Hi Ryo, I've attached a Python script that squares the values of a density map. Opening the script (File / Open) creates a copy of the active map (the one highlighted in the volume dialog) with density values squared. I've tested it with Chimera 1.4. You could save the squared map to a file with the volume dialog File / Save Map As... menu entry. The script is also on the Chimera scripts web page. http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts Tom
Hi chimera users, I want to calculate the square value for the volume of the electron density because I want to calculate the variance map. Do anyone know whether we can calculate the square value of the volume by chimera? And if we can, could you teach me how to calculate? Thanks for your time and help, Ryo
# Make a new map by squaring the values of the currently active map. # Get the currently active volume from VolumeViewer import active_volume v = active_volume() # Square the density values. import numpy m = v.full_matrix().astype(numpy.float32) m[:] = m*m # Make a new map. from VolumeData import Array_Grid_Data from VolumeViewer.volume import volume_from_grid_data g = Array_Grid_Data(m, v.data.origin, v.data.step, v.data.cell_angles) c = volume_from_grid_data(g)