The vop command edits volume data to create a new volume data set. Volume-model is the model number (preceded by #) of the existing volume data set or map. The original map is undisplayed and the new one 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.
Option keywords for vop 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.
Some options apply only to certain operations.
modelId N
Open the new data set as model N (must be an integer). The default is the next available number.
inPlace true|false
Whether to overwrite the existing data set in Chimera instead of creating a new one. Regardless of this setting, the existing data will only be overwritten if it was created in Chimera rather than read from a file.
useSubregion true|false
Use the displayed volume subregion rather than the full data set. In this context, a zone is not considered a subregion.
useStep true|false
Use the displayed volume subsample (step > 1) rather than the full data set.
fillValue value
Set all values in erased regions 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.
center x,y,z
Specify a reference point for volume operations in physical units (such as Å). It is overridden by iCenter if both are specified; the default is the center of the volume data box. The coordinates should be separated by commas but not spaces.
iCenter i,j,k
Specify a reference point for volume operations in grid units. It overrides center if both are specified; the default is the center of the volume data box. The coordinates should be separated by commas but not spaces. Values can be fractional.
onGrid other-map
Specify the grid on which to resample the data, where other-map is a volume model number preceded by #. The useSubregion and useStep options refer to this map when resampling is performed.
map other-map
Specify a second map with values to subtract from those of the first map, where other-map is a volume model number preceded by #. Values are paired simply on the basis of grid indices, so the two maps must have the same number of points in each dimension. Physical location and grid point spacing are ignored. If either useSubregion or useStep is true, both maps must have the same subregion and step. The resample operation may be useful for generating an appropriate map to subtract.
Fourier transform. Only the magnitudes of the complex Fourier components are included in the new data set; the phases are discarded and the constant component is set to zero. The box containing the Fourier transform (with axes in units of reciprocal space) is centered on the original data and scaled to have the same total volume. Some properties of the original data are evident from the Fourier transform. High-frequency components are near the edges of the box, low-freqency components near the center. Volume data is typically oversampled (voxel size two to three times smaller than the actual data resolution) and this causes the Fourier transform to have nonzero values only in the middle half or third of its bounding box. The missing wedge in electron microscope tomograms can also be seen. Spikes radiating along the principal axes in the Fourier transform are caused by nonperiodicity of the original data.