Appendix B. Markush Structures

As a fundamental feature of the system, the Markush and non-Markush structures are stored in separate structure tables, but have the same method for corporate ID generation and storage hierarchy. They support the same additional data attached to the preparation level as well.

For a list of supported Markush features in JChem storage please consult the link provided below:


All the Markush structures submitted to registration fall to Staging intentionally, they always have to be reviewed. None of the structure related operations are performed on the structure: e.g. salt/solvate stripping from the structure itself would not work, on the other hand the specified and attached salts are properly considered.


All the Markush structures submitted to registration from the Bulkloader page fall to Staging. None of the structure related operations are performed on the structure: e.g. selected structure checkers and fixers; salt/solvate stripping from the structure itself would not work (as in the case of automatic single registration).


The Markush submissions are displayed the same way as the non-Markush ones in the ’Staging table’. The status of a Markush structure is typically "Markush structure found", except for those cases where the validation process fails prior to the Markush check, e.g. because of an invalid ID provided.


Individual submissions in the Staging Area are displayed in a uniform style, regardless of the fact if it is a Markush structure or not. The structure editing area shows the Markush structure if available, that can be freely edited here.

  • ’Save’, ’Restore’, ’Assign’, ’Unlock’, ’Register with CN’ actions work as expected.

  • ’Show possible hits’ action shows all the Markush structure hits – and only those ones – if the submission contains a Maskush input; it shows only non-Markush hits if the input structure is not Markush. The same options are available that can be used for the non-Markush structures, and all the Markush matches will be presented that have an overlap with the input one.

  • ’Register’ action: the same feature applies for the matchlist dialog during the registration as in the case of ’Show possible hits’ above.

  • The system would not allow the registration of Markush structures as part of multi-component structures.

  • Some of the system switchers and structure checkers/fixers of the page would not be applicable in case of Markush structures (like ’Analyze Salt Solvate Fragments’), those will be automatically bypassed.


All the features work as before, with the same modifications on the matchlist that are descibed above, on the Submission page. The same storage hierarchy is created for Markush and non-Markush structures.

  • Structure shown as Markush in the relevant cases.

  • When Markush structure is amended to a non-Markush one (or vice versa) the new structure is taken account when providing the matches, the original structure and its type is completely disregarded.


Audit structure images (and the ones provided in the summary and history dialogs as well) show the appropriate images, even Markush if needed.

Salt Search

Salt search functionality is not affected by the Markush structures, the use of Markush structures as salts/solvates is not allowed.