Hi Swapnil,
print "*** Executing cctbx"
p2 = Popen(cmmd2, shell=True, bufsize=bufsize, stdin=PIPE, stdout=PIPE, stderr=PIPE) output2 = p2.communicate(input = allout)
Here input (allout) is not empty but still output2 is coming empty which causes problems in next processing.
Could you show the cmnd2 command? Note that you need to use "cctbx.python". This is a thin launcher that updates PYTHONPATH and PATH before starting python. If you use just "python" the cctbx imports will not work. BTW: three days ago I checked in support for efficiently copying cctbx arrays to Numpy arrays, in case you want to go back and forth between cctbx modules and other modules based on Numpy. You need cctbx bundles 2010_11_14_2256 or later for this. Ralf