15. Import mask protocol
Protocol designed to import a mask in Scipion from a file of user’s computer. Modifying the size of a previous mask is possible simply by changing the mask’s sampling rate.
- Requirements to run this protocol and visualize results:
- Scipion plugin: scipion-em
- Scipion menu: It does not appear in Model building view. Press
fand the pop up window to search a protocol will be opened (Fig. 15.8 (A)). Write any word related with the title of the protocol that you are looking for in the Search box. In this particular case we have written mask. Several protocols have been found related with this searching word. Select the first one dessigned for the purpose that we are interested in (pwem - import mask).
- Protocol form parameters (Fig. 15.8 (B)):
- Import section
- Mask path: Open the browser on the right to select in your computer the path to the previously saved mask.
- Pixel size (“sampling rate”) (Å/px): Write the new sampling rate value in the box.
- 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 Scipion viewer, will allow you to visualize the slices window of the mask (Fig. 7.3). The ShowJ window menu (File -> Open with ChimeraX) allows to open the selected map in ChimeraX graphics window.
- slices: ShowJ
- Summary content:
- Protocol output (below Scipion framework):pwem - import mask -> ouputMask;VolumeMask (x, y, and z dimensions, sampling rate).
- SUMMARY box:Mask file imported from: The specific selected path to the mask in your computer should appear here.