10. Create 3D Mask protocol

Protocol designed to create a mask, i.e., a wrapping surface able to delimit a volume or subunit of interest, in order to modify the density values within or outside it. This mask can be created with a given geometrical shape (sphere, cube, cylinder…) or obtained from operating on a 3D volume or a previous mask.

  • Requirements to run this protocol and visualize results:
    • Scipion plugin: scipion-em
    • Scipion plugin: scipion-em-xmipp
  • Scipion menu:
    Model building -> Preprocess map (Fig. 10.7 (A))
    Protocol **xmipp-create 3d mask**. A: Protocol location in *Scipion* menu. B, C: Protocol form.

    Fig. 10.7 Protocol xmipp-create 3d mask. A: Protocol location in Scipion menu. B, C: Protocol form.

  • Protocol form parameters (Fig. 10.7 (B: Mask generation; C: Postprocessing)):
    • Mask generation
      • Mask source: Selection of one of the next three possible types of sources for the mask, the map volume provided by the user, a specific geometrical design or a feature file.
        1. Volume
          • Input volume: Electron density map previously downloaded or generated in Scipion.
          • Operation: Approach applied to generate the mask:
            1. Threshold: By establishing a particular density Threshold (write here this threshold value).
            2. Segment: Segmentation process according to:
              • Number of voxels (write here that value).
              • Number of aminoacids (write here that value).
              • Dalton mass (write here that value).
              • Automatic
          • Only postprocess: Use only the methods described in the tap Postprocessing (see below).
        2. Geometry
          • Sampling Rate (Å/px): Size of voxel dimensions in Å.
          • Mask size (px): Mask dimensions in number of pixels.
          • Mask type: Sphere, box, crown, cylinder, Gaussian, raised cosine and raised crown. Dimensions of each one of these geometric shapes have to be assigned in pixels: Radius of the sphere (half size of the mask by default); box size; inner and outer radius of the crown, raised cosine and raised crown (half size of the mask by default); height of cylinder (mask size by default); Gaussian sigma (mask size/6 by default); and border decay or fall-off of the two borders of the crown (0 by default).
          • Shift center of the mask?: By selecting “Yes”, the mask will be shifted to a new origin of coordinates X, Y, Z.
        3. Feature File: Select with the browser the feature file in your computer.
    • Postprocessing
      • Remove small objects: Selection of “Yes” allows to ignore ligands of the map volume below a certain size (in voxels).
      • Keep largest component: By selecting “Yes” a mask will be generated considering only the largest element of the map volume, ignoring the rest.
      • Symmetrize mask: By selecting “Yes” a symmetrized mask will be generated according to a specific symmetry group (look at XMIPP Symmetry). c1 symmetry indicates no symmetry, by default.
      • Apply morphological operation: Slight modifications of the mask can be applied by dilation or erosion of the density region (Structural element size: One voxel by default). Combinations of dilation and erosion allow closing or opening empty spaces of density in the map volume.
      • Invert the mask: This option allows to invert the values of density regarding the wrapping surface of the mask, masking the outer part instead the inner part.
      • Smooth borders: Mask borders can be smoothed by applying a convolution of the mask with a Gaussian. The Gaussian sigma (in pixels) has to be supplied.
  • Protocol execution:
    Adding specific mask 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. This label will be shown in the output summary content (see below). 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 ShowJ, the default viewer, will open the mask by slices (Fig. 7.3). ShowJ window menu (File -> Open with ChimeraX) allows to open the mask volume in ChimeraX graphics window.
  • Summary content:

    • Protocol output (below Scipion framework):
      xmipp3 - create 3d mask -> ouputMask;
      VolumeMask (x, y, and z dimensions, sampling rate).
    • SUMMARY box:
      Details about Mask creation and Mask processing.