You cannot install updates while the software is running. If you have closed all CCDC programs but the updates still won't install, try rebooting your computer to clean up any stuck processes.
Sometimes there may be issues with connecting to our update servers for a variety of reasons, and we do try to improve this process as we discover issues.
If you are unsuccessful in obtaining updates from the Mercury (or Hermes) Help > Check for Updates... menu, it is possible to download updates from the CCDC website and apply them manually.
To install the updates manually the Downloads page from the Support and Resources section of the website (https://www.ccdc.cam.ac.uk/support-and-resources/downloads/) includes a "Data and Software Updates" section with the update installers available. On Linux you must make the updater executable before running it.
You are also able to run the automatic updater manually from a terminal/command prompt using:
'autoupdate --settings_file [path to CSDS installation]\update_data.ini'
'autoupdate --settings_file [path to CSDS installation]\update_software.ini'