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**

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

**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**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**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•scaleFactorskeyword specifies a multiplier for each map (default1.0); 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

gridmapis a model number preceded by #. Ifgridmapis not specified, it defaults to the first involume-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 togridmap: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.

boundingGrid- whether to adjust (extend or shrink) the grid ofgridmapto bound the input maps (defaulttruewhen adding maps without specifying agridmap, otherwisefalse)gridStep- whether to use the full resolution ofgridmap(step size1, 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 ofgridmap(all, default) or a specified subregion. A subregion can be specified by:

namepreviously assigned withvolume(seenameRegion) orVolume Viewer(seeNamed regions)- grid indices
i1–i2along the X axis,j1–j2along the Y axis, andk1–k2along the Z axis. Grid indices must be integers separated by commas but not spaces.

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 N^{3}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 integersNseparated by commas only._{x},N_{y},N_{z}

For each marker or atom in•atom-spec, extract a surrounding cube of data. The edge length of each cube is the sizedplus (ifuseMarkerSizeis true) the diameter of its central marker or atom. Thesizeis specified in physical units of length and can be omitted (defaultd=0.0) only whenuseMarkerSizeis 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:•Unspecified dimensions will be kept the same as the input map.

atomBoxspanning the specified atoms plus any extrapadin each dimension (dis in units of physical distance, default5.0)boxor just individual dimensionsx,y, and/orzin the X,Y,Z coordinate system of the input mapfboxor just individual dimensionsfxetc.in fractional coordinates where 0.0-1.0 spans each dimension of the input mapiboxor just individual dimensionsixetc.in grid indices of the input map. The input map's grid indices start at 0.

Calculate the 3D Fourier transform.•

Perform Gaussian filtering with half-width•σ. The half-width is specified in physical units such as Å (default1.0).

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•binSizeand must be odd integers. Supplying a single integer N (default3) indicates a box size of NxNxN grid points. Boxes with different numbers of grid points in each dimension can be specified by supplying three integersNseparated by commas only. The_{x},N_{y},N_{z}iterationsoption indicates how many cycles of smoothing to perform (default1).

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(default0.0) in steps ofincrement(default0.04) forNframes(default25). 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 theplayRangebounds (default is the entire range:0.0,1.0), the morph display will "bounce" back and forth. ThescaleFactorskeyword specifies a multiplier for each map (default1.0); as many values as input maps must be supplied. TheconstantVolumeoption specifies adjusting the threshold (contour level) automatically to keep the enclosed volume constant. TheaddModeoption 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. ThehideOriginalMapsoption 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•centeror in grid units withiCenter. 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.iCenteroverridescenterif both are given. The values in the erased regions will be set tovalue(default0). 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•~octantabove.

Permute grid axes to the specified•order, which can be any of the 6 ordered combinations ofx,y, andz. The original order isxyz.

Resample values on the grid of another map, where•gridmapis 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 foradd.

Scale values by a multiplicative factor•f(default1.0), shift values by adding aconstant(default0.0), and/or cast them to a different data value type. When values are both shifted and scaled, the shift is applied first. Thevalue-typedefaults to the current type and can be 8-, 16-, or 32-bit signed integer (int8,int16, orint32), 8-, 16-, or 32-bit unsigned integer (uint8,uint16, oruint32), or 32- or 64-bit floating-point (float32orfloat64).

Subtract the values of•othermapfrommap, both specified by model number preceded by #. ThescaleFactorskeyword specifies multipliersf1andf2formapandothermap, respectively; two values must be supplied, separated by a comma but not spaces. Alternatively, theminRMSoption can be used to scaleothermapautomatically to minimize the root-mean-square sum of the resulting (subtracted) values at grid points within the lowest contour ofothermap.The new map can be created on the grid of another, where

gridmapis a model number preceded by #. Ifgridmapis not specified, it defaults tomap. 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 foradd, except thatboundingGridalways defaults tofalse.

Reverse the order of the Z planes.

modelIdN

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

stepN|Nx,Ny,Nz

Whether to use the full resolution of the data (step size1, 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.

subregionname|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:

namepreviously assigned withvolume(seenameRegion) orVolume Viewer(seeNamed regions)- grid indices
i1–i2along the X axis,j1–j2along the Y axis, andk1–k2along the Z axis. Grid indices must be integers separated by commas but not spaces.

inPlacetrue|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 previousvopcommand) rather than read from a file. In the case of map addition, the model to overwrite is thegridmap(the model whose grid will be used for the result).