Chem3D Users Manual - CambridgeSoft

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Administrator 2. Adjust the slider to the desired resolution. The new radius is the middle value listed at the bottom of the Radius tool. Setting Surface Mapping The Mapping Property provides color-coded visualization of Atom Colors, Group Colors, Hydrophobicity, Partial Charges, or Electrostatic Potential (derived from partial charges) superimposed upon the solvent-accessible surface. Surface Color is color you have chosen with the Surface Color tool. Atom Color is based on the displayed atom colors, which may or may not be the default element colors. Element Color is based on the default colors in the Elements Table. Group Color is based on the colors (if any) you specified in the Model Explorer when creating groups. Hydrophobicity is displayed according to a widely-used color convention derived from amino acid hydrophobicities 1 , where the most hydrophobic (lipophilic) is red and the least hydrophobic (lipophobic) is blue. The following table shows molecule hydrophobicity. Amino Acid Hydrophobicity Cys 2.0 Trp 1.9 Ala 1.6 Thr 1.2 Gly 1.0 Ser 0.6 Middle (White) Pro –0.2 Tyr –0.7 His –3.0 Gln –4.1 Asn –4.8 Glu –8.2 Lys –8.8 Amino Acid Hydrophobicity Phe 3.7 Most hydrophobic (Red) Met 3.4 Ile 3.1 Leu 2.8 Val 2.6 1. Engelman, D.M.; Steitz, T.A.; Goldman, A., “Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins”, Annu. Rev. Biophys. Biophys. Chem. 15, 321-353, 1986. Asp –9.2 Arg –12.3 Least hydrophobic (Blue) The Partial Charges and Electrostatic Potential (derived from the partial charges) properties are taken from the currently selected calculation. If you have performed more than one calculation on the model, you can specify which calculation to use from the Choose Result submenu of the Calculations menu. Solvent Accessible Surface The solvent accessible surface represents the portion of the molecule that solvent molecules can access. When viewed in the ball and stick representation, a molecule may appear to have many nooks and crannies, but often these features 68 •Displaying Models <strong>CambridgeSoft</strong> Molecular Surface Displays
are too small to affect the overall behavior of the molecule. For example, in a ball-and-stick representation, it might appear that a water molecule could fit through the big space in the center of a benzene molecule. The solvent accessible surface (which has no central hole) shows that it cannot. The size and shape of the solvent accessible surface depends on the particular solvent, since a larger solvent molecule will predictably enjoy less access to the crevices and interstices of a solute molecule than a smaller one. To determine the solvent-accessible surface, a small probe sphere simulating the solvent molecule is rolled over the surface of the molecule (van der Waals surface). The solvent-accessible surface is defined as the locus described by the center of the probe sphere, as shown in the diagram below. surface is called the solvent-excluded volume. These surfaces are shown in the following illustration. The Connolly Surface of icrn is shown below: van der Waals surface Solvent accessible surface Solvent probe Connolly Molecular Surface The Connolly surface, also called the molecular surface, is similar to the solvent-accessible surface. Using a small spherical probe to simulate a solvent, it is defined as the surface made by the center of the solvent sphere as it contacts the van der Waals surface. The volume enclosed by the Connolly Total Charge Density The Total Charge Density is the electron density in the space surrounding the nuclei of a molecule, or the probability of finding electrons in the space around a molecule. The default isocharge value of 0.002 atomic units (a.u.) approximates the molecule’s van der Waals radius and represents about 95% of the entire three-dimensional space occupied by the molecule. The Total Charge Density surface is the best visible representation of a molecule’s shape, as determined by its electronic distribution. The Total Charge ChemOffice 2005/<strong>Chem3D</strong> Displaying Models • 69 Molecular Surface Displays
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License Information ChemOffice, Che
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· Licensed users of ChemOffice Ent
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computer, except as provided below.
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Q: IS IT OK TO COPY MY COLLEAGUE’
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A Guide to CambridgeSoft Manuals An
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Administrator Setting Molecular Sur
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Administrator Methods Available in
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Administrator Defining Atom Types.
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Administrator • CambridgeSoft
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Desktop Software Enterprise Solutio
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SOLUTIONS Enterprise Solutions APPL
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Desktop to Enterprise Solutions Che
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SOFTWARE E-Notebook Ultra Ultimate
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SOFTWARE ChemDraw Ultra Ultimate Dr
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SOFTWARE Chem3D Ultra Ultimate Mode
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SOFTWARE ChemFinder/Word • Search
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SOFTWARE The Merck Index • Encycl
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SOLUTIONS •Development and deploy
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MANAGEMENT •Custom organization o
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MANAGEMENT • Indexes chemical str
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MANAGEMENT • E-Notebook Enterpris
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DISCOVERY • Accessed through your
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DISCOVERY • Integrated with Regis
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DISCOVERY • Reagent lists can be
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DISCOVERY •Effectively manages da
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DISCOVERY • Catalog driven data m
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DATABASES • Fully structure-searc
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DATABASES • Encyclopedic referenc
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DATABASES • Extensive collection
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SERVICES · Business Case Developme
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CS ChemOffice ® Desktop to Enterpr
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Chem3D Users Manual - CambridgeSoft

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