Jmol Virtual Molecular Model Kit

Molecular Editor Info

Start with: ethane cyclohexane benzene NIH PubChem
Append: ethane cyclohexane benzene NIH PubChem
Compare: duplicate compare  Query: name smiles molfile
Model: move/measure delete correctH  Opt: Jmol NIH optOff
Atom: C H N O S P F Cl Br X delete invert drag   FC: inc dec
Bond: break single double triple increase rotate pickingOff
Utility: size erase clear  More Info: models controls bonds
Problems: manual  Model Clipboard: Copy Paste Append


Feedback Area & Script Command Field: Run Script

  

 

Intro | Draw | Edit | Tools | Image

Jmol Virtual Molecular Model Kit

Image Capture Info

Jmol 3D Capture | NIH 2D Capture

Intro | Draw | Edit | Tools | Image

Jmol Virtual Molecular Model Kit

Model Tools Info

Atom Colors: ; cpk; partial charge
Style: wireframe; ball&stick; background color
Clean-up: erase; clear; reset; reload
Surfaces: vdW; MEP 100; MEP 65  Dipoles: bonds; molecular
MO: homo; lumo; mo(-); mo(+) (MO files only)
Anim: SN2; cyclohexane flip; ethane rotation
Anim: quit; pause; resume
Templates: LIN; TPL; SQP; TET; TBP; OCT Info

Pre-Assembled MM
Library Menu

Set Append Pre-Assembled MO
Library Menu

MM Load MO Load

Search Databases for Displayed Model
HNMR | AKA Query Tool Info
 

Intro | Draw | Edit | Tools | Image

Jmol Virtual Molecular Model Kit

2D to 3D Editor Info

You have to enable Java and JavaScript on your machine !

Courtesy of Peter Ertl, Novartis

Compare   Depict   Load 3D: NIH   PubChem  Jmol

Intro | Draw | Edit | Tools | Image

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Calculate Stoichiometry Expression


Save: MultiUser | Restore: MultiUser  Info


Virtual Molecular Model Kit

Introduction Info

Welcome to the Virtual Molecular Model Kit (VMK). The VMK is designed to be used as a presentation tool and a resource for model kit experiments. The VMK has all the functionality of traditional teaching models and more. Models in 3D can be constructed using the Molecular Editor or the JME 2D to 3D Editor. The VMK connects to the NCI/NIH Chemical Resolver and PubChem. These services provide access to millions of unique chemical structures which can be loaded directly into the VMK display window. Models in the display window link to specific data sources via the AKA link of the Model Tools. All VMK control panels can be accessed from the following links:

Molecular Editor

Model Tools

2D to 3D Editor

Image Capture

Click the Info link on each control panel for video help


Jmol: an open-source Java viewer for chemical structures in 3D
JME Structure Drawing Applet: courtesy of Peter Ertl, Novartis
NIH Chemical Identifier Resolver: NIH - NCI/CADD Group
ISU CheMagic: Otis Rothenberger, Illinois State University
USM O=CHem: Thomas Newton, University of Southern Maine

Jmol VMK Journal | Problem Manual