Compound Registration FAQ

T he FAQ (Frequently asked questions ) page contains listed questions and answers, commonly asked about the Compound Registration.

  1. How can I register a compound with parent multiplicity 2 and salt multiplicity 3?

    On the Registration or Submission page you can add the salt or solvate with the appropriate multiplicity, then you can set also the parent multiplicity. Please note, that only positive integer numbers can be set for salt multiplicities and positive numbers with one decimal can be set for solvate multiplicities (the decimal places in case of salts/solvates can be configured).

  2. Can I register multicomponent structures?

    Yes, different types of multi-component compounds exist, based on the level of accurac y of the composition information: alternates, formulation and mixtures. A multi-component compound is distinct from a structure having multiple fragments within a structure field that has been registered as a single compound (without registering each fragment individually). An alternate is a multi-component compound without quantitative composition information. A formulation is a multi-component compound with exact quantitative composition information. A mixture is a multi-component compound with semi-quantitative composition information.

  3. Can I register multifragment structures?

    Multifragment structures can be registered, and are handled as a single molecule. Fragments representing salts/solvates can be automatically extracted and converted to the proper salt/solvate and multiplicity information during the registration process.

  4. Can I register dimer structures by drawing the monomer and setting 2 for the parent multiplicity?

    No. Greater than 1 parent multiplicities must be used with salt/solvate info. For registering dimer structures you must draw or import the dimer.

  5. Can I register peptides?

    Yes, a text file, which contains only one type of sequence (only one or only three lettered sequences but not both) can be pasted or imported in order to register it. It is possible to register in a contracted, expanded or ungrouped form. In case if autoregistration is not possible, you can register it from the Staging area (manual registration).
    For more details please consult:

  6. Can I register polymers?

    Yes, the simplest form of a polymer (without detailed structural information related to the crossing bonds) can be registered. Just draw the repeating unit, click the Group tool on the tooolbar, select the atoms you want to be included and set the Monomer (mon) as group type.
    Unfortunately, structural repeating unit (SRU) type polymers, due to molecular weight calculations issues, cannot be registered.
    For more details please consult:

  7. Can I register Markush structures?

    Yes, it is possible to register Markush structures within the system. The registered Markush structures are stored separately, but treated the same way as all the other ones: parents, versions and preparations are created; Markush matches are offered during the registration, etc. There are two major limitations: (1) Markush structures cannot be registered automatically, all of them are forced to be reviewed, (2) Markush structures cannot be used as components in multi-component structures.
    Searching with Markush structures is possible on the Search page, even against the non-Markush structures (in that case all members of the Markush query will be returned as hits, even if they are only part of a multi-component structure).

  8. Can I bulk register structures?

    Yes, there is a specific Upload option for this purpuse. You can load an SDFile and map its fields to the appropriate Compound Registration fields (or use a previously saved mapping template), and you can even reset the system switchers and the Structure Checker and Autofixer options on the fly. The original and fixed structures can be previewed before initiating the registration.
    Please note that currently only Single type compounds can be uploaded.

  9. Can I configure the system to store my compounds only on 2 levels (parent-lot)?

    It is possible to configure the system to hide the version level on all the GUI pages and in all confirmation messages, so from the user perspective the system behaves like the data would be stored only on 2 hierarchy levels. You can also configure the system to generate registration IDs on the lot (preparation/batch) level (e.g.CXN1234-01), which takes care of the lot counter even if you move a lot from one parent to another (it is regenerated according to the new parent). In addition, you can configure the downstream service to neglect the version level, so your downstream systems do not need to even know about it. And, which is the most important: if later you decide to upgrade your system to a 3-level hierarchy, it can be simply done by a configuration!

  10. Can I autoregister a preparation (lot) under a given Id?

    Yes, use the Register with CN option, which is available on the Registration and Submission pages.

