Job: Particle Subtraction
Last updated
Last updated
Subtract projections of a masked sub-volume from particle images.
Use input particles with a gold-standard half set
Ensure that the region to be subtracted is well-aligned
The mask must have a soft edge
A particle subtraction job is used to remove unwanted signal from particle images. The input volume is projected in the fitted pose for each input particle. This projection is then subtracted from the particle image, yielding an image of the particle as if it did not have the masked out region.
Particles must be from a previous refinement job with half-set splits (i.e., homogeneous or non-uniform refinement). Results may improve if per-particle scale factors have been optimized.
Volume must include both half maps. The volume must be the same size as the particle images.
The mask should cover the region of the volume that is to be subtracted from the images. Like other masks which “cut through” map density, the mask must have a soft edge. However, if your mask is too large it may incorporate noise from regions of the map with no appreciable signal. Thus, the size of the mask must be carefully tuned.
It is essential that the windowing parameters in a Particle Subtraction job match those of the input refinement. The volume is multiplicatively scaled to match the contrast of each particle image, and using different windowing parameters may result in an incorrect scaling factor.
We recommend a minimum soft padding width of where resolution is the volume’s GSFSC resolution in Å and apix is the volume’s pixel size in Å, but you may need to test several masks to find the optimal result. More advice on mask making is available in .
We recommend performing a using the subtracted particle sets as a sanity check that the correct parts of the image have been subtracted.
Particle subtracted images are often most useful in .