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.
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.
Reduction level, merges N^3 beads on output This option is mutally exclusive with --maxbeads.
Maximum number of graphs in output (default: 1, unlimited if --threshold is specified).
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.
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.
Number of spherical harmonics to use when predicting the theoretical scattering (default: 15)
Number of points in scattering vector (default: 256)
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 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.
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.