Command: molmap

Usage:
molmap  atom-spec  resolution  options

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. Another way to generate a low-resolution representation of an atomic structure is with measure inertia. See also: fitmap, sym

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

molmap #1 3.5
molmap protein 6

Options

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, or cube with N specified.

onGrid  gridmap
Create the new map on the grid of another, also using its current step size. This option overrides any gridSpacing and edgePadding values.

cube  N | true | false
Whether to enforce making the grid cubic, with the same number of points in X, Y, and Z (default false). If true, an even number of points will always be used. If an integer N is given:

• N points will be used in each dimension
• if edgePadding but not gridSpacing is specified, the spacing will be adjusted to include the requested padding
• if edgePadding and gridSpacing are both specified, the edgePadding will be ignored and the grid box may not cover the molecule if the spacing is too small given the number of points N

The cube option is ignored if onGrid is used.

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

balls  true | 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 the resolution. If false (default), for each atom use a Gaussian function with height proportional to the atomic number and width proportional to the resolution. The balls option 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 fine resolution but taking care to use an edgePadding value larger than the VDW radii (e.g., molmap protein 0.5 balls t edge 2.5).

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.

replace  true | false
Whether to overwrite any map previously created by molmap from the same set of atoms.

symmetry sym-type
Create a map corresponding to a symmetrical multimer of the structure. By default, no symmetry is used. Most sym-type options 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 #N – use the biological assembly information from another atomic model or the symmetry assignment of a volume model (such as from volume symmetry or measure symmetry)
  • Example: #4
• cage model (from Cage Builder) 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  vector-spec
Specify axis of symmetry vector (default z).

• center  point-spec
Specify center of symmetry point (default 0,0,0).

coordinateSystem  model-spec
Specify a reference coordinate system for interpreting specifications of axis and center of symmetry. The default is the atomic model containing the specified atoms.