I have been using IJC for sometime and love the Substructure search feature. All of a sudden I dont have that option anymore. The other search types are listed (superstructure, exact fragment...) but no substructure. I have just updated to the newest version but still nothing. What do I do?
I suspect that what has happened is that you have imported data that contains structures with query features.
When a file is imported IJC tries to guess the best structure table type to use based on the contents of the file.
For normal molecules the table type "Molecules" would be used. If the data contains reactions then the table type "Reactions" will be used, and if the data contains query structures then the table type "Query structures" will be used.
Each of these specific table types allows searching to be more specific to the type of data. For instance, for query structures substructure search makes no sense, and superstructure is the default search type.
What has probably happened is that your data probably contains a small number of query features (list atoms, generic atom types etc.) which has caused the query strucutres table type to be chosen by default.
When this happens you need to manually set the table type to "Any structures" which is the catch all table type, and will handle substructure searching.
You do this by changing the Table contents property of the JChem table when you create it. See here for details:
I hope this helps