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EM2DAM manual

em2dam

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© ATSAS Team, 2011-2012

Table of Contents

Manual

The following sections shortly describe how to run EM2DAM from the command-line on any of the supported platforms, the required input and the produced output files.

Introduction

EM2DAM (Electron Microscopy density map to Dummy Atom Model) converts an electron microsopy density map into a dummy atom model suitable for refinement against SAXS data. A density cutoff may be specified explicitely, or EM2DAM may use either experimental SAXS data or employs an ab initio heuristic to determine a suitable density threshold cutoff. The output model may be used as a starting model for refinement with DAMMIN.

Running em2dam

Usage:

$ em2dam <MAP> [DAT] [OPTIONS]

OPTIONS known by EM2DAM are described in next section, the required argument EMFILE in the section on input files.

Command-line arguments and options

EM2DAM takes an EM density map and an optional corresponding experimental SAXS dataset as arguments.

EM2DAM recognizes following command-line options:

Short optionLong optionDescription
-t --threshold=<X> Cutoff threshold (default: minimum density); if not specified the cutoff with the best fit to the experimental data (if any) is used, or a heuristic is employed to find a suitable threshold. This option is mutally exclusive with --maxgraphs.
-r --reduction=<N> Reduction level, merges N^3 beads on output This option is mutally exclusive with --maxbeads.
--maxgraphs=<N> Maximum number of graphs in output (default: 1, unlimited if --threshold is specified).
--maxbeads=<N> Maximum number of beads in output (default: 100.000, unlimited if --reduction is specified). If maxbeads is specified, the reduction level is determined dynamically to output at most maxbeads.
--damstart Make output model suitable as search volume for DAMMIN. Ideally use together with --reduction or --maxbeads; merged volume elements with at least some density are considered as "solvent" in the resulting output file and may be used by DAMMIN.
--lm=<N> Number of spherical harmonics to use when predicting the theoretical scattering (default: 15)
--ns=<N> Number of points in scattering vector (default: 256)
--sm=<X> Maximum scattering vector (default: 0.5 A-1)
-p --prefix=<PREFIX> Output filename prefix (default: basename of input map).
-v --version print version information and exit.
-h --help Print a summary of arguments and options and exit.

em2dam input files

MAP is expected to be an electron microscopy density map. Default values, except threshold, are read from header of MRC file. The experimental SAXS data may be in any of the supported data formats as long as scattering vector, experimental intensity and errors are available.

em2dam output files

EM2DAm creates two kind of output files the model itself and its theoretical scattering pattern as by dam2is.html. If experimental SAXS data is provided a fit against the experimental data is provided. On output, each filename starts with a customizable prefix that gets an extension appended.

Examples

$ em2dam emd_1654.map -p rubisco -t 3.0

Convert a density map in into a bead model using a density cutoff threshold of 3.0. Generated output files are rubisco.pdb and rubisco.dat.

$ em2dam emd_1654.map -p rubisco -t 3.0 --maxbeads=5000 --damstart

Convert a density map in into a bead model with at most 5000 beads, using a density cutoff threshold of 3.0. Generated output files are rubisco.pdb and rubisco.dat, the former may be used as input file for DAMMIN.


  Last modified: July 18, 2017

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