Managing and editing molecules

  • Updated

With molecule entities, you can edit your chemical structures and review their properties. You can also archive, add and remove tags, and review and restore previous versions of your molecules. This article covers these processes and managing/editing molecules.

View physicochemical properties

You can view a molecule’s properties calculated by RDKit by opening the molecule and clicking the Physicochemical properties tab.

  • Atom counts

  • Calculated octanol/water ratio (cLogP)

  • Molecular weight (MW)

  • Topological polar surface area (TPSA)

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View visual representations of chemical structures

To view the visual representation of a chemical structure, open the molecule and click the Chemical Structure tab. In this tab, you can also view the chemical formula and canonicalized SMILES string.

Edit chemical structure of molecules

From the chemical structure tab, users are able to edit the chemical structure. To edit the chemical structure, the user can draw a new chemical structure through MarvinJS or import a new molecule:

Note: Salts do not display on chemical structures at this time.

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View and restore previous versions

Molecules are versioned like other entities on Benchling, where a new version of a molecule is created when a user updates its chemical structure.

To view, rename, and restore previous versions of a molecule:

  1. Open the molecule, then click the clock icon in the right-side panel.

  2. Select the version you want to review. The version will display in the Chemical Structures tab in read-only mode.

  3. To clone, restore, or rename a version, click:

    • Clone from version to create a new file with this version.

    • Reset to version to restore this version.

    • Update version after entering a version name to rename the version.

Rename, move, archive, and tag molecules

To move, archive, or rename a molecule:

  1. Click the i icon in the right-side panel.

  2. In the pop-up window, click:

    • Update information after entering a new name or selecting a different folder.

    • Archive to archive the molecule.

To manage tags:

  1. Click the i icon in the right-side panel.

  2. Click the Tags tab in the pop-up window.

    • Enter a tag name and optional value, then click Add to create and add a tag to the molecule.

    • Hover over a tag and click the X to remove a tag from the molecule.

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