This menu contains operations that handle geometry-related tasks. These include measurements of interatomic distances, bond angles and dihedral angles. Each of these functions has a toolbar shortcut. Using Preferences dialog, it is possible to set quick distance/angle calculation, where the values are computed for the currently selected atoms. For instance, if two atoms are selected, the distance is computed without displaying the dialog for picking the atoms.

Detecting steric clashes

Sirius has the ability to detect steric clashes and hydrogen bonds within the loaded structures. Both dialogs use very similar selection mechanisms and differ only in the specifics of each search. For example, in the steric clash detection dialog, the user may select the cutoff distance, and in the hydrogen bond detection dialog the maximum length of a hydrogen bond can be specified. Both dialogs provide the ability to define two groups of atoms between which the interaction should be detected. If the search should be restricted to intramolecular interactions, the right half of the selection panel is disabled. For instance, if an entire structure is selected for hydrogen bonding check, all intramolecular hydrogen bonds will be detected. On the other hand, if two separate groups of atoms need to be defined, the "intermolecular" option should be selected. In this case, interaction between the groups will be evaluated.

Detecting hydrogen bonds

Hydrogen bonds can be detected either in intramolecular or intermolecular context. They are located using interatomic distances, as well as geometry constraints that limit acceptable hydrogen bonding arrangements by 60 degree deviation in either direction. Once the hydrogen bonds are displayed, they can be picked in the display and managed individually via Display Marker Manager (Components -> Manage display markers).