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Are there any differences between substructure searches in WebCSD and ConQuest?

Solution

Note: The following information applies only to WebCSD version 1 (legacy WebCSD).

​Although the substructure search engine behind WebCSD is entirely new and does not work in the same way as ConQuest, the results of substructures searches using these two programs are generally identical.

It is important to note though that there is a subtle difference between the two search programs - a WebCSD substructure search currently requires that the fragments drawn are within the same connectivity. ConQuest on the other hand by default will allow a user to define fragments in unconnected moieties (e.g. co-crystals, solvates or salts) and even allows one to define contacts between these non-covalently-bonded fragments. Identical substructure search behaviour between the two systems can be achieved by using the option in the ConQuest sketcher to request "All Atoms in Same Molecule" under the "Atoms" menu.