You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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.
The text was updated successfully, but these errors were encountered:
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.
The text was updated successfully, but these errors were encountered: