Usage:
vop operation arguments options

The vop command edits volume data to create a new volume data set. The original map is undisplayed and the new map is displayed with the same threshold and color as the original. Map display can be adjusted and the map saved to a file using Volume Viewer or the command volume. See also: mask, Volume Filter, Segment Map

Examples:

vop add #1-25 onGrid #0
vop add #1,2,5 onGrid #5 inPlace true
vop add #1,2 boundingGrid false
vop gaussian #3 sd 5
vop subtract #2 #4 modelId #5
vop unbend #0 #1 z 200 200

The operation can be:

• add - add two or more maps
• bin - reduce data size by averaging over cells of multiple grid points
• boxes - extract cubic regions centered on markers
• cover - extend map to cover specified atoms or box
• flatten - scale values to make first moments zero
• fourier - Fourier transform
• gaussian - Gaussian filtering
• laplacian - Laplacian filtering
• median - set each value to the median of values in a surrounding box
• morph - morph maps
• ~octant - erase positive octant
• octant - erase all but the positive octant
• permuteAxes - permute axes
• resample - resample on the grid of another map
• scale - scale, shift, and/or cast to a different data value type
• subtract - subtract another map from the first
• unbend - unbend a map near a path formed by markers/links or atoms/bonds
• zFlip - reverse order of Z planes

• vop add volume-spec [ scaleFactors f1,f2,... ] [ onGrid gridmap ] [ boundingGrid true|false ] [ gridStep N | Nx,Ny,Nz ] [ gridSubregion name | i1,j1,k1,i2,j2,k2 | all ] general-options

Add two or more maps to create a new map. The scaleFactors keyword specifies a multiplier for each map (default 1.0); as many values as input maps must be supplied, separated by commas but not spaces.

The new map can be created on the grid of another, where gridmap is a model number preceded by #. If gridmap is not specified, it defaults to the first in volume-spec (the first of the maps being added). The input maps are resampled on the grid by trilinear interpolation, and the resulting values summed for each grid point. Further options related to gridmap:

• boundingGrid - whether to adjust (extend or shrink) the grid of gridmap to bound the input maps (default true when adding maps without specifying a gridmap, otherwise false)
• gridStep - whether to use the full resolution of gridmap (step size 1, default) or a specified subsample (step size > 1). Step sizes must be integers. If a single number is supplied, it is used along all three axes; if three numbers are supplied (separated by commas but not spaces), they are used along the X, Y, and Z axes, respectively.
• gridSubregion - whether to use the full extents of gridmap (all, default) or a specified subregion. A subregion can be specified by:
  • name previously assigned with volume (see nameRegion) or Volume Viewer (see Named regions)
  • grid indices i1–i2 along the X axis, j1–j2 along the Y axis, and k1–k2 along the Z axis. Grid indices must be integers separated by commas but not spaces.

If the new map is large, for example a whole tomogram, the command may fail for lack of memory. The whole new map must fit in memory.

Average over cells of multiple grid points in the original map to produce a smaller map. Supplying a single integer N (default 2) indicates partitioning the map into bins of NxNxN grid points and averaging the N³ values per bin to produce a new map with 1/N as many points in each dimension. Cells with different numbers of grid points in each dimension can be specified by supplying three integers N_x,N_y,N_z separated by commas only. See also: segment

For each marker or atom in atom-spec, extract a surrounding cube of data. The edge length of each cube is the size d plus (if useMarkerSize is true) the diameter of its central marker or atom. The size is specified in physical units of length and can be omitted (default d=0.0) only when useMarkerSize is true.

Extend a map to cover specified atoms or to fill a rectangular box. It is assumed that the input map is periodic along all three axes. The output dimensions can be specified as:

• atomBox spanning the specified atoms plus any extra pad in each dimension (d is in units of physical distance, default 5.0)
• box or just individual dimensions x, y, and/or z in the X,Y,Z coordinate system of the input map
• fbox or just individual dimensions fx etc. in fractional coordinates where 0.0-1.0 spans each dimension of the input map
• ibox or just individual dimensions ix etc. in grid indices of the input map. The input map's grid indices start at 0.

Unspecified dimensions will be kept the same as the input map.

Scale data values by factor (1 + a*i + b*j + c*k) where i,j,k are the grid indices and a,b,c are calculated to zero out the first moments of the resulting map (make its mass balance at the center of the grid).

Calculate the 3D Fourier transform.

Perform Gaussian filtering with half-width σ. The half-width is one standard deviation of the 3D isotropic Gaussian function, specified in physical units such as Å (default 1.0). The value-type defaults to the current type and can be 8-, 16-, or 32-bit signed integer (int8, int16, or int32), 8-, 16-, or 32-bit unsigned integer (uint8, uint16, or uint32), or 32- or 64-bit floating-point (float32 or float64).

Perform Laplacian filtering.

Smooth the data by setting each value to the median of the values in a box centered at that point. Values at points for which the surrounding box extends outside the data are simply set to zero. Box dimensions are specified in grid units with binSize and must be odd integers. Supplying a single integer N (default 3) indicates a box size of NxNxN grid points. Boxes with different numbers of grid points in each dimension can be specified by supplying three integers N_x,N_y,N_z separated by commas only. The iterations option indicates how many cycles of smoothing to perform (default 1).

