recursive_gmconvert
Implements divide-and-conquer gmm computation as in [1].
dependencies
EMAN2 (blake.bcm.edu/emanwiki/EMAN2), used to compute the FSC.
gnuplot (www.gnuplot.info/)
installation
- clone the repository or download the zip and extract it (we refer to the root of the source tree as
SRC_DIR). - compile gmconvert:
cd ${SRC_DIR}/gmconvert/src ; make ; cd - - if you need to run some commands before executing the scripts, place them in modules.sh
usage:
${SRC_DIR}/recursive_gmconvert.sh -f map_filename -t threshold -n num_gaussians -N num_iterations [-i first_iteration] [-s]Required arguments:
-f map_filename: the file name of the input EM map
-t threshold: the density threshold
-n num_gaussians_or_file: If the argument is a number, then number of gaussians per sub-process, if argment is a file then read a sequence of number of gaussians from file
-0 num_gaussians0: number of gaussians for first iteration
-N num_iterations: number of recursion levels
Optional arguments:
-i first_iteration: initial recursion level (defaults to 1)
-s: enable serial mode
-h: display this message
Unless you enable serial mode (-s flag), all the scripts assume that you are running a cluster with the slurm queuing system.
Output:
The script creates a sub-directory (called i) for each recursion level i, and the output files are called i/i.gmm and i_imp.gmm.
i/i.gmm contains the gmm in gmconvert format, and i_imp.gmm contains the gmm in IMP format (the conversion is handeld by gmconvert2imp.sh), which can be read in IMP using IMP.isd.gmm_tools.decorate_gmm_from_text function.
other scripts:
get_maps.sh is used to run a batch of recursive_gmconvert.sh on a list of emdb entries read from standard input. It will fetch the data from the emdb and run the divide-and-conquer GMM calculation.
Example 1: get_maps.sh -n 2 -N 2 -s <<< 1883
Example 2: get_maps.sh -n 2 -N 2 -s < input.txt
In example 2, input.txt contains one emdb entry per line.
Arguments:
All arguments from recursive_gmconvert.sh, except -f and -t
References
[1] Bayesian multi-scale modeling of macromolecular structures based on cryo-electron microscopy density maps
Samuel Hanot, Massimiliano Bonomi, Charles H Greenberg, Andrej Sali, Michael Nilges, Michele Vendruscolo, Riccardo Pellarin
doi: https://doi.org/10.1101/113951
[2] Multiple subunit fitting into a low-resolution density map of a macromolecular complex using a gaussian mixture model.
Kawabata, T. , Biophys J 2008 Nov 15;95(10):4643-58.
http://www.cell.com/biophysj/fulltext/S0006-3495%2808%2978604-1
[3] EMAN2: an extensible image processing suite for electron microscopy.
G. Tang, L. Peng, P.R. Baldwin, D.S. Mann, W. Jiang, I. Rees & S.J. Ludtke.
(2007) J Struct Biol. 157, 38-46. PMID: 16859925