Frequently Asked Questions

    License

    Why can Marvin JS not find a valid license?

    There are multiple causes why this can happen. As the client-side license is granted through the web services, you must connect them manually if you are not using the bundled version (the version does the connecting automatically). It is also possible to get this error when you are using a custom web services endpoint. In this case, make sure the license path is correctly added through the marvin.Sketch.license call. For more information about license installation, see Installation and Upgrade. If none of the above applies, it is likely you want to use the legacy licensing. In this case, please contact Sales or our Support.

    Copy - Paste from/to Marvin JS

    Why do I lose items during copying (cutting) from Marvin JS application and pasting it?

    In Marvin JS, two copy formats are available: MRV or Mol V2000. If your administrator chose the latter, all the items which are not supported by Mol V2000 format, will be lost. Inside the application, we recommend using Duplication action (can be found in the Selection Context menu) or (if it is possible) to ask your administrator to change the copy format from MOL to MRV.

    When I press Cut/Copy/Paste buttons, instead of the action, I get a message which says I need to use the keyboard shortcuts. Why is that?

    This message appears in browsers which (by security reasons) do not give direct access for JavaScript applications to your system clipboard. In these cases, Marvin JS will remind you to use the keyboard shortcuts which will make the copy/paste function available via browser actions.

    I cannot paste my structure copied from MarvinSketch. How can I solve this?

    In Marvin Sketch, the MRV format is the default copy format in Windows OS. Although it is still possible to copy structures in OLE format. Microsoft OLE format is a binary format, which - because of security reasons - is not allowed to be copied or pasted by any of the browsers. There are some workarounds to paste your structures into Marvin JS canvas:

    1. By using the Copy as functionality that is available from the context menu or by pressing Ctrl+K, you can specify copy format. Please consider that Marvin JS only supports MRV and MOL V2000 formats natively, for pasting other formats, the appropriate web service should be installed. Marvin Sketch will remember your last choice, thus for successive copying, you only need to remember the Ctrl(Command)+K and Enter combination.
    2. In Marvin Sketch Ctrl(Cmd)+M shortcut is reserved for MRV copy. You can use this shortcut instead of Ctrl(Command)+C action for copying the selected structure.
      Copy paste workflow between Marvin JS and MarvinSketch

    I cannot paste my structure copied from other vendor's applications. How could I do this anyway?

    Some chemical editors handle the structures in special binary formats (e.g. SKC, CDX...), which are not allowed to paste by any browsers, because of security reasons. In most of these applications, there is an option that allows us to copy as another, text-based format. For example Mol V2000, Mol V3000, SMILES, SMARTS, etc. Copy your structure as one of the text formats, and you can easily paste these into Marvin JS. It is also a good solution, if you save your structure to the binary format, then open it via Import dialog or just Drag&Drop your file from your file system to Marvin JS canvas.

    How can I copy molecule names as text?

    You can display texts in Marvin JS in text-boxes. Copy your text into the clipboard, then open Marvin JS, select the Text tool and left-click on the Canvas. Paste the molecule name into the opening Text dialog, then press the OK button.

    Reactions

    How can I export my drawing as a reaction?

    If the structure on the canvas contains only a single step reaction, then it will be automatically exported as a reaction file by Marvin JS as default. This means, there will be separate blocks for reactants, products, and agents in the exported file; making it possible to use the file in a reaction search. In this case, only those file formats are available in the Export dialog which supports reactions (MRV, RXN, SMILES, CXSMILES, SMARTS, CXSMARTS, CML, RXN V3000, SDF, CSSDF, CDX, SKC).

    How multi-step reactions are exported? Can Marvin JS export multi-step reactions?

    Multi-step reactions are exported as graphical structures in MRV, CDX, SKC format. It means, Marvin JS can save these types of reactions, but roles like reactions/products/agents are not distinguished.

    How can separate components be handled together during reaction export? (For example in case of salts.)

    • Reactants or products: Marvin JS handles components which have no plus sign between as one 'merged component' during export automatically.
    • Agents: Agents should be selected manually to be handled together. Please check this page to see how: How to merge agents?