WebCSD 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)

Visualizer 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 visualizer allows the measurement of distance, angles and torsions. To display measurements, first highlight the required atoms in the visualizer. 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.

Opening structure in external viewer

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

To set that you want mol2 files to open in Mercury, follow the standard process to configure file associations for your operating system.

Windows 10/11

1. Right-click on the mol2 file
2. Select "Open With"
3. Click "Choose an app on your PC"
4. Browse to mercury.exe. The default location is in C:\Users\USERNAME\CCDC\ccdc-software\mercury
5. Click "Always"