Chem3D Users Manual - CambridgeSoft

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Administrator Surface Type Solid Description The surface is displayed as an opaque form. Solid is a good choice when you are interested in the details of the surface itself, and not particularly interested in the underlying atoms and bonds. Surface Type Translucent Description The surface is displayed in solid form, but is partially transparent so you can also see the atoms and bonds within it. Translucent is a good compromise between surface display styles. Setting Molecular Surface Isovalues Wire Mesh Dots The surface is displayed as a connected net of lines. Wire Mesh is a good choice when you want to focus on surface features, but still have some idea of the atoms and bonds in the structure. The surface is displayed as a series of unconnected dots. Dots are a good choice if you are primarily interested in the underlying structure and just want to get an idea of the surface shape. Isovalues are, by definition, constant values used to generate a surface. For each surface property, values can be calculated throughout space. For example, the electrostatic potential is very high near each atom of a molecule, and vanishingly small far away from it. Chem3D generates a surface by connecting all the points in space that have the same value, the isovalue. Weather maps are a common example of the same procedure in two dimensions, connecting locations of equal temperature (isotherms) or equal pressure (isobars). To set the isovalue: 1. From the Surfaces menu, choose Isocontour. NOTE: The exact name of this command reflects the type of isovalue in each window. For example, for Total Charge Density Surfaces, it is “Isocharge”. The Isocontour slider appears. 2. Adjust the slider to the new isovalue. The new isovalue is the middle value listed at the bottom of the Isocontour tool. 66 •Displaying Models CambridgeSoft Molecular Surface Displays
Setting the Surface Resolution The Surface Resolution is a measure of how smooth the surface appears. The higher the resolution, the more points are used to calculate the surface, and the smoother the surface appears. However, high resolution values can also take a long time to calculate. The default setting of 30 is a good compromise between speed and smoothness. To set the resolution: 1. From the Surfaces menu, choose Resolution. The Resolution slider appears. Setting Solvent Radius The Solvent Radius can be set from 0.1 to 10 Å using the slider. The default solvent radius is 1.4 Å, which is the value for water. Radii for some common solvents are shown in the following table: Solvent Water 1.4 Methanol 1.9 Radius (Å) Ethanol 2.2 Acetonitrile 2.3 2. Adjust the slider to the desired resolution. The new resolution is the middle value listed at the bottom of the Resolution tool. Setting Molecular Surface Colors How you set the color depends on what type of surface you are working with. For Solvent Accessible, Connolly Molecular, or Total Charge Density surfaces, do the following: 1. On the Surfaces menu, choose Surface Color. The Surface Color dialog box appears. 2. Select the new color. 3. Click OK. For the other surface types, where you must specify two colors, do the following. 1. On the Surfaces menu, choose Alpha Color or Beta Color. The Alpha or Beta Color dialog box appears. 2. Select the new color. 3. Click OK. Acetone 2.4 Ether 2.4 Pyridine 2.4 DMSO 2.5 Benzene 2.6 Chloroform 2.7 To set the solvent radius: 1. From the Surfaces menu, choose Solvent Radius. The Radius slider appears. ChemOffice 2005/Chem3D Displaying Models • 67 Molecular Surface Displays
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ChemOffice.Com ® ChemOffice ® Che
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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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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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SOLUTIONS •Adds chemical data typ
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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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