Scripts: cube.py

#
# Extend a map by zero padding to make it have equal grid points along x,y,z dimensions.
# For a map of size 96,101,88 (1a0m from EDS) a command that does this is
#
#   vop cover #0 ibox -2,0,-6,98,100,94 useSymmetry false cellSize 200,200,200
#
# This script just produces the right arguments for the input map dimensions and runs vop cover.
# Run this script using Chimera command
#
#   run /tmp/cube.py #2
#
def cubify(v):
    xs,ys,zs = v.data.size
    s = max((xs,ys,zs))
    xo,yo,zo = (s-xs)//2,(s-ys)//2,(s-zs)//2
    command = ('vop cover %s ibox %d,%d,%d,%d,%d,%d useSymmetry false cellSize %d,%d,%d'
               % (v.oslIdent(),-xo,-yo,-zo,s-xo-1,s-yo-1,s-zo-1,s,s,s))
    from chimera import runCommand
    runCommand(command)

vspec = arguments[0]
from chimera import specifier
from VolumeViewer import Volume
for v in specifier.evalSpec(vspec).models():
    if isinstance(v, Volume):
        cubify(v)