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Command: molmap

Usage:
molmap  atom-spec  resolution  options

The command molmap generates a density map from the specified atoms. By default, each atom is described as a 3D Gaussian distribution of width proportional to the resolution and amplitude proportional to the atomic number. A map of the combined densities is generated and opened as a volume data set. The symmetry option allows generating a map for a symmetrical multimer of the structure. Map display can be adjusted and the map saved to a file using the command volume. See also: fitmap, sym

The molmap command is based on the pdb2mrc program in EMAN.

Options

Option keywords and Boolean (truth) values can be truncated, with synonyms for true: True, 1, and synonyms for false: False, 0. A vertical bar “|” designates mutually exclusive values, and default settings are indicated with bold.

gridSpacing  s
The grid spacing s (default resolution/3) is the separation of points along the X, Y, and Z axes of the generated map. This option is ignored if onGrid is used.
edgePadding  p
The edge padding p (default 3*resolution) sets map dimensions relative to the bounding box of the atom centers. Each face of the volume data box is offset outward by p from the corresponding bounding box face. This option is ignored if onGrid is used.
onGrid  gridmap
Create the new map on the grid of another, where gridmap is a model number preceded by #. This option overrides any gridSpacing and edgePadding values.
cutoffRange  r
How many standard deviations σ (default 5) of each Gaussian distribution to include in the map. Omitting the tails speeds up map calculation.
sigmaFactor  f
Together with the resolution, the sigma factor f determines the width of the Gaussian distribution used to describe each atom:
σ = f(resolution)
By default, f = 1/(π * 2½) ≈ 0.225 which makes the Fourier transform (FT) of the distribution fall to 1/e of its maximum value at wavenumber 1/resolution. Other plausible choices:
balls  true | false
If true, use a flat value of 1 within the VDW radius of each atom, surrounded by the downslope of a Gaussian (a half-normal distribution) with height 1 and width proportional to the resolution. If false (default), for each atom use a Gaussian function with height proportional to the atomic number and width proportional to the resolution. The balls option can be used to make a map with isosurfaces that approximate the VDW envelope of the atoms when contoured at positive levels ≤ 0.2. A fairly close approximation can be achieved with a fine resolution but taking care to use an edgePadding value larger than the VDW radii (e.g., molmap protein 0.5 balls t edge 2.5).
displayThreshold  m
Set the initial contour level to enclose a fraction m (default 0.95) of the total mass in the map. The fraction equals the sum of grid point values above the contour level divided by the sum of all grid point values.
replace  true | false
Whether to overwrite any map previously created by molmap from the same set of atoms.
symmetry sym-type
Create a map corresponding to a symmetrical multimer of the structure. By default, no symmetry is used. Most sym-type options have additional sub-options or parameters:
axis axis
Specify axis of symmetry (default z), where axis can be:
center center
Specify center of symmetry (default 0,0,0), where center can be:
coordinateSystem N
Specify a reference model (default is the atomic model containing the specified atoms) by model number N preceded by #. The reference coordinate system is used for interpreting specifications of axis and center of symmetry.

UCSF Resource for Biocomputing, Visualization, and Informatics / June 2016