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