foldhunter

This program is used to quantitatively fit a subunit/domain into a large structure density map at intermediate resolution.

foldhunter <map> <model> <outputmap> [da=<angle>] [startangle=<alt,az,phi>] [range=<angle range>|<r1,r2,r3>] [smart] [sphere_region=<x0,y0,z0,r>] [cyl_region=<x0,y0,z0,rmin,rmax,h>] [keep=<solution_num>] [mask=<x0,y0,z0,r>] [apix=<angstrom_per_pixel>] [res=<angstrom>] [peakwidth=<pixels>] [finestda=<finest angle stepsize>] [time] [int=<file>] [log=<filename>] [verbose]

Parameters:


<map>input file, single 3D map in MRC format, usually the reconstruction map
<model>input file, single 3D map in MRC format, the probe map e.g. from PDB atomic structure blurred to similar resolution to <map>
<outputmap>the output density map in MRC format, is the rotated and then translated probe map according to the best match parameters
[da=<angle>]angular search step size in degree
[startangle=<alt,az,phi>]starting angles, search will be around it (+-range/2), in degree
[range=<angle range>|<r1,r2,r3>]range of the search will cover, single value will set three ranges the same, or three different ranges could be set, in degree
[smart]if smart is set, the search will go deep around the best orientation with finer angular step size until angular step size is smaller than 1 degree or finestda
[sphere_region=<x0,y0,z0,r>]only consider solutions in given spheric region, in pixel, relative to center of the map
[cyl_region=<x0,y0,z0,rmin,rmax,h>]only consider solutions in given cylinder shell region, in pixel, relative to center of the map
[keep=<solution_num>]number of the top matches will be outputed, default to 20
[mask=<x0,y0,z0,r>]won't consdier solutions inside the masked spheric region, in pixel, relative to center of the map
[apix=<angstrom_per_pixel>]Angstrom/voxel, if set, the output for translation will be in Angstrom, otherwise in pixel
[res=<angstrom>]the resolution of map, only effective when da is not set and used to calculate the maximal angular step size. default to 8 Angstrom
[peakwidth=<pixels>]pixels assumed for each match peak width, to avoid too close peaks being considered, default to 5 pixels
[finestda=<finest angle stepsize>]smallest angular step size that 'smart' feature will use,d efault to 1 degree
[time]will monitor the time spent in the 6 dimension search loop
[int=<file>]filename for intermediate data output
[log=<filename>]the file to send the intermediate outputs, if not set, stdout (screen) will be used
[verbose]output the intermediate information and the time spent in the orientation search will be monitored

Usage:

foldhunter <ref.mrc> <probe.mrc> <probe-out.mrc> da=20

Description

This is first sequential version, the recent improvements are all on the later parallelized version foldhunterP, please check foldhunterP and Helixhunter and Foldhunter for more information.


EMAN Manual page, generated Fri Feb 8 16:12:24 2002