[Chimera-users] Sum of volume data values

Thomas Goddard goddard at cgl.ucsf.edu
Wed Apr 12 16:17:06 PDT 2006

Hi Eran,

  Ok, here is code to read an MRC file and print the sum of map values
without using Chimera.  You need Python, the Numeric Python module which
handles multidimensional arrays and the VolumeData module from Chimera.
Numeric is obtained from sourceforge:


The VolumeData module is in your Chimera distribution.


Here's an example running the script where I've set PYTHONPATH to have
access to the VolumeData module:

	% env PYTHONPATH=/usr/local/chimera/share python2.4 volumesum2.py
	Sum of values of groel.mrc  =  21720.8984375

Send future questions to chimera-users at cgl.ucsf.edu so others who
have similar problems can benefit.  I get that email just as fast.


file volumesum2.py follows:

# Script to print the sum of volume data values.
# Does not need Chimera, just the VolumeData module and Numeric and Python.

path = 'groel.mrc'

# Read the MRC volume data and get the 3-D Numeric array.
from VolumeData.mrc.mrc_format import MRC_Data
data = MRC_Data(path)
m = data.matrix()

# Compute the sum of the elements of the volume matrix.
import Numeric
sum = Numeric.sum(m.flat)

# Print the sum
print 'Sum of values of', path, ' = ', sum


> Date: Wed, 12 Apr 2006 14:46:14 -0700
> From: Eran Shacham <eshacham at burnham.org>
> To: Thomas Goddard <goddard at cgl.ucsf.edu>
> Subject: Re: Sum of volume data values
> Hey Tom,
> Thanks for your reply. However, I would like to do that from within a 
> script I already wrote. i.e I would like to integrate a read_in method 
> for an MRC file, access it values and then calculate the sum. I would 
> like to avoid doing that by opening my file in Chimera at this stage of 
> the program. Can it be done by importing some of your code?
> Thanks,
> Eran.

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