Edit internal coordinates

Meanings of buttons and entries in the internal coordinate editing window: Adding coordinates:
When the 'Edit internal coordinates' window is openened your mouse is set to picking mode, i.e. you can click on atoms in the VMD window to select bonds angles and dihedrals and impropers. If you select an existing bond it will be removed, if you select an existing angle, dihedral or improper, the selection will be ignored. The type of coordinate to be added is specified by the buttons in the 'Edit' window. The autogeneration of angles and dihedrals containing the newly added bond can also be requested.

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.