  11. How can I register a compound without structure, or with only partially known structure?

    The Chemically Significant Text (CST) field is especially for that purpose. CST only records cannot be autoregistered, if the CST is used for the first time. The records will fall to the Staging area with "UnknownCST" status message, from where they can be registered (manual registration). If the CST is present in the Chem. Sig. Text dictionary (Administration page), the record can be autoregistered.
    If the structures of two compounds are the same (or empty), but the CSTs are different, than these compounds are considered as 2D matches (not as duplicates).

  12. Is JChem Oracle Cartridge supported on the back-end?

    The DB storing of the Registry contains normal JChem tables, and the direct support of the Cartridge is not needed, because the Registry tabled can be directly joined to other JChem Cartridge tables, if required.

  13. Can I use other editor than Marvin JS on the GUI pages?

    Yes, Marvin applet and ChemDraw are supported, but for the latter one you need a valid installation of ChemDraw on your computer.

  14. I changed the Structure editor to Marvin applet, but I cannot use it in Chrome.
    Applets are not supported by Chrome. Marvin applet can be used in InternetExplorer or FireFox, although it is much slower than the Marvin JS.

  15. I changed the Structure editor to ChemDraw, but I cannot use it in my 64-bit InternetExplorer, althought it works fine in FireFox and Chrome.

    ChemDraw has not support for 64-bit plugin. FireFox and Chrome are 32-bit, and therefore the ChemDraw plugin works fine in it.

  16. Why does the VersionFix page appear in certain cases?

    In the case when the automatic version fix cannot be performed, a version fix page will appear. In a version fix page the user can decide and manually correct the version structure (according to the parent structure).

  17. What to do if my compound fell to staging due to a quality check, but I believe that this is the correct structure?

    You should switch off the Perform Quality Checks option on the Submission page. You need to have the corresponding privileges to do so.

  18. What to do if my compound fell to the Staging Area because of a Structure Checker error that not belongs to the quality checks (e.g. Racemate Checker error)?

    If you have an automatic fixer defined for this checker, you can select it from the popup list of that checker, and, than it will be applied on the fly when you register your structure (in case of the Racemate Checker the Convert to Unknown fixer can be a possible option). You can test the effect of the fixers using the Show Possible Hits option.
    If you do not find any appropriate fixer for the checker, you have to modify the structure to pass the failing structure checker, or you can contact a Registrar to fix the submission for you.

  19. Can I modify a submission in the Staging area without registering it?

    Yes. Submissions can be modified (e.g. LnbRef, Molweight, Restriction, CST, structure) and then saved. These will be marked as "Saved submissions" in the Staging and their original structure can be restored later or they can be registered.

  20. Can I have a detailed status message in the Staging area about the submissions?

    For the submissions in the Staging area a status message is displayed in the last column. When hovering over the status message a detailed message is also displays for the given submission. If a submission is opened from the Staging in the Submission page, the short and detailed message is also displayed.

  21. What are the meanings of the different molecular weights indicated in the result table on the Search page?

    Molweight (structure) refers to the molecular weight of the preparation structure (neutral, charged or isotopic), whereas the Molweight (structure + salt) refers to the molecular weight of the preparation structure together with the salt or solvate which belongs to the version/lot.

  22. Can I add a salt or isotope to an already registered compound?

    Yes, on the Details page, from version or lot level, salts/solvates and/or isotopes can be added to the structure. Then click on the Amend button. If the amendment was initiated from lot level and it was the only lot of the version, the Ids will be kept. Otherwise the lot will be moved under another version. If the amendment was performed on version level, the Ids will be kept.

  23. If I add a salt or isotope on the Details page to an already registered structure, my compound will receive a new parent Id?

    No. In case of salt/solvate and/or isotope additions, which can be performed only from lot or version level, the parent Id (PCN) will be always kept.

  24. Can I amend an already registered single type compound to be a multi-component compound?

    Yes. From version or lot level single compounds can be amended to multi-component ones. The multi-component compound might keep the PCN (in case when amending a version of a single version tree or in case when amending a lot of a only lot of an only version tree), whereas the components (if they were not present yet in the DB) will receive new parent Ids, to which the components are linked in the multi-component compound.

