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Sample Workflows and Usage ​

Below are some examples of workflows that can be accomplished in Nanome v2, including using MARA to open and prep structures.

Opening from MARA ​

  • Log into MARA and Nanome with the same account credentials.
  • Create a new MARA chat.
  • Prompt MARA to load a structure of your choice and MARA will render the structure in the Molstar Visualizer.
    • Example Prompt: "Load 67o" --> loads in Molstar viewer panel.
  • Click the button to "Open in XR", and a message will appear in MARA.
  • Go to the Nanome app in your XR headset - the structure will be there as a new workspace named after the chat.

Note: The workspace will be set to 'Private' permission level, so it cannot be shared.

Limitation: Each 'open in headset' action from MARA will create a new workspace. Representations might not be exact between Molstar and Nanome. In those cases, our team is happy to help. Please reach out to us at support@nanome.ai to help us build solutions for representations.

Sharing Workspace ​

  • Open Collaboration and click ‘Permissions’. There are two main methods to do this:
    • Set the workspace code from ‘Private’ to ‘Viewer’ or ‘Editor’ depending on your needs, then tell your colleagues the code.
    • Invite a user directly by email if they have a Nanome account. (This must be an exact email match, there is no auto-completion.)
  • Each user that joins with the code or was added via email will appear in the workspace list.
    • Each user permission can be individually managed (including setting to none).

Displaying Interactions Between Structures ​

  • Make sure your structures show up as entries in the main section of the Application Menu.
  • Find one of the entries, then click on the '3 dots' button to the right of the entry name.
  • Select 'Add inter-entry interactions' from the pop-up menu, then choose the other entry you want to view and click 'Run'.
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Aligning Proteins in XR ​

  • Make sure your proteins show up as entries in the main section of the Application Menu.
  • Select one protein in the entry list, then click on the 'align' button to the right of the entry name.
  • In the pop-up menu, select the protein you want to align with, then click 'Align'.
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