617__)

vwrOptions:

{ "name":"jmolApplet1513","applet":true,"documentBase":"https://chem.libretexts.org/Ancillary_Materials/Interactive_Applications/Molecular_and_Protein_Interactive_Figures/GLmol_3Dmol_and_JSmol_multiple","platform":"J.awtjs2d.Platform","fullName":"jmolApplet1513__400852418685617__","codePath":"https://awesomefiles.libretexts.org/Molecules/JSmol/j2s/","display":"jmolApplet1513_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"400852418685617","bgcolor":"white" }

setting document base to "https://chem.libretexts.org/Ancillary_Materials/Interactive_Applications/Molecular_and_Protein_Interactive_Figures/GLmol_3Dmol_and_JSmol_multiple"

Jmol Version: 14.29.3 2018-02-03 09:25

java.vendor: Java2Script (HTML5)

java.version: 2018-01-28 23:38:52 (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:jmolApplet1513 (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"

callback set for APPLETREADYCallback Jmol._readyCallback 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 null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

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 popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet1513__400852418685617__ ready

script 1 started

zoomLarge = false

antialiasDisplay = true

callback set for errorCallback myCallback ERROR

errorCallback = "myCallback"

Viewer cachePut cache://localLOAD_https://files.rcsb.org/download/1blu.pdb

Viewer cachePut https://files.rcsb.org/download/1blu.pdb

Viewer cachePut cache://localLOAD_https://files.rcsb.org/download/1blu.pdb

Viewer cachePut https://files.rcsb.org/download/1blu.pdb

FileManager.getAtomSetCollectionFromFile(https://files.rcsb.org/download/1blu.pdb)

The Resolver thinks Pdb

ELECTRON TRANSPORT 16-APR-96 1BLU

STRUCTURE OF THE 2[4FE-4S] FERREDOXIN FROM CHROMATIUM VINOSUM

found biomolecule 1: A

biomolecule 1: number of transforms: 1

SF4 = IRON/SULFUR CLUSTER

Setting space group name to P 31 2 1

1BLU

Time for openFile(=1blu): 276 ms

reading 712 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

712 atoms created

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

Time for creating model: 59 ms

ELECTRON TRANSPORT 16-APR-96 1BLU

STRUCTURE OF THE 2[4FE-4S] FERREDOXIN FROM CHROMATIUM VINOSUM

found biomolecule 1: A

SF4 = IRON/SULFUR CLUSTER

1BLU

spinY = 10.0

Script completed

Jmol script terminated

Viewer cachePut cache://localLOAD_https://files.rcsb.org/download/1d66.pdb

Viewer cachePut https://files.rcsb.org/download/1d66.pdb

FileManager.getAtomSetCollectionFromFile(https://files.rcsb.org/download/1blu.pdb)

The Resolver thinks Pdb

ELECTRON TRANSPORT 16-APR-96 1BLU

STRUCTURE OF THE 2[4FE-4S] FERREDOXIN FROM CHROMATIUM VINOSUM

found biomolecule 1: A

biomolecule 1: number of transforms: 1

SF4 = IRON/SULFUR CLUSTER

Setting space group name to P 31 2 1

1BLU

Time for openFile(=1blu): 26 ms

reading 712 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

712 atoms created

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

Time for creating model: 25 ms

ELECTRON TRANSPORT 16-APR-96 1BLU

STRUCTURE OF THE 2[4FE-4S] FERREDOXIN FROM CHROMATIUM VINOSUM

found biomolecule 1: A

SF4 = IRON/SULFUR CLUSTER

1BLU

spinY = 10.0

Script completed

Jmol script terminated

FileManager.getAtomSetCollectionFromFile(https://files.rcsb.org/download/1d66.pdb)

The Resolver thinks Pdb

TRANSCRIPTION/DNA 06-MAR-92 1D66

DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX

found biomolecule 1: D, E, A, B

biomolecule 1: number of transforms: 1

CD = CADMIUM ION

Setting space group name to P 43 21 2

1D66

Time for openFile(=1d66): 43 ms

reading 1762 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

1762 atoms created

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

Time for creating model: 50 ms

TRANSCRIPTION/DNA 06-MAR-92 1D66

DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX

found biomolecule 1: D, E, A, B

CD = CADMIUM ION

1D66

spinY = 10.0

Script completed

Jmol script terminated

GLmol

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