error when install pdbfixer1.5 on centos7:
removing '/usr/lib/python2.7/site-packages/pdbfixer-1.5-py2.7.egg' (and everything under it)
creating /usr/lib/python2.7/site-packages/pdbfixer-1.5-py2.7.egg
Extracting pdbfixer-1.5-py2.7.egg to /usr/lib/python2.7/site-packages
Sorry: TypeError: compile() expected string without null bytes
Sorry: TypeError: compile() expected string without null bytes
Sorry: TypeError: compile() expected string without null bytes
Sorry: TypeError: compile() expected string without null bytes
Sorry: TypeError: compile() expected string without null bytes
Sorry: TypeError: compile() expected string without null bytes
Sorry: TypeError: compile() expected string without null bytes
Sorry: TypeError: compile() expected string without null bytes
pdbfixer 1.5 is already the active version in easy-install.pth
pdbfixer is already can active by comline.
but it can not read PDB.
return another error..:
Traceback (most recent call last):
File "./repair.py", line 107, in
repair(pdbfile)
File "./repair.py", line 83, in repair
fixer = PDBFixer(filename=pdbfile)
File "/usr/lib/python2.7/site-packages/pdbfixer-1.5-py2.7.egg/pdbfixer/pdbfixer.py", line 277, in init
templatePdb = app.PDBFile(os.path.join(templatesPath, file))
File "/usr/lib64/python2.7/site-packages/simtk/openmm/app/pdbfile.py", line 160, in init
self.positions = self._positions[0]
IndexError: list index out of range
How exactly did you install it? Did you previously have another version installed? It looks like it thinks you have two copies installed by two different means.
error when install pdbfixer1.5 on centos7: removing '/usr/lib/python2.7/site-packages/pdbfixer-1.5-py2.7.egg' (and everything under it) creating /usr/lib/python2.7/site-packages/pdbfixer-1.5-py2.7.egg Extracting pdbfixer-1.5-py2.7.egg to /usr/lib/python2.7/site-packages Sorry: TypeError: compile() expected string without null bytes Sorry: TypeError: compile() expected string without null bytes Sorry: TypeError: compile() expected string without null bytes Sorry: TypeError: compile() expected string without null bytes Sorry: TypeError: compile() expected string without null bytes Sorry: TypeError: compile() expected string without null bytes Sorry: TypeError: compile() expected string without null bytes Sorry: TypeError: compile() expected string without null bytes pdbfixer 1.5 is already the active version in easy-install.pth
pdbfixer is already can active by comline. but it can not read PDB.
return another error..: Traceback (most recent call last): File "./repair.py", line 107, in
repair(pdbfile)
File "./repair.py", line 83, in repair
fixer = PDBFixer(filename=pdbfile)
File "/usr/lib/python2.7/site-packages/pdbfixer-1.5-py2.7.egg/pdbfixer/pdbfixer.py", line 277, in init
templatePdb = app.PDBFile(os.path.join(templatesPath, file))
File "/usr/lib64/python2.7/site-packages/simtk/openmm/app/pdbfile.py", line 160, in init
self.positions = self._positions[0]
IndexError: list index out of range
please help.