  25. Can I amend a multi-component compound?

    Yes. Multi-component compounds can be amended from lot or version level. They cannot be amended from parent level.

  26. What will happen with the component structures in case when amending a multi-component compound?

    When the components are registered also as single compounds in the DB, and we try to amend a multi-component compound, first a warning is received, that "Components from this compound are already used elsewhere:..." To continue, we need to click on the "Continue amending the structure" button. After the performing the modifications (and clicked on the Amend), the "Who keeps the original PCN?" question is received. For the modified component, which exists also as a single compound in the DB, two options: "Modified" and "Other" are available. If choosing "Modified", the PCN of the modified component will be kept, while the lot under it will be moved under a new PCN. If "Other" is chosen, the modified component will receive a new PCN and the original one will be kept for the original component.

  27. What are the match actions in case when amending a compound and having an exact match?

    In case of exact match, the only option is to Accept the match. If other matches (e.g. 2D) are also present, no other match options are available for those.

  28. What are the match actions in case when amending a compound and having a 2D match?

    In the case when there is no exact match and there is one or more 2D / Tautomer / 2D&Tautomer match(es), the match actions are Accept, Replace or Unique. If the Amendment was initiated from lot or version level, all three match actions are valid. In case of parent level amendment only Accept and Unique options are valid.

  29. Can I amend a compound from version level when there is no lot under it?

    No. Version level amendment is not allowed for versions without lots. "Empty level error. Editing is disabled, when the lot level is empty." message should be received.

  30. Can I amend a compound from parent level when there are no versions under it?

    No. Parent level amendment is not allowed for parents without versions and lots. There are 2 cases:
    a.) For p arents, which are NOT components of multi-component compounds:
    "Empty level error. Editing is disabled, when the version level is empty." message should be received.
    b.) For p arents, which ARE components of multi-component compounds:
    "Parent used elsewhere. This structure is only used as a component of a multi-component structure (...). Please edit those structures instead." message should be received.

  31. How to search for an AMF component on the Search page?

    AMF components can be found on the Search page only if they were registered as single type preparations.

  32. What are the mandatory fields for a registration on the Registration page?

    Valid, unique external Ids (LotId and LnbRef, if the system is configured this way), valid source (configurable) and structure and/or CST is needed for a registration.

  33. Can I have Project based access to the registered compounds?
    Yes, the system can be configured in a way that Project based access is enabled. In this case registered compounds will be available to be viewed or to be modified only if the logged in user has the specify role for it. No registration will be possible using newly given Project name(s) as additional data. Otherwise, when Project based access is disabled, Project fields can be freely used as additional data, no filtering is made.

  34. Can I change the content of the additional data dropdown fields?

    Additional data fields in general, can be configured only by privileged user. If considering Project, as additional data in dropdown fields, there are two cases:
    a.) If Project based access is enabled
    If Projects were created on the Administration page (Access control tab), those will be present in the Project dropdown fields from Registration, Submission pages, only if the user has write role within the projects. Otherwise, a user who has no access to the Administration tab, cannot enter Project as additional data.
    b.) If Project based access is disabled
    If Projects were created on the Administration page (Access control tab), those will be present in the Project dropdown fields from Registration, Submission pages, regardless of the user and the specified role of the user within a project. A user who has no access to the Administration tab, can enter also other data than the previously defined ones.

  35. How can I migrate the compounds from my old registration system?

    There are 2 options:
    a.) We can provide a few migration algorithms that you can use instantly for direct migration, or modify it to fit your needs;
    b.) The BulkLoader page has an option to keep the original PCN and CN provided with the record, if there is no match to a previously registered compound.

  36. Is it possible to load all of my salts/solvates in a single action into the dictionary?

    Yes, similarly to compound upload, salt/solavtes can be bulk loaded from the Upload page of the application. Salts and/or solvates can be imported from an SDFile after mapping its fields to the appropriate Compound Registration fields (Name and salt solvate flag).