foldhunterP

Description

This is the parellel version (pthreads) of foldhunter

This program is classified as experimental at this point. Expect a forthcoming publication with more details. We do not suggest using it until it has been better characterized.

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, from the probe map that is rotated and then translated according to the best match parameters
[numcpu=<number of CPU]number of processors to use, default to 5
[da=<angle>]angular step size
[startangle=<alt,az,phi]starting angles, search will be around it, 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
[log=<filename>]the file to send the intermediate outputs, if not set, stdout (screen) will be used
[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
[spher_region=<x0,y0,z0,r>]only consider solutions in given spheric region, in pixel, relative to center of the map
[keep=<solution_num>]number of the top matches will be outputted, default to 20
[cyl_region=<x0,y0,z0,r,h>]only consider solutions in given cylinder region, in pixel, relative to center of the map
[mask=<x0,y0,z0,r>]won't consdier solutions in side 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
[peakwidth=<pixels>]pixels assumed for each match peak, to avoid too close peaks being considered, default to 5 pixels
[int=<file>]fileanme for intermediate data
[time]if time specified, the intermediate output will be suppressed, and the time spent in the orientation search will be monitored
[finestda=<finest angle stepsize>]smallest angular step size that 'smart' feature will use,d efault to 1 degree

Usage:

foldhunterP ref.mrc probe.mrc out.mrc numcpu=8

foldhunterP ref.mrc probe.mrc out.mrc da=20 smart

foldhunterP ref.mrc probe.mrc out.mrc da=1 startangle=35.7,99.3,234.7 range=10.0

Description

This program tries to find the best match for a probe density map (such as a known structure from PDB) to be docked into the reference map which is usually a low resolution reconstruction map by cryoEM, this will hopefully give more information about how the domains arrange in larger context.

The requirements for the two input maps are that they are cubic, same size, similar resolution.

The methodology is simply cross correlation and the correlation coefficients are used as the criterion to find the best matches. The final outputs are just simple the top matches, there is no intention to build intelligence to determine if the matches are correct. Make sure to visually inspect the top matches. Experience already showed that the correct match needs not to be the best match.

The program outputs the Euler angles and the translations for each match, but only actually transforms the probe map and outputs to the output map. When viewed together with the reference map, this output map will overlap the corresponding domain in reference map if the solution is correct.

For other matches, one needs to manually transform to match the equivalent domain in reference map. Be sure to transform in correct order: rotate first, then translate. proc3d could be used to do these transforms, but unfortunately proc3d does it in reversed order (translate first, then rotate), be be sure to transform in two steps instead of one step if proc3d is used.

More specifically, to transform the model map to match the corresponding part in the reference map:

1: rotate the model by the 3 rotation angles

e.g. proc3d model out1 rot=30,60,80

2: translate the output of step 1 by the 3 translations

e.g. proc3d out1 out trans=3,-4,5


EMAN Manual page, generated Mon Jan 10 23:35:08 2000