subtom_maskcorrected_FSC_bfactor
Calculates “mask-corrected” FSC and sharpened refs.
subtom_maskcorrected_fsc_bfactor(
'ref_a_fn_prefix', ref_a_fn_prefix ('even/ref/ref'),
'ref_b_fn_prefix', ref_b_fn_prefix ('odd/ref/ref'),
'motl_a_fn_prefix', motl_a_fn_prefix ('even/combinedmotl/allmotl'),
'motl_b_fn_prefix', motl_b_fn_prefix ('odd/combinedmotl/allmotl'),
'fsc_mask_fn', fsc_mask_fn ('FSC/fsc_mask.em'),
'output_fn_prefix', output_fn_prefix ('FSC/ref'),
'filter_a_fn', filter_a_fn (''),
'filter_b_fn', filter_b_fn (''),
'do_reweight', do_reweight (0),
'do_sharpen', do_sharpen (0),
'plot_fsc', plot_fsc (0),
'plot_sharpen', plot_sharpen (0),
'filter_mode', filter_mode (1),
'pixelsize', pixelsize (1.0),
'nfold', nfold (1),
'filter_threshold', filter_threshold (0.143),
'rand_threshold', rand_threshold (0.8),
'box_gaussian', box_gaussian (1),
'iclass', iclass (0),
'iteration', iteration (1))
Takes in two references ref_a_fn_prefix
_#.em and ref_b_fn_prefix
_#.em
where # corresponds to iteration
and a FSC mask fsc_mask_fn
and
calculates a “mask-corrected” FSC. This works by randomizing the structure
factor phases beyond the point where the unmasked FSC curve falls below a given
threshold (by default 0.8) and calculating an additional FSC between these phase
randomized maps. This allows for the determination of the extra correlation
caused by effects of the mask, which is then subtracted from the normal masked
FSC curves. The curve will be saved as a Matlab figure and a PDF file, and if
plot_fsc
is true it will also be displayed.
The script can also output maps with the prefix output_fn_prefix
that have
been sharpened with b_factor
if do_sharpen
is turned on. This setting
has two threshold settings selected using filter_mode
, FSC (1) and pixel
(2). FSC allows you to use a FSC-value filter_threshold
as a cutoff for the
lowpass filter, while using pixels allows you to use an arbitrary resolution
cutoff in filter_threshold
. The sharpening curve will be saved as a Matlab
figure and a pdf file, and if plot_sharpen
is true it will also be
displayed.
This function estimates the B-factor to apply versus applying an ad-hoc B-factor by fitting a curve to the drop in resolution as the number of particles decreases. This is detailed in Rosenthal and Henderson, 2003, doi:10.1016/j.jmb.2003.07.013
Finally this script can also perform and output reweighted maps if
do_reweight
is true, and the pre-calculated Fourier weight volumes
filter_a_fn
and filter_b_fn
.
Example
subtom_maskcorrected_fsc_bfactor(...
'ref_a_fn_prefix', 'even/ref/ref', ...
'ref_b_fn_prefix', 'odd/ref/ref', ...
'motl_a_fn_prefix', 'even/combinedmotl', ...
'motl_b_fn_prefix', 'odd/combinedmotl', ...
'fsc_mask_fn', 'FSC/fsc_mask.em', ...
'output_fn_prefix', 'FSC/ref', ...
'filter_a_fn', '', ...
'filter_b_fn', '', ...
'do_reweight', 0, ...
'do_sharpen', 1, ...
'plot_fsc', 1, ...
'plot_sharpen', 1, ...
'filter_mode', 1, ...
'pixelsize', 1.35, ...
'nfold', 6, ...
'filter_threshold', 0.143, ...
'rand_threshold', 0.8, ...
'box_gaussian', 3, ...
'iclass', 0, ...
'iteration', 1)