sxlocres

Local Resolution: Compute local resolution of a map.


Usage

Usage in command line

sxlocres.py  firstvolume  secondvolume  maskfile  outputfile  --wn=WINDOW_SIZE  --step=SHELL_STEP_SIZE  --cutoff=RES_CRITERION  --radius=RADIUS  --fsc=OUTPUT_FILE_PATH  --res_overall=RESOLUTION  --out_ang_res=OUTPUT_FILE_PATH  --apix=PIXEL_SIZE  --MPI


Typical usage

sxlocres exists in for both MPI and non-MPI versions.

mpirun -np 32  sxlocres.py 'refinementdir/main002/vol0.hdf'  'refinementdir/main002/vol2.hdf locres.hdf' --cutoff=0.5 --radius=28 --res_overall=0.3  --fsc='fscvol.txt' --MPI


Input

Main Parameters

firstvolume
First half-map: A sub-map computed from about half of input projection data. In case of quasi-independent half-refinements, it has to one of the two generated structures. (default required string)
secondvolume
Second half-map: A sub-map computed from about half of input projection data. In case of quasi-independent half-refinements, it has to one of the two generated structures. (default required string)
maskfile
3D mask: Defines the region for which local resolution will be computed. It is advisable to eliminate irrelevant regions surrounding the structure. (default none)
outputfile
Output volume: Each voxel contains the associated resolution. It is expressed in absolute frequency units. (default required string)
--wn
Window size [Pixels]: Size of window within which local real-space CCC (equivalent to FSC) is computed. (default 7)
--step
Fourier shell step size [Pixels]: Values larger than 1.0 increase the speed and stability of the local resolution map, but decrease its reciprocal space resolvability. (default 1.0)
--cutoff
Local resolution criterion: Specify the resolution cut-off of the local resolution map. The map will contain, for each voxel, the value of spatical frequency at which local resolution at this voxel dropped below the specified cut-off level. Low values (say 0.14) result in a noisy and tus difficult to interpret local resolution map. (default 0.5)
--radius
Mask radius [Pixels]: In case no mask is provided, a hard sphere of this radius will be used. By default, radius = box_size/2 - (--wn). (default -1)
--fsc
FSC output file: Contains the overall FSC curve computed by rotational averaging of local resolution values. It is truncated to --res_overall. By default, the program does not save the FSC curve. (default no curve)
--res_overall
Overall resolution [1/Pixel]: Specify overall (or global) resolution in absolute frequency (>=0.0 and <=0.5) for calibration of the average local resolution. Use the absolute frequency corresponding to the standard FSC resolution estimation. See Description section in the wiki page for details. By default, the program will not calibrate the average local resolution. (default -1.0)


Advanced Parameters

--out_ang_res
Save Angstrom local resolution: Additionally creates a local resolution file in Angstroms. (default False)
--apix
Pixel size of half-maps [A]: Effective only with --out_ang_res options. (default 1.0)
--MPI
Use MPI: (default False)


Output


Description

Local resolution values are computed within small windowed areas (size wn3). Due to small window size the values are inaccurate and tend to underestimate resolution. Therefore, the option --res_overall allows to calibrate the average value of all local resolutions to the overall resolution, as estimated by the FSC between half-maps. This value has to be independently obtained by the user. Command sximgstat.py computes (masked) FSC from half-maps and one can read the absolute frequency corresponding to 0.5 (or other) cut-off threshold.


Method


Reference


Developer Notes


Author / Maintainer

Pawel A. Penczek


Keywords

Category 1:: APPLICATIONS


Files

SPARX/bin/sxlocres.py


See also

Maturity

Stable:: Has been evaluated and tested. Please let us know if there are any bugs.


Bugs

There are no known bugs so far.