CTF refinement

[Giovanni Cardone]

Dear users,

several improvements have been done with regards to the defocus
refinement. The major change is in the way it is executed. In the
previous versions 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

PS: this is the second attempt in sending the email. If already
received, please disregard.