helixhunter2OMP

This program is used to find possible alpha-helices region in medium resolution (8Angstrom) density map

helixhunter2OMP <input> <output> <a/pix> [minlen=<Angstrom>] [maxlen=<Angstrom>] [hlxnum=<int>] [sigma=<number>] [percen=<0-1>] [view] [list=<filename>] [dejavu=<filename>] [cosec=<filename>] [verbose] [docylccffirst] [cpu=<n>] [cyl] [int=<file>] [da=<angle>] [res=<Angstrom>] [type=<0-2>] [len=<number>] [ccf] [vectavg[=<angstrom>]]

Parameters:


<input>input file, single 3D map in any format that EMAN supports, usually the reconstruction map
<output>output file, Open Inventor format, explicitly describing each helix
<a/pix>the sampling for input file, Angstrom/pixel
[minlen=<Angstrom>]the minimal length of density region to qualify for a helix, in Angstrom
[maxlen=<Angstrom>]the maximal length of density region to qualify for a helix, in Angstrom
[hlxnum=<int>]the number of helices wanted, the correct threshhold would be automatically searched
[sigma=<number>]threshhold set to number of sigma above mean for pre-threshholding the map
[percen=<0-1>]threshhold set to percent of the maximal density for pre-threshholding the map, this is prefered when both are set
[view]will automatically call ivview to show the result Inventor file
[list=<filename>]also output a simple text file describing the helices: 9 white space delimited parameters for each helix(order: 3 center, 4 quaternions, radius, length)
[dejavu=<filename>]also output a DejaVu secondary structure elements file, see DejaVu document for more details
[cosec=<filename>]also output a COSEC secondary structure element file, see COSEC document for more details
[verbose]show intermediate output for monitoring progress and more working details
[docylccffirst]to do exhaustive cross correlation search with prototypic helix first, following parameters are useful only if this is set
[cpu=<n>]number of CPUs to use. cross-correlation step is parallelized with OpenMP
[cyl]output a protoypic helix density map in MRC format
[int=<file>]prefix for the 3 output MRC maps from the resulted cross correlation search,
[da=<angle>]angular step size for the search, default to appropriate number for the resolution and map size
[res=<Angstrom>]resolution of the density map, default to 8 Angstrom
[type=<0-2>]type of prototypic helix, default to 2
[len=<number>]the length of prototypic helix, default to 16.2 Angstrom (3turns)
[ccf]using straight cross correlation function instead of the default MCF(mutual correlation function)
[vectavg[=<angstrom>]]the score map will be locally vector averaged after the seach, default to 3x3x3 Angstrom kernel size

Usage:

helixhunter2 input.mrc output.iv 1.5

helixhunter2 input.mrc output.iv 1.5 verbose view dejavu=dejavu.sse list=helices.txt percen=0.8

helixhunter2 input.mrc output.iv 1.5 verbose view docylccffirst da=5 percen=0.5

Description

This program is classified as experimental at this point. The parallelization is done with OpenMP, which means it only work on shared memory systems. This is not compiled by default.

This programs trys to find the helices density regions in a medium resolution density map. There are two modes for this program: the default is to work directly on the density map by segmenting the high density regions, analyzing the properties for each region, and making decisions if the region is qualitied as a helix; the second mode is to pre-process the density map by exhaustive cross correlating with prototypic helix at all possible orientations, re-weighting the original densities, and then adopt the first mode to find the helices. While the default mode is very fast which usually takes less than 10 seconds and the second mode would take much longer time which usually in minutes to tens of minutes range, the second mode usually gives superior results. The parameters that need to pay attention to are the two threshhold parameters percen and sigma, the higher the threshhold, the less numer of and the longer helices would be found, and the lower the threshhold, the more numer of and the shorter and ofter non-helix regions are found.

Visit web page Helixhunter and Foldhunter for more information.


EMAN Manual page, generated Tue Oct 8 21:38:48 2002