Load brick

load_brick is an API-only function to load an array of data as a map into PyMOL.

Volume visualization of a map (artificial data)

Example

from pymol import cmd
from chempy.brick import Brick
import numpy

# grid spacing in Angstrom
yourgridspacing = (0.2, 0.2, 0.2)

# numpy array with some artificial data
yourdata = numpy.zeros((100, 100, 100))
yourdata[20:80, 20:80, 20:80] = 1.0
yourdata[40:60, 40:60, 40:60] = 2.0

# load into PyMOL
brick = Brick.from_numpy(yourdata, yourgridspacing)
cmd.load_brick(brick, 'yourmap')

# visualize
cmd.volume('yourvolume', 'yourmap', [\
      0.5, 'blue', 0.4, \
      0.6, 'blue', 0.0, \
      1.4, 'red', 0.0, \
      1.5, 'red', 0.9, \
    ])