12. Extract asymmetric unit protocol

Protocol designed to obtain in Scipion the smallest asymmetric subunit of an electron density map having certain types of rotational symmetry.
WARNING: This protocol requires the starting volume located in the center of coordinate axes to equal the center of symmetry with the origin of coordinates.
  • Requirements to run this protocol and visualize results:
    • Scipion plugin: scipion-em
    • Scipion plugin: scipion-em-xmipp
    • Scipion plugin: scipion-em-chimera
  • Scipion menu:
    Model building -> Preprocess map (Fig. 12.12 (A))
    Protocol **xmipp3-extract asymmetric unit**. A: Protocol location in *Scipion* menu. B: Protocol form.

    Fig. 12.12 Protocol xmipp3-extract asymmetric unit. A: Protocol location in Scipion menu. B: Protocol form.

  • Protocol form parameters (Fig. 12.12 (B)):
    • Input Volume: Volume already downloaded in Scipion from which the asymmetric unit will be extracted.
    • Symmetry: In this protocol, symmetry refers only to rotational symmetry, also known in biology as radial symmetry. This symmetry is the property of volumes to preserve their shape after a partial turn around a symmetry axis.
    Types of rotational symmetry included in this protocol are shown in Fig. 12.13. Two names appear in each case, the first one corresponds to XMIPP nomenclature of symmetry because we are using XMIPP package, and the second one (in brackets) follows the general Scipion nomenclature. Current nomenclature is ChimeraX’s nomenclature, which is, in turn, the same symmetry nomenclature of the International Union of Cristallography.
    Protocol **xmipp3-extract asymmetric unit**. Types of rotational symmetry.

    Fig. 12.13 Protocol xmipp3-extract asymmetric unit. Types of rotational symmetry.

    • Cyclic symmetry Cn (Cn): Only one symmetry axis goes through the geometric center of the volume. Two more form parameters are shown when this type of symmetry is selected:
      • Symmetry Order: Number of times (n) in which a volume shows the same shape when the volume rotates around the symmetry axis from 0 to 360º. If the same shape is only obtained after turning 360º, then n = 1. This means that the volume has no symmetry. 360º/n determines the rotation angle.
      • offset: Starting angle around Z axis.
    • Dihedral symmetry Dn (Dxn): Two perpendicular symmetry axes go through the geometric center of the volume. As in the case of cyclic symmetry, two more form parameters are shown when this type of symmetry is selected:
      • Symmetry Order: Number of times (n) in which a volume shows the same shape when the volume rotates around both symmetry axes from 0 to 360º. Analogously, 360º/n determines the rotation angle.
      • offset: Starting angle around Z axis.
    • Tetrahedral symmetry T (T222): Four symmetry axes go from each vertex to the opposing face center (order 3), and three symmetry axes join opposing edges (order 2). Symmetry order = 12.
    • Octahedral symmetry O (O): Three symmetry axes join opposing vertices (order 4), four symmetry axes join opposing face centers (order 3), and six symmetry axes join opposing edges (order 2). Symmetry order = 24.
    • Icosahedral symmetries I1 (I222), I2 (I222r), I3 (In25), I4 (In25r): Six symmetry axes join opposing vertices (order 5), 10 symmetry axes join baricenters of opposing faces (order 3), and 15 symmetry axes join opposing edges (order 2). Symmetry order = 60. Each type of icosahedral symmetry depends on its initial orientation. Check in CHIMERAX each icosahedral symmetry by writing in the command line:
      shape icosahedron radius 50 orientation
      (222: default, order 2 axes follow XYZ coordinate axes;
      222r: idem rotated 90º around Z axis;
      n25: an order 2 axis and an order 5 axis follow Y and Z axes, respectively,
      n25r: idem rotated 180º around X axis).
    • Inner Radius (px): Minimal distance from the geometric center that delimits inwards the part of the electron density map that will be included in the extracted volume. A wizard symbol on the right side of this parameter can be helpful to select this radius.
    • Outer Radius (px): Maximal distance from the geometric center that delimits outwards the part of the electron density map to be included in the extracted volume. In other words, the part extracted of the map electron density will be between the Inner and the Outer Radius. Again, the wizard symbol on the right side of this parameter can be helpful to select this radius.
    • Expand Factor: Additional fraction of the asymmetrical unit cell that will be included in the extracted volume.
  • Protocol execution:
    Adding specific extracted volume label is recommended in Run name section, at the form top. To add the label, open the protocol form, press the pencil symbol at the right side of Run name box, complete the label in the new opened window, press OK and, finally, close the protocol. If you want to run again this protocol, do not forget to set to Restart the Run mode.
    Press the Execute red button at the form bottom.
  • Visualization of protocol results:
    After executing the protocol, press Analyze Results and a small window will be opened (Fig. 12.14). This window allows you to select between chimerax (ChimeraX graphics window) and slices (ShowJ, the default Scipion viewer), to visualize the volume.
    Menu to select a visualization tool.

    Fig. 12.14 Menu to select a visualization tool.

    • chimerax: ChimeraX graphics window
      Initial whole volume and extracted volume appear referred to the origin of coordinates in ChimeraX. To show the relative position of the volume, the three coordinate axes are represented; X axis (red), Y axis (yellow), and Z axis (blue) (Fig. 5.3). Coordinate axes, initial volume, and extracted map asymmetric unit are model numbers #1, #2 and #3, respectively, in ChimeraX Models panel. Volume coordinates and pixel size can be checked in ChimeraX main menu Tools -> Volume Data -> Map Coordinates: Origin index/ Voxel size.

      |WARNING: Take into account that coordinates appear in pixels while they have been introduced in Å.

    • slices: ShowJ
      Each volume can be independently visualized by selecting it in the upper menu as the arrow indicates in Fig. 12.15.
      Protocol **xmipp3-extract asymmetric unit**. Volume selection with ShowJ.

      Fig. 12.15 Protocol xmipp3-extract asymmetric unit. Volume selection with ShowJ.

  • Summary content:
    • Protocol output (below Scipion framework):
      xmipp3 - extract asymmetric unit -> ouputVolume;
      Volume (x, y, and z dimensions, sampling rate).
    • SUMMARY box:
      Empty.