Virtual Model Kit: Control Panel

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Virtual Model Kit: Introduction

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Welcome to the CheMagic O=CHem virtual molecular model kit (VMK). The VMK is designed to have all of the teaching power of a traditional student model kit and much more.

The VMK is also a window to the world of chemical information. Models in the VMK are quickly linked to PubChem, NIST, ChemSpider, and Google. Models can also be loaded into the VMK via direct connection to several popular data sources.

The VMK Control Panel is set to display help comments with each button click. The comments appear at the bottom of the page. Uncheck this box to turn this feature off.

The VMK is powered by JSmol, the NCI/CADD Chemical Identifier Resolver, the JSME Molecular Editor, the JSpecView data viewer, the H-NMR predictor, the PubChem database, the Protein Data Bank (PDB), the Crystallographic Open Database (COD), and the ChemSpider database. The VMK is written in HTML5. It works best with Safari, Firefox, or Chrome browsers.

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Virtual Model Kit: JSME Drawing Editor

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Virtual Model Kit: Misc Control Links

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CIF File Symmetry Operations:

reload molecular    unit cell    block    block cell

PDB Style (color inherited) Structures:

cartoon rockets    ribbons    rockets    strands    trace

PDB Style (color set) Schemes:

(cpk) spacefill    (cpk) ball & stick    (cpk) sticks
(cpk) wireframe    (Jmol) cartoon    (Jmol) trace

PDB Select:

display header    display commands    type commands

Modify Background:

background black     background white     background gray

Modify Atom-Click Color:

pink     green     blue     cpk

Useful Animations: Click to play animation.

Diels-Alder    aromatic-chlorination    keto-enol

butene-bromination    cyclohexane-flip

stop    pause    resume

Virtual Model Kit: Measure

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While this measure screen is active, measurements can be made by clicking the following control links:

When measurements are made from this screen, they are saved until they are deleted. The control links below manage the display of these measurements. These display controls can be executed by clicking the links on this Measure screen or by entering them in the script text field on the main Control Panel. In general, control links displayed with italicized text can also be executed by entering them in the main Control Panel script field:

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Virtual Model Kit: Model Editor

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H    C    N    O    P     S    F    Cl    Br    I    X

single    double    triple    break    connect

drag    correctH    MMFF    Resolver

atom    model    increase    decrease

duplicate    invert    compare    center

Virtual Model Kit: IR Spec

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Connecting to NIST

Virtual Model Kit: Mass Spec

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Connecting to NIST

  |   Restore Model

Virtual Model Kit: NMR Spec

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Connecting to Database

Virtual Model Kit: Image

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Connecting to Database

Virtual Model Kit: Search & Data

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Connecting to PubChem

Virtual Model Kit: Blank4