voltool

The voltool command provides utilities to facilitate the manipulation and analysis of 3D volumetric data (density maps). All commands have the option to load the density map file from disk (-i filename) or work on maps which have already been loaded into VMD (-mol molid with optional -vol volume id which defaults to 0) to avoid unnecessary file i/o.

The input map format can be any that VMD reads (e.g., .ccp4, .mrc, .situs, .dx), while the output format (-o filename) must currently be in .dx.

map operations using an atomic structure:

• fit selection -res resolution [-i input density map] [-mol molid] [ -vol volume ID] [-thresholddensity threshold value] :
  Performs rigid body fitting of an atom selection to the given density map. First, the center of mass of the selection is moved to the center of mass of the density, followed by a brute-force rotational search. Structures are ranked according to their cross-correlation score.

• cc selection [-allframes] [-i input density map] [-mol molid ] [ -vol volume ID] [-thresholddensity threshold value] :
  Computes the MDFF cross correlation between a selection from an all-atom molecular structure, and a density map. This command uses multi-core CPU and GPU-accelerated algorithms for fast computation, as described in: http://dx.doi.org/DOI:10.1039/C4FD00005F The -thresholddensity option ignores voxels with values below x threshold in the simulated density map. This option is used to ignore density which is further away from the atom selection, which can often be noise.

• sim selection [-o output density map] [-res target resolution in Å] [-spacing grid spacing] : Compute a simulated density map from an atom selection on an all-atom molecular structure.

• mask selection [-res resolution of map in Å] [-cutoff cutoff distance in Å] [-i input density map] [-mol molid ] [ -vol volume ID] [-thresholddensity threshold value] :
  Creates a binary mask around the atom selection by simulating a map of given resolution, then removing all voxels from the input map that do not fall within the mask and the given cutoff.

operations on one map

• write [-i input density map] [-mol molid ] [ -vol volume ID] [-o output file] : Write volumetric data to a file (currently .dx is only supported output format).

• com [-i input density map] [-mol molid ] [ -vol volume ID] : get center of mass of density

• moveto -pos {x y z} coordinates [-i input density map] [-mol molid ] [ -vol volume ID] [-o output file]: move density center of mass to a specified coordinate

• move -mat 4x4 transform matrix [-i input density map] [-mol molid ] [ -vol volume ID] [-o output file]: apply specified 4x4 transformation matrix to density

• trim -amt {x1 x2 y1 y2 z1 z2} amount to trim on each axis [-i input density map] [-mol molid ] [ -vol volume ID] [-o output file]: trim edges of a density

• crop -amt {minx miny minz maxx maxy maxz} min/max coordinates [-i input density map] [-mol molid ] [ -vol volume ID] [-o output file]: crop density to values given in coordinate space

• clamp [-min min value] [-max max value] [-i input density map] [-mol molid ] [ -vol volume ID] [-o output file]: clamp out of range voxel values

• smult -amt scalar [-i input density map] [-mol molid ] [ -vol volume ID] [-o output file]: multiply every voxel by a scaling factor

• sadd -amt scalar [-i input density map] [-mol molid ] [ -vol volume ID] [-o output file]: add a scaling factor to every voxel

• range -minmax {min max} min/max values [-i input density map] [-mol molid ] [ -vol volume ID] [-o output file]: rescale voxel values to a given range

• downsample [-i input density map] [-mol molid ] [ -vol volume ID] [-o output file]: downsample by x2 (x8 total reduction)

• supersample [-i input density map] [-mol molid ] [ -vol volume ID] [-o output file]: supersample by x2 (x8 total increase)

• sigma [-i input density map] [-mol molid ] [ -vol volume ID] [-o output file]: transform map to sigma scale

• binmask [-threshold threshold value] [-i input density map] [-mol molid ] [ -vol volume ID] [-o output file]: make a binary mask of the map

• smooth -sigma radius [-i input density map] [-mol molid ] [ -vol volume ID] [-o output file]: multiply every voxel by a scaling factor

• pot [-threshold threshold value] [-i input density map] [-mol molid ] [ -vol volume ID] [-o output file]: convert a density map to an MDFF potential

• hist [-nbins number of histogram bins] [-i input density map] [-mol molid ] [ -vol volume ID]: Calculates a histogram of the density map and returns a list of frequencies and bin midpoints.

• info origin | cellaxes | cellvolume | xsize | ysize | zsize | minmax | mean | sigma | integral [-i input density map] [-mol molid ] [ -vol volume ID]: Gets information about the density map specified by the first argument:
  origin: x,y,z coordinates of the map's origin.
  cellaxes: the axes of one individual cell/voxel as a list of lists.
  cellvolume: the volume of one individual cell/voxel.
  xsize/ysize/zsize: length (number of voxels) of the axis in the given direction.
  minmax: list containing the minimum and maximum voxel values.
  mean, sigma: mean and standard deviation of the voxel values.
  integral: integral of the map (product of the mean and the volume of all cells).
  

operations on two maps These commands, except for correlate, have the default behavior of computing the result with the intersection of the two maps and interpolating the values from them. The -union option can be used to instad use the union of the two input maps, and -nointerp can be used to turn off interpolation.

• add [-i1 input density map] [-mol1 molid ] [ -vol1 volume ID] [-i2 input density map] [-mol2 molid ] [ -vol2 volume ID] [ -union] [ -nointerp ] [-o output file]:
  add two maps together

• diff [-i1 input density map] [-mol1 molid ] [ -vol1 volume ID] [-i2 input density map] [-mol2 molid ] [ -vol2 volume ID] [ -union] [ -nointerp ] [-o output file]:
  subtract map2 from map1

• mult [-i1 input density map] [-mol1 molid ] [ -vol1 volume ID] [-i2 input density map] [-mol2 molid ] [ -vol2 volume ID] [ -union] [ -nointerp ] [-o output file]:
  multiply map1 and map2

• avg [-i1 input density map] [-mol1 molid ] [ -vol1 volume ID] [-i2 input density map] [-mol2 molid ] [ -vol2 volume ID] [ -union] [ -nointerp ] [-o output file]:
  average two input maps into one

• correlate [-i1 input density map] [-mol1 molid ] [ -vol1 volume ID] [-i2 input density map] [-mol2 molid ] [ -vol2 volume ID]:
  calculates the cross-correlation coefficient between two maps