Manual

The following sections briefly describe how to run EM2DAM from the command- line, 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 [OPTIONS] <MAP> [SASDATA]

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 accepts the following command line arguments:

Argument	Description
MAP	Exactly one electron microscopy map data (.map) file.
SASDATA	Exactly one experimental SAS data (.dat) file.

Absolute as well as relative path to data files are accepted. Instead of a file name, the argument may be given as ‘-‘ to read data from stdin.

EM2DAM recognizes following command-line options:

Short option	Long option	Description
-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 N beads.
	--damstart	Make output model suitable as search volume forDAMMIN. 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: \(0.5 \AA^{-1}\))
-p	--prefix <PREFIX>	Output filename prefix (default: basename of input map).
	--model-format <FMT>	Format of the output models, one of: cif, pdb (default: cif)
-v	--version	print version information and exit.
-h	--help	Print a summary of arguments, options, and exit.

em2dam input files

EM2DAM requires at least a electron microscopy map data (.map) file. Default values for options, except threshold are read from the MAP.

Optionally, a experimental SAS data (.dat) file may be provided. If present, it is used to tune the parameters to fit the experimental data.

em2dam output files

EM2DAM writes multiple output files each with the defined prefix:

Extension	Description
.dat	The calculated scattering of the Dummy Atom Model. Only present if no SASDATA was provided.
.fir	Fit of the simulated scattering curve versus the experimental data. Only present if SASDATA was provided.
.pdb or .cif	A Dummy Atom Model representation of the particle found in the MAP. Output format depends on the output-format option. If the damstart option is provided, the model is suitable to be used as a search volume for DAMMIN.

Please note that existing files with the same file name will be overwritten without further notice.

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.