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Tool: Build Structure

The Build Structure tool builds and modifies atomic structures. The equivalent commands are build and bond. See also: Rotamers, Modeller Comparative, rna, torsion

Build Structure can be opened from the Structure Editing section of the Tools menu and manipulated like other panels (more...). Sections:

  • Start Structure
  • Modify Structure
  • Adjust Bonds

    Start Structure

    The Start Structure section of Build Structure adds new atoms or molecules independent of any pre-existing atoms. See also: open, angle, torsion

    Options are to Add:

    Modify Structure

    The Modify Structure section of Build Structure can change the element, valence (number of directly attached atoms), and/or geometry (spatial arrangement of attached atoms) of a single selected atom at a time. Hydrogens are appended as needed to fill the valence. Building outward can be done by successive cycles of modifying a hydrogen attached to the previously modified atom.

    Clicking Apply changes the selected atom as specified:

    Clicking the Delete button at the bottom of Modify Structure removes any selected atoms and bonds. See also command: delete, menu: Actions... Delete

    Adjust Bonds

    The Adjust Bonds section of Build Structure allows adding and deleting covalent bonds. A bond can also be deleted using its selection context menu. See also: bond, delete

    Covalent Bond Radii

    Approximate covalent bond radii are used to guess the connectivity of untemplated residues (when not specified in the input structure file) and to generate crude bond lengths for building atomic structures.

    Selected covalent bond radii (Å)
    H 0.23
    B 0.83
    C 0.68
    N 0.68
    O 0.68
    F 0.64
    Si 1.20
    P 1.05
    S 1.02
    Cl 0.99
    Se 1.22
    Br 1.21
    I 1.40

    A complete list, obtained many years ago from documentation from the Cambridge Crystallographic Data Centre, can be found in Table III of:

    Determination of molecular topology and atomic hybridization states from heavy atom coordinates. Meng EC, Lewis RA. J Comput Chem 12:891 (1991).

    UCSF Resource for Biocomputing, Visualization, and Informatics / September 2020