Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision | ||
|
auto3dem:userguide [2016/01/13 14:12] gcardone [po2r] |
auto3dem:userguide [2016/01/19 13:04] (current) admin [auto] |
||
|---|---|---|---|
| Line 236: | Line 236: | ||
| **freeze_res**: non-zero value freezes the resolutions used in PPFT, and PO2R (resolution used in P3DR will still be based on the results from PSF). | **freeze_res**: non-zero value freezes the resolutions used in PPFT, and PO2R (resolution used in P3DR will still be based on the results from PSF). | ||
| - | **fsc_hithresh**: cutoff value for FSC used in estimating map resolution. | + | **fsc_cutoff**: cutoff value for FSC used in estimating map resolution. If not specified it is set either to 0.143 (gold_standard set to 1) or to 0.5 (gold_standard set to 0). |
| - | **fsc_lothresh**: cutoff value for FSC used to set resolution limits in P3DR, PSF, and PO2R. | + | **fsc_hithresh**: cutoff value for FSC used to set resolution limits in PPFT and PO2R. |
| + | |||
| + | **fsc_lothresh**: cutoff value for FSC used in filtering the map in P3DR. | ||
| **gauss_adj**: parameter used to set width of Gaussian falloff in P3DR (reciprocal angstroms). | **gauss_adj**: parameter used to set width of Gaussian falloff in P3DR (reciprocal angstroms). | ||
| Line 445: | Line 447: | ||
| **magref_reset**: 1 to ‘forget’ magnification assigned to data, 0 to refine around the current estimated value. | **magref_reset**: 1 to ‘forget’ magnification assigned to data, 0 to refine around the current estimated value. | ||
| - | **magref_step**: size of magnification refinement step (microns). | + | **magref_step**: size of magnification refinement step (fraction). |
| **mask_map**: name of binary map to use for focused refinement. Only used for modes //local// and //ticos_equiv//. Default is ‘none’, a reserved string indicating that no mask is used. | **mask_map**: name of binary map to use for focused refinement. Only used for modes //local// and //ticos_equiv//. Default is ‘none’, a reserved string indicating that no mask is used. | ||
| Line 454: | Line 456: | ||
| <WRAP center round box 75%> | <WRAP center round box 75%> | ||
| ''local'': local refinement (//nangle// steps of //dangle// degrees along each direction)\\ | ''local'': local refinement (//nangle// steps of //dangle// degrees along each direction)\\ | ||
| - | ''mag'': magnification refinement (//nmagref// steps of //magref//_step microns along each direction)\\ | + | ''mag'': magnification refinement (//nmagref// steps of //magref//_step fraction along each direction)\\ |
| ''global'': global search in one asymmetric unit (on a grid with step of //gangle// degrees)\\ | ''global'': global search in one asymmetric unit (on a grid with step of //gangle// degrees)\\ | ||
| ''ticos_equiv'': restricted search to the 60 symmetry related orientations. | ''ticos_equiv'': restricted search to the 60 symmetry related orientations. | ||
| Line 569: | Line 571: | ||
| | auto | freeze_annulus | 0 | | | auto | freeze_annulus | 0 | | ||
| | auto | freeze_res | 0 | | | auto | freeze_res | 0 | | ||
| + | | auto | fsc_cutoff | 0.143 if gold_standard=1, 0.5 otherwise | | ||
| | auto | fsc_hithresh | 0.5 | | | auto | fsc_hithresh | 0.5 | | ||
| | auto | fsc_lothresh | 0.3 | | | auto | fsc_lothresh | 0.3 | | ||