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**.

gridSpacings

The grid spacings(default) is the separation of points along the X, Y, and Z axes of the generated map.resolution/3

edgePaddingp

The edge paddingp(default3*) sets map dimensions relative to the bounding box of the atom centers. Each face of the volume data box is offset outward byresolutionpfrom the corresponding bounding box face.

cutoffRanger

How many standard deviations σ (default5) of each Gaussian distribution to include in the map. Omitting the tails speeds up map calculation.

sigmaFactorf

Together with theresolution, the sigma factorfdetermines the width of the Gaussian distribution used to describe each atom:σ =By default,f(resolution)f=1/(π * 2which makes the Fourier transform (FT) of the distribution fall to 1/^{½}) ≈ 0.225eof its maximum value at wavenumber 1/resolution. Other plausible choices:

- 1/(π * (2/log2)
^{½}) ≈ 0.187 makes the FT fall to half maximum at wavenumber 1/resolution- 1/(2 * 2
^{½}) ≈ 0.356 makes the Gaussian width at 1/emaximum height equal theresolution- 1/(2 * (2log2)
^{½}) ≈ 0.425 makes the Gaussian width at half maximum height equal theresolution

displayThresholdm

Set the initial contour level to enclose a fractionm(default0.95) 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.

modelIdN

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.

replacetrue|false

Whether to close any map previously created bymolmapfrom the same set of atoms.

showDialogtrue|false

Whether to show theVolume Viewerdialog after creating the map.

See also:
**volume**,
**measure correlation**,
**meshmol**