Morph between two or more maps (this is the command-line implementation of Morph Map, except that more than two maps can be handled). For a reasonable result, the input maps should have the same grid dimensions, spacing, and numbers of points. A morphing fraction of 0.0 corresponds to the first map and a fraction of 1.0 corresponds to the last, with intermediate maps evenly spaced within that range. There is smooth interpolation between each adjacent pair of maps.

The morph display will proceed from start-fraction (default 0.0) in steps of increment (default 0.04) for N frames (default 25). By default (playDirection 1), the initial direction of play is from low to high fractions. If the number of frames and step increment are more than needed to reach the playRange bounds (default is the entire range: 0.0,1.0), the morph display will "bounce" back and forth. The scaleFactors keyword specifies a multiplier for each map (default 1.0); as many values as input maps must be supplied. The constantVolume option specifies adjusting the threshold (contour level) automatically to keep the enclosed volume constant. The addMode option specifies treating the second map as a delta to be added to the first instead of linearly interpolating between the two. It is not recommended for inputs of >2 maps. The hideOriginalMaps option specifies hiding the input maps.

Erase values inside the positive octant (all grid points with X,Y,Z coordinates greater than the center). The center can be specified in physical units (such as Å) with center or in grid units with iCenter. The default is the center of the volume data box. The coordinates should be separated by commas but not spaces, and the values can be fractional. iCenter overrides center if both are given. The values in the erased regions will be set to value (default 0). A different value may improve contour surface appearance; for example, large negative values produce flatter surfaces where an octant has been cut away from a map of positive values.

Erase values outside the positive octant. Options are as described for ~octant above.

Permute grid axes to the specified order, which can be any of the 6 ordered combinations of x, y, and z. The original order is xyz.

Resample values on the grid of another map, where gridmap is a model number preceded by #. Values on the grid are obtained by trilinear interpolation of the input map. The other arguments are as described above for add.

Scale values by a multiplicative factor f (default 1.0), shift values by adding a constant (default 0.0), and/or cast them to a different data value type. When values are both shifted and scaled, the shift is applied first. The value-type defaults to the current type and can be 8-, 16-, or 32-bit signed integer (int8, int16, or int32), 8-, 16-, or 32-bit unsigned integer (uint8, uint16, or uint32), or 32- or 64-bit floating-point (float32 or float64).

Subtract the values of othermap from map, both specified by model number preceded by #. The scaleFactors keyword specifies multipliers f1 and f2 for map and othermap, respectively; two values must be supplied, separated by a comma but not spaces. Alternatively, the minRMS option can be used to scale othermap automatically to minimize the root-mean-square sum of the resulting (subtracted) values at grid points within the lowest contour of othermap.

The new map can be created on the grid of another, where gridmap is a model number preceded by #. If gridmap is not specified, it defaults to map. The input maps are resampled on the grid by trilinear interpolation, and the resulting values subtracted for each grid point. The remaining arguments are as described above for add, except that boundingGrid always defaults to false.

Unbend a map near a path formed by markers/links or equivalently, atoms/bonds. The path-spec should be an atom-spec that specifies a single chain of atoms (markers) connected by bonds (links). The path will be mapped to the Z axis of the result. The new-y parameter defines what axis in the existing volume will be mapped to the Y axis of the result, and can be given as:

• x - X-axis
• y - Y-axis
• z - Z-axis
• x,y,z (three values separated by commas only) - an arbitrary vector
• 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.

The xsize and ysize parameters give the X and Y dimensions of the new map in physical units (typically Å). The gridSpacing s is the separation between grid points in the new map (default is the minimum spacing along the three axes of the input map). A cubic spline is placed through the path points and the input volume is interpolated on planes perpendicular to the splined path.

Reverse the order of the Z planes.

modelId N
Open the new data set as model number N (an integer, optionally preceded by #). The default is the lowest unused number.

step N | Nx,Ny,Nz
Whether to use the full resolution of the data (step size 1, default) or a specified subsample (step size > 1). Step sizes must be integers. A step size of 1 indicates all data points, 2 indicates every other data point, 3 every third point, etc. If a single number is supplied, it is used along all three axes; if three numbers are supplied (separated by commas but not spaces), they are used along the X, Y, and Z axes, respectively.

subregion name | i1,j1,k1,i2,j2,k2 | all
Whether to use the full extents of the data (all, default) or a specified subregion. A subregion can be specified by:

• name previously assigned with volume (see nameRegion) or Volume Viewer (see Named regions)
• grid indices i1–i2 along the X axis, j1–j2 along the Y axis, and k1–k2 along the Z axis. Grid indices must be integers separated by commas but not spaces.

inPlace true|false
Whether to overwrite the existing data set in Chimera instead of creating a new one. Not all operations accept this option. Regardless of this setting, the existing data will only be overwritten if it was created in Chimera (for example with a previous vop command) rather than read from a file. In the case of map addition, the model to overwrite is the gridmap (the model whose grid will be used for the result).