Jmol Virtual Molecular Model Kit

Molecular Editor Info

Start with:  C2H6    C2H4    C2H2    C6H12    C6H6    NIH    PubChem 
Append:  C2H6    C2H4    C2H2    C6H12    C6H6    NIH    PubChem 
Compare:  duplicate   compare   Query:  name    smiles   sdf 
Model:  move/meas  {  translate   rotate   X Y Z -X -Y -Z }  delete 
Optimize:  Jmol   NIH   correct hydrogen   optimize off 
Atom:  C   H   N   O   S   P   F   Cl   Br   X   delete   drag   +    -  
Bond:  break   single   double   triple   increase   rotate   off 
Utility:  erase   clear   invert    Movie:  begin   capture   end 
Model Clipboard:  copy   paste   append   MEP:  on 100   on 65   off 

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    Utility:  erase   clear   reset 
Style:  wireframe   ball & stick   background color 
Surfaces:  vdW   partial charge    Dipoles:  bonds   molecular 
MO:  homo   lumo   <   >     Databases:  HNMR   AKA Query Tool  Info
Templates:  LIN   TPL   SQP   TET   TBP   OCT  Info
Animations:  SN2   cyclohexane   ethane      quit   pause   resume 

Movies:      Run Movie
Pre-Assembled MM
Library Menu

Set Append Pre-Assembled MO
Library Menu

MM Load MO Load

 

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