Hi, I am trying to run povme on my system but I am getting an error:
OUTPUTBASENAME: example_
PARAMETERS DEFINED
ABOUT TO LOAD RECEPTORS
Reading frames from 1X7R.pdb
Further processing frame 1
Further processing frame 2
Further processing frame 3
Further processing frame 4
Further processing frame 5
RECEPTORS LOADED
Generating the pocket-encompassing point field
Saving the point field as a PDB and NPY file
Point field saved to ./POVME_test_run/example_frameInfo/example_inclusion.pdb to permit visualization
Point field saved to ./POVME_test_run/example_frameInfo/example_inclusion.npy to optionally load for the volume calculation
Saving the contiguous-pocket seed points as a PDB and NPY file
Contiguous-pocket seed points saved to ./POVME_test_run/example_frameInfo/example_seed.pdb to permit visualization
Point field saved to ./POVME_test_run/example_frameInfo/example_seed.npy to optionally load for the volume calculation
Calculating the pocket volume of each frame
STARTING CALC VOLUME
Traceback (most recent call last):
File "/home/cmbc/miniconda2/bin/POVME3.py", line 2205, in
if name == "main": dorun = runit(sys.argv)
File "/home/cmbc/miniconda2/bin/POVME3.py", line 1970, in init
tmp = Multithreading([(index, pdb_object, parameters) for index, pdb_object in index_and_pdbs], parameters[NumProcessors], MultithreadingCalcVolumeTask)
File "/home/cmbc/miniconda2/bin/POVME3.py", line 146, in init
for item in inputs: single_thread.value_func(item, None)
File "/home/cmbc/miniconda2/bin/POVME3.py", line 1089, in value_func
coloredMaps = my_peel.color_povme_map(pts, parameters[GridSpacing], skin=color_skin_distance)
File "/home/cmbc/miniconda2/lib/python2.7/site-packages/POVME/packages/binana/peel.py", line 3397, in color_povme_map
minX = np.min(povmeMatrix[:,0])
File "/home/cmbc/miniconda2/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 2618, in amin
initial=initial)
File "/home/cmbc/miniconda2/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 86, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
But when I run povme on the basic example provided , it ran smoothly.
Kindly help me in resolving this issue as I am facing this problem since 2 days.
Hi, I am trying to run povme on my system but I am getting an error:
OUTPUTBASENAME: example_
PARAMETERS DEFINED
ABOUT TO LOAD RECEPTORS
Reading frames from 1X7R.pdb
Further processing frame 1
Further processing frame 2
Further processing frame 3
Further processing frame 4
Further processing frame 5
RECEPTORS LOADED
Generating the pocket-encompassing point field
Saving the point field as a PDB and NPY file
Point field saved to ./POVME_test_run/example_frameInfo/example_inclusion.pdb to permit visualization
Point field saved to ./POVME_test_run/example_frameInfo/example_inclusion.npy to optionally load for the volume calculation
Saving the contiguous-pocket seed points as a PDB and NPY file
Contiguous-pocket seed points saved to ./POVME_test_run/example_frameInfo/example_seed.pdb to permit visualization
Point field saved to ./POVME_test_run/example_frameInfo/example_seed.npy to optionally load for the volume calculation
Calculating the pocket volume of each frame
STARTING CALC VOLUME
Traceback (most recent call last):
File "/home/cmbc/miniconda2/bin/POVME3.py", line 2205, in
if name == "main": dorun = runit(sys.argv)
File "/home/cmbc/miniconda2/bin/POVME3.py", line 1970, in init
tmp = Multithreading([(index, pdb_object, parameters) for index, pdb_object in index_and_pdbs], parameters[NumProcessors], MultithreadingCalcVolumeTask)
File "/home/cmbc/miniconda2/bin/POVME3.py", line 146, in init
for item in inputs: single_thread.value_func(item, None)
File "/home/cmbc/miniconda2/bin/POVME3.py", line 1089, in value_func
coloredMaps = my_peel.color_povme_map(pts, parameters[GridSpacing], skin=color_skin_distance)
File "/home/cmbc/miniconda2/lib/python2.7/site-packages/POVME/packages/binana/peel.py", line 3397, in color_povme_map
minX = np.min(povmeMatrix[:,0])
File "/home/cmbc/miniconda2/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 2618, in amin
initial=initial)
File "/home/cmbc/miniconda2/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 86, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
But when I run povme on the basic example provided , it ran smoothly.
Kindly help me in resolving this issue as I am facing this problem since 2 days.