I do quite a few overlap analyses of compound sets in Instant JChem and would like to ignore salts when I run the analyses. Is there any way of doing this. Currently, I run high similarity searches but am not certain this picks up everything and is tedious to deconvolute. Thanks
Yes, the best way to do this is to use a standardizer on the JChem table being searched.
There is a standardizer action called "Remove fragment" that lets you do this (e.g. keep the largest fragment). When you define this standardizer on the table being queried (the target table) then the structures in that table as well as the query structures will have the salts removed before doing the search.
See here for more information about standardizer: https://www.chemaxon.com/products/standardizer/
Also note that standardizer needs a licence. If you do not have one then please contact sales at chemaxon dot com.