Construction of masks
Dynamo uses several types of masks in different pipelines.
Masks are used in Dynamo for several purposes: indicating the active part of the template for alignment, restricting the area of the aligned particles that will count for classification, avoiding FSC artifacts, placing aligned averages back in a tomogram....
In some tasks, the masks are expected to be simple geometrical shapes. In other occasions, it might be necessary to have a finer control on the process of constructing a mask. Dynamo includes several tools:
Use dmask to open a GUI with several geometrical options: spheres, ellipsoids, tubes, cylinders. dmask can be used from the command line.
There are other commands for specific geometries: dsphere, dshell, dcylinder....
You can edit a template and draw on its 2D slices handdraw lines each enclosing an area of interest. There a different ways to convert such an area into a 3d volume
Here, you would enclose an area on a 2d slice that includes the Z axis (i.e., a section from an X-view or a Z-view), and then let Dynamo rotate the area around the central Z axis to create a revolution solid.
This can be done with dynamo_mapview. Open your template, go to an X view, select one slice and press on [shift+S]. A second window will pop up, zooming into the selected slice. When you finish, the message area will tell you the name of the file containing the the created revolution solid.
Slide by slide
By thresholding and smoothing
A mask can be define to XXXXX
Combination of masks
It is easy to create combinations of masks using logical operators: or just "adds" masks.
Alternatively, you can use the compact syntax in dynamo_mask_combine
Depicting mask overlays
When you design a mask, it is frequently useful to check how it relates to a given template.