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Administrator Example 3 In Example 3, however, the hashed bond is ambiguous because both atoms on the hashed bond are attached to more than two bonds. In this case the hashed bond is treated like a solid bond. Wavy bonds are always treated like solid bonds. H-Dots and H-Dashes are also used to indicate stereochemistry. H-Dots become hydrogen atoms attached to carbon atoms by a wedged bond. H-Dashes become hydrogen atoms attached by a wedged hashed bond. Example 4 H H H H H Example 4 shows cis-decalin on the left and trans-decalin on the right as they would be drawn in ChemDraw to be read in by Chem3D. Of course, you can specify a cis fusion with two H-Dots instead of two H-Dashes. As a general rule, the more stereo bonds you include in your model, the greater is the probability that Chem3D will make correct choices for chirality and dihedral angles. When converting two-dimensional structures, Chem3D uses standard bond lengths and angles as specified in the current set of parameters. If Chem3D tries to translate strained ring systems, the ring closures will not be of the correct length or angle. Labels Chem3D uses the atom labels in a two-dimensional structure to determine the atom types of the atoms. Unlabeled atoms are assumed to be carbon. Labels are converted into atoms and bonds using the same method as that used to convert the text in a text box into atoms and bonds. Therefore, labels can contain several atoms or even substructures. cis-decalin trans-decalin 618• 2D to 3D Conversion <strong>CambridgeSoft</strong> Labels
Appendix F: File Formats Editing File Format Atom Types Some file formats contain information describing the atom types that the file format understands. Typically, these atom types are ordered by some set of numbers, similar to the atom type numbers used in the Atom Types table. If the file format needs to support additional types of atoms, you can supply those types by editing the file format atom types. Chem3D 9.0 uses XML tables for storing file formats. You can edit these tables in any text editor or in Chem3D by selecting the table you want to edit from the Parameter Tables list on the View menu. TIP: The .xml files are in the path ...\Chem3D\C3D Items\ Name Each atom type is described by a name. This name is a number found in files of the format described by the file format. All names must be unique. The records in the table window are sorted by name. NOTE: While names are similar to atom type numbers, they do not have to correspond to the atom type numbers of atom types. In some cases, however, they do correspond. Description The second field contains a description of the atom type, such as C Alkane. This description is included for your reference only. The remaining fields (Symbol, Charge, Maximum Ring Size, Rectification type, Geometry, Number of Double Bonds, Number of Triple Bonds, Number of Delocalized Bonds, Bound to Order and Bound to Type) contain information corresponding to the information in an Atom Types table. File Format Examples The following sections provide examples of the files created when you save Chem3D files using the provided file formats. Alchemy File The following is a sample Alchemy file 1 (Alchemy) created using Chem3D for a model of cyclohexanol. The numbers in the first column are line numbers that are added for reference only. 1 19 ATOMS 19 BONDS 2 1 C3 -1.1236 -0.177 0.059 3 2 C3 -0.26 -0.856 -1.0224 4 3 C3 1.01 -0.0491 -1.3267 5 4 C3 1.838 0.1626 -0.0526 6 5 C3 0.9934 0.8543 1.0252 7 6 C3 -0.2815 0.0527 1.3275 8 7 O3 -2.1621 -1.0585 0.3907 9 8 H -1.4448 0.8185 -0.3338 10 9 H -0.8497 -0.979 -1.9623 11 10 H 0.0275 -1.8784 -0.6806 12 11 H 1.6239 -0.5794 -2.0941 13 12 H 0.729 0.9408 -1.7589 1. Alchemy III is a registered trademark of Tripos Associates, Inc. Appendices <strong>ChemOffice</strong> 2005/Appendix File Formats • 619 Editing File Format Atom Types
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