Chimera Commands Index

molmap  atom-spec  resolution  options

The command molmap generates a density map from the specified atoms. 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 data set in Volume Viewer. A map corresponding to a symmetrical multimer of the structure can be generated with the symmetry option. Map display can be adjusted and the map saved to a file using Volume Viewer or the command volume. See also: measure correlation, meshmol, fitmap, Fit to Segments

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


Option keywords for molmap can be truncated to unique strings, and their case does not matter. Synonyms for true: True, 1. Synonyms for false: False, 0. A vertical bar “|” designates mutually exclusive options, 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:
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.
modelId N
Open the map as model number N (an integer, optionally preceded by #). Submodel specifications #N.N (# required) can also be given. If the source atoms belong to a single model, the default is the same main model number as the atoms but with the next unused submodel number; if the atoms belong to multiple models, the default is the next unused main model number.
replace true|false
Whether to close any map previously created by molmap from the same set of atoms.
showDialog true|false
Whether to show the Volume Viewer dialog after creating the map.
symmetry sym-type
Create a map corresponding to a symmetrical multimer of the structure. By default, no symmetry is used. Specifications of sym-type are case-independent, and most types 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 molecule 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.