Builder Preferences

This tab allows you to set preferences that control the inclusion of hydrogens, adjustment of bonds and zoom level in building operations, and several other related settings.

Allow united atom types while building

The use of united atom types can cause problems for users who do not want implicit hydrogen atoms in their structures, such as Jaguar users. United atom types with implicit hydrogens are assigned by default when hydrogens are deleted from heavy atoms. If this option is cleared, united atom types are never assigned when atoms and bonds are explicitly deleted, atoms are retyped, or structures are drawn freehand. Instead, the atom types remain unchanged, or explicit radical types are assigned if they are available. United atom types are used regardless of this option if a hydrogen treatment that requires united atom types is applied, or when reading in a structure file (such as a PDB file) that does not have explicit hydrogens present.

Adjust bond lengths when atom type is changed

When atom types are changed, bond lengths are automatically adjusted to give a "reasonable" bond length. This behavior is undesirable if the geometry is already correct (such as from a crystal structure) and it is only necessary to change the atom types. Clearing this option prevents the adjustment of bond lengths.

Adjust number of hydrogens following build operations

The number of hydrogen atoms is adjusted by default to maintain a normal valence during formal charge, bond order, or retyping changes. This behavior is not always desirable, and can be prevented by clearing this option.

Automatically minimize adjusted hydrogens following bond order operations

Perform a short minimization on hydrogens that are added or removed due to bond order changes. This alleviates unrealistic geometries that can occur when changing the bond order.

Automatically minimize fragments after adding

Perform a short minimization on new fragments after they are added to a structure, or the structure is adjusted by using items on the New Fragment menu like Flip to Alternate H or Change Connection Point. This action should alleviate clashes with the existing structure.

Delete terminal atoms

When deleting an atom, terminally attached atoms can be deleted or retained. If this option is selected, they are deleted. For example, if you delete the carbon atom of a methyl group, the hydrogen atoms attached to the methyl group are also deleted if this option is selected. If you delete the middle carbon atom in propane, the two hydrogens attached to this atom are deleted, but the carbon atoms are not because they are not terminal atoms.

Include alternate positions in local transformations

When translating or rotating a set of atoms (local transformation) that include atoms with alternate positions, change the coordinates in the same way for both alternate positions. Deselect this option to transform the displayed location and not the alternate.

Include zero-order bonds when defining molecules

When determining which atoms are bonded together to form molecules, consider atoms that are joined by zero-order bonds to belong to the same molecule. This option is selected by default.

These settings determine how geometry minimization is performed.

Freeze unselected atoms during geometry minimization

Freeze the atoms that are not selected in the Workspace when geometry minimization is done. By default, atoms within 5 Å of the selected atoms are restrained with a moderate restraint, and atoms within 5 Å of these atoms are restrained with a much tighter restraint, with the remaining atoms are frozen.