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**,
**SegFit**

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

molmap #1 3.5

molmap protein 6

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. This option is ignored ifresolution/3onGridis used.

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. This option is ignored ifonGridis used.

onGridgridmap

Create the new map on the grid of another, also using its current step size. Thegridmapis specified by model number preceded by #. This option overrides anygridSpacingandedgePaddingvalues.

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 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.

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.

symmetrysym-type

Create a map corresponding to a symmetrical multimer of the structure. By default, no symmetry is used. Specifications ofsym-typeare case-independent, and most types have additional sub-options or parameters:

biomt- use biological unit information, if any, from the molecule model containing the specified atoms- symmetry of model
#- use biomt information from another molecule model or the symmetry assignment of a volume modelN

- Example:
#4- cage model polygon symmetry
#orN,pM#- place copies at equivalent positions relative to each M-sided polygon in the cage model with ID numberN,pnMN. Thepform places one copy per M-sided polygon, whereasMpnplaces M copies per M-sided polygon using CMMsymmetry about the center of the M-sided polygon nearest the original copy.

- Examples:
#2,p6or#2,pn5- cyclic symmetry
Caround axis and centern

- Example:
C3- dihedral symmetry
Daround axis and centern

- Example:
d7- tetrahedral symmetry
T[,around centerorientation]where

- Example:
t,z3orientationcan be:

222(default) - with two-fold symmetry axes along the X, Y, and Z axes, a three-fold along axis (1,1,1)z3- a three-fold symmetry axis along Z, another three-fold axis in the YZ plane such that rotation about the X axis by ~110° is a symmetry operation (EMAN convention)- octahedral symmetry
Oaround center- icosahedral symmetry
I[,around centerorientation]where

- Example:
i,n25orientationcan be:

222(default) - with two-fold symmetry axes along the X, Y, and Z axes2n5- with two-fold symmetry along X and 5-fold along Zn25- with two-fold symmetry along Y and 5-fold along Z2n3- with two-fold symmetry along X and 3-fold along Z222r- same as 222 except rotated 90° about Z2n5r- same as 2n5 except rotated 180° about Yn25r- same as n25 except rotated 180° about X2n3r- same as 2n3 except rotated 180° about Y- helical symmetry
H,around axis and centerrise,angle,n[,offset]where

- Example:
h,43.5,21,6,-2riseis the translation along the axis per subunit,angleis the rotation in degrees per subunit, andnis how many copies total (including the original) the resulting segment of infinite helix should contain. The integeroffset(default0) allows extending the helix in both directions. The example above would given= 6 copies total, with two copies in the negative axis direction, one at the identity position, and three in the positive axis direction.- translational symmetry
shift,along axis – or –n,distanceshift,n,x,y,zwhere

- Example:
shift,3,26.7nis how many copies total (including the original) the result should contain. The translation can be expressed as adistancealong the axis or as a vectorx,y,zin the reference coordinate system.- the product of symmetry groups, each specified as described above and separated by
*to indicate multiplying each symmetry matrix of one group with each symmetry matrix of another; can be generalized to multiple symmetry groups (not just two)

- Example:
c2*h,42,21,9,-4

axisaxis

Specify axis of symmetry (defaultz), whereaxiscan be:

x- X-axisy- Y-axisz- Z-axisx,y,z(three values separated by commas only) - an arbitrary vector in the reference coordinate system- an
atom-specof exactly two atoms (not necessarily bonded or in the same model) or one bond. A bond can only be specified by selecting it and using the wordselected,sel, orpicked; any atoms also selected at the time will be ignored.

centercenter

Specify center of symmetry (default0,0,0), wherecentercan be:

x,y,z(three values separated by commas only) - an arbitrary point in the reference coordinate system- an
atom-specof any combination of atoms and surface pieces. The center of the bounding sphere of the specified items will be used.

coordinateSystemN

Specify a reference model (default is the molecule model containing the specified atoms) by model numberNpreceded by #. The reference coordinate system is used for interpreting specifications of axis and center of symmetry.