Deleting coordinates:
You can delete the coordinates that are currently selected in the
coordinate list by clicking the delete button (or hitting the Del
key while the focus is on Paratool's main window. Bonds can also be
removed by clicking on the two participation atoms. Note that deleting
a coordinated implies the removal of all dependent
coordinates. E.g. if you delete a bond, all angles, dihedrals and
impropers containing that bond will also be removed.
Delete all internal coordinates:
With this button yu can completely clear the internal coordinate
list. However, the bondlist in VMD defining which bonds are displayed
graphically is not affected, whereas if you delete selected bonds
their counterparts in VMD's bondlist are removed.
Fix/Unfix coordinates
With these buttons you can fix or unfix selected internal coordinates
in subsequent geometry optimizations. This can be useful for potential scans.
Bond regeneration:
VMD's bondlist is regenerated based on atom distances, all removed
bonds and their dependent coordinates will also be removed from the
internal coordinate list. The maximum atom distance for a bond can be
specified.