Chem3D 8.0 Manual - CambridgeSoft

Administrator2. The first line of a Cartesian coordinate file isfollowed by one line of data for each atom in themodel. Each line describing an atom beginswith the symbol for the atom. This symbol mustcorrespond to a symbol in the Elements table.The symbol can include a charge, such as N+.The symbol is followed by the serial number.3. The serial number is followed by the threecoordinates of the atom. If you have specifiedcrystal cell parameters in the first line of thefile, then these numbers are the fractional cellcoordinates. Otherwise, the three numbers areX, Y, and Z Cartesian coordinates.4. Following the coordinates is the atom typenumber of the atom type for this atom. Thisnumber must correspond to the code of an atomtype record specified in the file format atomtype table. For more information, see “EditingFile Format Atom Types” on page 33.5. Following the atom type number is theconnection table for the atom. You can specifyup to ten other atoms. The connection table fora Cartesian coordinate file can be listed in oneof two ways: by serial number or by position.Connection tables by serial number use theserial number of each atom to determine thenumber that appears in the connection table ofother atoms. All serial numbers must, therefore,be unique.Connection tables by position use the relativepositions of the atoms in the file to determinethe number for each atom that will appear in theconnection table of other atoms. The first atomis number 1, the second is 2, etc.6. To create multiple views of the same set ofatoms, you can flow the descriptions of theatoms with an equal number of linescorresponding to the same atoms with differentcoordinates. Chem3D generates independentviews using the additional sets of coordinates.Samples of Cartesian coordinate files withconnection tables by position and serial number fora model of cyclohexanol are shown below. Toclearly illustrate the difference between the twoformats, the serial number of the oxygen has beenset to 101.19C 1 0.706696 1.066193 0.50882 1 2 4 7 8C 2 -0.834732 1.075577 0.508789 1 1 3 9 10C 3 -1.409012 0.275513 -0.668915 1 2 6 11 12C 4 1.217285 -0.38632 0.508865 1 1 5 13 14C 5 0.639328 -1.19154 -0.664444 1 4 6 15 16C 6 -0.89444 -1.1698 -0.646652 1 3 5 17 18O 101 1.192993 1.809631 1.59346 6 1 19H 9 1.052597 1.559525 -0.432266 5 1H 10 -1.211624 2.125046 0.457016 5 2H 11 -1.208969 0.640518 1.465607 5 2H 12 -2.524918 0.2816 -0.625809 5 3H 13 -1.11557 0.762314 -1.629425 5 3H 14 0.937027 -0.8781 1.470062 5 4H 15 2.329758 -0.41023 0.437714 5 4H 16 1.003448 -2.24631 -0.618286 5 5H 17 1.005798 -0.76137 -1.627 5 5H 18 -1.295059 -1.73161 -1.524567 5 6H 19 -1.265137 -1.68524 0.271255 5 6A36 • CambridgeSoftFile Format Examples