CTF refinement

[Giovanni Cardone]

Several improvements have been done with regards to the defocus refinement. The major change is in the way it is performed. Before the refinement, if requested, was done only on a micrograph basis, and it was performed at each iteration, after the alignment.

In the new version 4.04 of Auto3DEM it is possible to refine the defocus on a micrograph or particle basis, depending on the value of the parameter per_ptle_ctf. In order to perform the refinement, in the settings file (generally the one ending with _master or _continue) you need to set 'auto ctf_refine' to 1. In this way auto3dem will perform the refinement as the first of the iterations indicated, and it will reset ctf_refine to 0 afterwards: this means that if more than one iteration is requested in the settings, the first will do the defocus refinement, and the following ones will perform the refinement specified by the mode. In order to refine the defocus also separately for each particle, the easiest way is to set 'auto per_ptle_ctf' to 1, which will switch all the programs to use the defocus estimate for each particle.

We also changed the parameters to control the refinement, i.e. the ones starting with 'pctfr'. Now it is possible to define the step search for the defocus axis and azimuth separately, and to specify if we want to estimate the defocus without assuming any astigmatism. Here below are reported the fields and their relative default values

per_ptle_ctf  = 0        # Disable per particle CTF

dfocus         = .05      # Step size for CTF refinement (defocus, microns)

nfocus         = 4        # Number of steps in each direction for the defocus search

dangle         = 1        # Step size for CTF refinement (astigmatism angle, degrees)

nangle         = 4        # Number of steps in each direction for the angular search

tempfac       = 0        # Temperature factor to apply to the map (recommended not to change)

ctfmode       = 2        # CTF correction mode (default: apply only phase reversal)

funcmode     = 3        # Metric to determine the optimum parameters (default: just phase comparison)

funcweight    = 0        # radial weigth factor in reciprocal space to apply to the metric (default: no weight applied) 

anastigm      = 0        # Anastigmatic (default: images are assumed astigmatic)

Sincerely,

Giovanni