Usage:
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, SegFit

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, also using its current step size. The gridmap is specified by 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 * 2^½) ≈ 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:

• 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/e maximum height equal the resolution
• 1/(2 * (2log2)^½) ≈ 0.425 makes the Gaussian width at half maximum height equal the resolution

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:

• biomt - use biological unit information, if any, from the molecule model containing the specified atoms
• symmetry of model #N - use biomt information from another molecule model or the symmetry assignment of a volume model
  • Example: #4
• cage model polygon symmetry #N,pM or #N,pnM - place copies at equivalent positions relative to each M-sided polygon in the cage model with ID number N. The pM form places one copy per M-sided polygon, whereas pnM places M copies per M-sided polygon using CM symmetry about the center of the M-sided polygon nearest the original copy.
  • Examples: #2,p6 or #2,pn5
• cyclic symmetry Cn around axis and center
  • Example: C3
• dihedral symmetry Dn around axis and center
  • Example: d7
• tetrahedral symmetry T[,orientation] around center
  • Example: t,z3
  where orientation can 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 O around center
• icosahedral symmetry I[,orientation] around center
  • Example: i,n25
  where orientation can be:
  • 222 (default) - with two-fold symmetry axes along the X, Y, and Z axes
  • 2n5 - with two-fold symmetry along X and 5-fold along Z
  • n25 - with two-fold symmetry along Y and 5-fold along Z
  • 2n3 - with two-fold symmetry along X and 3-fold along Z
  • 222r - same as 222 except rotated 90° about Z
  • 2n5r - same as 2n5 except rotated 180° about Y
  • n25r - same as n25 except rotated 180° about X
  • 2n3r - same as 2n3 except rotated 180° about Y
• helical symmetry H,rise,angle,n[,offset] around axis and center
  • Example: h,43.5,21,6,-2
  where rise is the translation along the axis per subunit, angle is the rotation in degrees per subunit, and n is how many copies total (including the original) the resulting segment of infinite helix should contain. The integer offset (default 0) allows extending the helix in both directions. The example above would give n = 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,n,distance along axis – or – shift,n,x,y,z
  • Example: shift,3,26.7
  where n is how many copies total (including the original) the result should contain. The translation can be expressed as a distance along the axis or as a vector x,y,z in 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

axis axis
Specify axis of symmetry (default z), where axis can be:

• x - X-axis
• y - Y-axis
• z - Z-axis
• x,y,z (three values separated by commas only) - an arbitrary vector in the reference coordinate system
• an atom-spec of 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 word selected, sel, or picked; any atoms also selected at the time will be ignored.

center center
Specify center of symmetry (default 0,0,0), where center can be:

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

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.