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3D Visualiser Information


Keyboard shortcuts

D : toggle the display of disordered atoms

F : toggle full-screen mode

G : toggle hit highlighting

H : toggle the display of hydrogen atoms

I : display instructions (in external website)

K : toggle rocking animation

P : toggle spin animation

R : reset display view (clearing measurement display)


Visualiser Mouse Controls

Left-click : Atom highlighting

Left-click and drag : rotate structure

Scroll wheel : zoom structure

Right-click : Change rotation centre

Right-click and drag : pan structure


Measurement instructions

The visualiser allows the measurement of distance, angles and torsions. To display measurements, first highlight the required atoms in the visualiser. The measurement buttons, in the bottom-left of the 3D viewer window, will become active - for example, highlighting two atoms will allow the option of displaying the distance between those two atoms; if three atoms are selected the option for an angle measurement is available.


It is also possible to display measurements using a double click on the last atom of the measurement selection. For example, to measure a distance highlight one atom with a single mouse click, and double click the second atom for the distance to be displayed.


Associating file types with programs

The storage format for 3D CSD structures is mol2, which opens using Mercury, our free visualisation software. Other programs in the CSD software portfolio which can also open mol2 files include enCIFer, and Hermes.

The instructions to open the CSD structure in Mercury are below.

When you install Mercury you can indicate that you want mol2 files to open by default in Mercury by selecting the checkbox during the installation.
The default installation location for Mercury.exe is in the CSD system folder in the C:\Program Files\CCDC\Mercury folder

To manually set that you want mol2 files to open in Mercury you should run through the following steps for your operating system.

Windows 10 / 11
  1. Right-click the Start button and choose Settings
  2. Select Apps from the list
  3. Choose Default apps from the left-hand menu
  4. Scroll down and select the Choose default apps by file type link
  5. Locate the file extension (e.g. .mol2) for which you want to change the default program
  6. In the Choose default apps by file window, pick Mercury to associate with the file extension
  7. Mercury should now open whenever you open a mol2 file