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Contents

Introduction
Generic options of Side-bar Applications
Side-panel Tools
Atom popup menu tools
Preferences

Introduction

This application contains tools for interactively querying the structure for distances, angles etc..

Generic options of side-panel applications

For all applications with a side-panel interface you can right-mouse click on the application name (Geometry) to give a pop-up menu with:
Hide/Show Hide or show the tools for the application. This can simplify the side-panel if you are not using Geometry for a while.
Close Remove the application completely from the side-panel.
Preferences Open a window with Preferences for the application.
Help Show the help page for the application.

Side-panel tools

When you click on a tool such as Distances it becomes the active tool and is highlighted in gold; clicking on it again or clicking on another tool will switch it off. While there is an active tool clicking on atoms and/or bonds with the left mouse button selects that atom or bond for the tool.

Distances
Pick pairs of atoms for their inter-atomic distance to be shown on the display.
Distances/angles
A new text display window labeled Geometry: Distances/angles is opened. A new line appears in the window for each atom picked and this lists: the model name and atom name of the picked atom; the distance from the atom to the previously picked atom; the bond angle defined by this and the two previously picked atoms; and the torsion angle defined by this and the three previously picked atoms. The distances between pairs of atoms are also shown on the display.
Clear contacts
Clears all interatomic distances from the display.
Export Vectors
Write the currently displayed interatomic distances to a .vector file.

Atom popup menu tools

While the geometry application is open the following tools are on the popup menu which appears when an atom is clicked with the right mouse button:

Geometry - first atom
Select the first atom for interatomic distance calculation
Geometry - next atom
Select the next atom and show the distance to the previous atom.
Contact around this atom/residue
Show close contacts around the picked atom or residue

Preferences

The Preferences window can be accesses by clicking on the side-panel title Geometry with the right-mouse button or it is in the Applications folder of the Preferences window.

You can set the Maximum contact distance and Minimum contact distance for the Contact around this atom/residue tool.
The Line/label colour can be changed