EMFOM
Function of the program :
Read in the structure factors from two equally separated EM reconstructions and calculated the figure of merit (FOM)14 of structure factors and use it to weight the structure factor from the non-separated reconstruction map. When the two structure factors, which can be regard as two data from different derivatives in X-ray crystallography, are very similar, the figure of merit will be close to 1 so that less weight down will occur for the amplitude. From the two structure factors, the phase possibility is also calculated. The best phase, centroid (center of gravity) of the probability distribution14, will be used as the phase for the FOM-weighted structure factor. By using this X-ray crystallographic strategy, bad structure factor are filtered out or weighted down which will lead to improvement of the map.
Purpose of the program:
To improve the final map of cryo-EM reconstructions.
Usage of the program:
- Usage: fom [option] all.asf odd.asf evn.asf out.asf
- Options:
| Options | explanations |
|---|---|
| -r high_resolution | Highest Resolution in Å |
| -l low_resolution | optional lowest resolution in Å |
| -k amp_scale_factor | Amp scale factor, Default 1.0 |
| -a angle_step_size | optional FOM angle search steps,-a -s only need one, angle_step_size = 360.0 / angle_steps |
| -q | working quietly, without progress output |
| -v | working verbosely, default, with many progress output |
| -b bin_number | resolution shell number for estimate Error, default 80 |
| -f | Soft filter using the default parameters |
| -e recipocal_step edge_cut_weight | Soft filter parameters,after reciprocal_step grids in reciprocal space, the weight drops to edge_cut_weight, Default recipocal_step=3.0;edge_cut_weight=0.000001 |
| -h | Print the help, no calculation |
BUG REPORT :
If you meet any bugs or problems of the programs, please email xc@purdue.edu.