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. Map display can be adjusted and the map saved to a file using Volume Viewer or the command volume.

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.
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.
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 model number as the atoms; if the atoms belong to multiple models, the default is the lowest unused 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.

See also: volume, measure correlation, meshmol