Focus Documentation

The parameters used in the maximum likelihood processing are shown in the above GUI. Once the parameters are set, clicking the “maximum likelihood” in the upper left panel starts the process. The obtained reference in each iteration of ML can be viewed by clicking the image name “SCRATCH/ML_reference_xxx.mrc” in the image window. When the ML processing is completed, the image window shows the final results including the references with and without envelop correction, and the unit cell map (ML result xxxx) generated from the amplitude and phase. Clicking “Generate Map” in the upper left panel generates the 2d crystal map from the amplitude and phase.

Parameters need to be set with caution:

* Total diameter of the window, diameter of the mask: large than one unit cell but smaller than two unit cells.

* Type of low-pass filter: useful when the particle number is small. “sharp cut off ” works well in most cases.

* Rotational symmetry: definitely relys on a precise phase origin.

The merger has the similar GUI as the previous one. But the process has two distinguished procedures, as shown below.

The maximum likelihood merger first generates a stack of unit cells for each crystal image, and save the stack as a binary file under the folder of the image. The parameters varying on crystals, for example, defocus and lattice are taken over from the the individual folder. The parameters that have common values to all the crystals are taken from the merger directory and should be set on the merger GUI. The common parameters include: window diameter, mask diameter, do_whiten, correct_CTF, percentage of particles. The window diameter should be large than 1.5*mask diameter to leave ample space for merging stacks with different phase origin.

Then the ML processing is applied to all the unit cells as a whole data set. The ML parameters are from the merger GUI. All the stacks are merged to the first stack.