Chem3D Users Manual - CambridgeSoft

Administrator
Setting Molecular Surface Types . . . . . . . . . . . . 65
Setting Molecular Surface Isovalues . . . . . . . . . 66
Setting the Surface Resolution . . . . . . . . . . . . . 67
Setting Molecular Surface Colors . . . . . . . . . . . 67
Setting Solvent Radius . . . . . . . . . . . . . . . . . . . 67
Setting Surface Mapping . . . . . . . . . . . . . . . . . . 68
Solvent Accessible Surface . . . . . . . . . . . . . . . . 68
Connolly Molecular Surface . . . . . . . . . . . . . . . 69
Total Charge Density . . . . . . . . . . . . . . . . . . . . . 69
Total Spin Density . . . . . . . . . . . . . . . . . . . . . . . 70
Molecular Electrostatic Potential . . . . . . . . . . . 70
Molecular Orbitals . . . . . . . . . . . . . . . . . . . . . . . 70
Visualizing Surfaces from Other Sources 71
Chapter 4: Building and Editing Models
Setting the Model Building Controls . . . . 73
Building with the ChemDraw Panel. . . . . 74
Unsynchronized Mode . . . . . . . . . . . . . . . . . . . 74
Name=Struct . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Building with Other 2D Programs . . . . . . . . . . 75
Building With the Bond Tools . . . . . . . . . . 75
Creating Uncoordinated Bonds. . . . . . . . . . . . . 76
Removing Bonds and Atoms . . . . . . . . . . . . . . 76
Building With The Text Tool . . . . . . . . . . . 77
Using Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Changing atom types . . . . . . . . . . . . . . . . . . . . 78
The Table Editor . . . . . . . . . . . . . . . . . . . . . . . 78
Specifying Order of Attachment. . . . . . . . . . . . 78
Using Substructures. . . . . . . . . . . . . . . . . . . . . . 78
Building with Substructures . . . . . . . . . . . . . . . 79
Example 1. Building Ethane with Substructures 79
Example 2. Building a Model with a Substructure
and Several Other Elements 80
Example 3. Polypeptides. . . . . . . . . . . . . . . . . . 80
Example 4. Other Polymers . . . . . . . . . . . . . . . 81
Replacing an Atom with a Substructure . . . . . . 81
Building From Tables . . . . . . . . . . . . . . . . . . 81
Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
Changing an Atom to Another Element . 82
Changing an Atom to Another Atom Type 83
Changing Bonds . . . . . . . . . . . . . . . . . . . . . . . 83
Creating Bonds by Bond Proximate Addition . 84
Adding Fragments . . . . . . . . . . . . . . . . . . . . . 84
View Focus. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Setting Measurements . . . . . . . . . . . . . . . . . . 85
Setting Bond Lengths . . . . . . . . . . . . . . . . . . . . 86
Setting Bond Angles . . . . . . . . . . . . . . . . . . . . . 86
Setting Dihedral Angles. . . . . . . . . . . . . . . . . . . 86
Setting Non-Bonded Distances (Atom Pairs) . 86
Atom Movement When Setting Measurements 86
Setting Constraints. . . . . . . . . . . . . . . . . . . . . . . 87
Setting Charges . . . . . . . . . . . . . . . . . . . . . . . . . 87
Setting Serial Numbers . . . . . . . . . . . . . . . . . 88
Changing Stereochemistry . . . . . . . . . . . . . . 88
Inversion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Reflection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Refining a Model . . . . . . . . . . . . . . . . . . . . . . . 90
Rectifying Atoms . . . . . . . . . . . . . . . . . . . . . . . . 90
Cleaning Up a Model . . . . . . . . . . . . . . . . . . . . . 90
Chapter 5: Manipulating Models
Selecting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Selecting Single Atoms and Bonds . . . . . . . . . . 91
Selecting Multiple Atoms and Bonds . . . . . . . . 92
Deselecting Atoms and Bonds . . . . . . . . . . . . . 92
Selecting Groups of Atoms and Bonds . . . . . . 92
Using the Selection Rectangle. . . . . . . . . . . . . . . 92
Defining Groups . . . . . . . . . . . . . . . . . . . . . . . . 93
Selecting a Group or Fragment . . . . . . . . . . . . . 93
Selecting Atoms or Groups by Distance . . . . . 94
Showing and Hiding Atoms . . . . . . . . . . . . . 94
Showing Hs and Lps . . . . . . . . . . . . . . . . . . . . . 95
Showing All Atoms . . . . . . . . . . . . . . . . . . . . . . 95
Moving Atoms or Models . . . . . . . . . . . . . . . 95
Moving Models with the Translate Tool . . . . . . 96
Rotating Models . . . . . . . . . . . . . . . . . . . . . . . . 96
X- Y- or Z-Axis Rotations . . . . . . . . . . . . . . . . . 97
Rotating Fragments . . . . . . . . . . . . . . . . . . . . . . 97
Trackball Tool. . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Internal Rotations . . . . . . . . . . . . . . . . . . . . . . . 97
Rotating Around a Bond . . . . . . . . . . . . . . . . . . 98
Rotating Around a Specific Axis . . . . . . . . . . . . 98
Rotating a Dihedral Angle . . . . . . . . . . . . . . . . . 98
Using the Rotation Dial . . . . . . . . . . . . . . . . . . . 99
Changing Orientation. . . . . . . . . . . . . . . . . . . 99
Aligning to an Axis . . . . . . . . . . . . . . . . . . . . . . 99
Aligning to a Plane. . . . . . . . . . . . . . . . . . . . . . . 99
Resizing Models . . . . . . . . . . . . . . . . . . . . . . . 100
Centering a Selection . . . . . . . . . . . . . . . . . . . . 100
Using the Zoom Control. . . . . . . . . . . . . . . . . 101
Scaling a Model . . . . . . . . . . . . . . . . . . . . . . . . 101
Changing the Z-matrix. . . . . . . . . . . . . . . . . 101
The First Three Atoms in a Z-matrix . . . . . . . 101
Atoms Positioned by Three Other Atoms . . . 102
Positioning Example . . . . . . . . . . . . . . . . . . . . 103
Positioning by Bond Angles. . . . . . . . . . . . . . . 103
Positioning by Dihedral Angle . . . . . . . . . . . . . 104
Setting Origin Atoms. . . . . . . . . . . . . . . . . . . . 104
Chapter 6: Inspecting Models
Pop-up Information. . . . . . . . . . . . . . . . . . . . 105
Non-Bonded Distances . . . . . . . . . . . . . . . . . . 106
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