Dialog Box - called from: Input1 Menu
This lists the current bonds. Click on individual items in the list, then on the buttons to revise, delete or add bonds. The Revise and Add Bonds buttons call up the Bond Data dialog.
To calculate bond distances and angles, for use in bond and polyhedra input, use the Coordination button in the Input Atoms dialog.
You can also click the Generate from Radii button, to derive bonds automatically.
PDB quick bonds check box. In the case of Protein Data Bank (PDB) structures, ATOMS is able to use the information on residues which is present in the file, as well as CONNECT records, to greatly decrease the time required to locate bonds, compared to standard ATOMS methods for crystals. However, if some bonds are missing or duplicated it may be necessary to uncheck this box.
Color mode. For stick bonds you can use either the color specified in the Bond Data dialog for the entire bond, or the atom colors in a half-and-half arrangement.