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.

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, wheregridmapis a 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

ballstrue |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 theresolution. If false (default), for each atom use a Gaussian function with height proportional to the atomic number and width proportional to theresolution. Theballsoption 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 fineresolutionbut taking care to use anedgePaddingvalue larger than the VDW radii (e.g.,molmap protein 0.5 balls t edge 2.5).

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.

replacetrue| false

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

symmetrysym-type

Create a map corresponding to a symmetrical multimer of the structure. By default, no symmetry is used. Mostsym-typeoptions have additional sub-options or parameters:

biomt- use “biological assembly” information from the atomic model containing the specified atoms

(currently this information is only read from PDB format, not mmCIF)- symmetry of model
#- use the biological assembly information from another atomic model or the symmetry assignment of a volume modelN

- Example:
#4- cage model (from
Cage Builder) 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)

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 models. The center of the bounding sphere of the specified items will be used.

coordinateSystemN

Specify a reference model (default is the atomic model containing the specified atoms) by model numberNpreceded 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