ChemDraw Chem3D: When I open a file containing X-ray diffraction data using the Cartesian Coordinates file Interpreter, the coordinates have shifted and the bond lengths are not what is expected from the data in the file.

When I open a file containing X-ray diffraction data using the Cartesian Coordinates file Interpreter, the coordinates of the structure that are built within CS Chem3D have shifted and the bond lengths are not what is expected from the data in the file.

This occurs when the settings found in the Build preferences dialog box are imposed on the structure. You should make sure that they are set correctly for your purposes before opening a file using any of the available file interpreters. For example, if you don't want the X,Y and Z coordinates shifted, deselect the Center in Window checkbox; if you don't want the standard measurements applied, such as bond length and bond angle, deselect the Apply Standard Measurements checkbox. If you do not want Chem3D to complete empty valences with hydrogens, deselect the Rectify checkbox. Lastly, you can change the bond proximate control to change the how far away to atoms must be before a bond is formed. When you choose the Cartesian Coordinate file interpreter within the Open file dialog box, you click the Options button, and check the settings there as well. For instance, if your X-ray data only contains the number of atoms, the atom symbols and the X,Y,Z coordinates, you should click the Missing connection table button, and deselect the Expect Atom Types and Expect Serial Numbers check boxes.