$ python access_dope.py creating representation Traceback (most recent call last): File "access_dope.py", line 27, in ? (m,prot)=create_representation() File "access_dope.py", line 7, in create_representation mp0= IMP.atom.read_pdb(IMP.atom.get_example_path('1fdx.B99990001.pdb'), m, IMP.atom.NonWaterNonHydrogenPDBSelector()) _IMP.IOException: Unable to find example file 1fdx.B99990001.pdb at /rose/space1/integratedModelling/share/doc/imp/examples/atom/1fdx.B99990001.pdb. IMP is not installed or set up correctly. $ python brownonian_statistic.py Traceback (most recent call last): File "brownonian_statistic.py", line 10, in ? maximum_diffusion_coefficient=\ NameError: name 'get_einstein_diffusion_coefficient' is not defined $ python cg_pdb.py Hierarchy Traceback (most recent call last): File "cg_pdb.py", line 8, in ? simplified= IMP.atom.create_simplified_along_backbone(IMP.atom.Chain(chain), 3) File "/rose/space1/integratedModelling/lib/python2.4/site-packages/IMP/atom/__init__.py", line 919, in __init__ this = _IMP_atom.new_Chain(*args) NotImplementedError: Wrong number of arguments for overloaded function 'new_Chain'. Possible C/C++ prototypes are: IMP::atom::Chain() IMP::atom::Chain(IMP::Particle *) $ python charmm_forcefield.py Traceback (most recent call last): File "charmm_forcefield.py", line 10, in ? ff = IMP.atom.get_heavy_atom_CHARMM_parameters() AttributeError: 'module' object has no attribute 'get_heavy_atom_CHARMM_parameters' $ python charmm_forcefield_verbose.py Traceback (most recent call last): File "charmm_forcefield_verbose.py", line 10, in ? ff = IMP.atom.get_heavy_atom_CHARMM_parameters() AttributeError: 'module' object has no attribute 'get_heavy_atom_CHARMM_parameters' $ python markers.py Traceback (most recent call last): File "markers.py", line 9, in ? s= IMP.atom.Selection(h, residue_indexes=[100,153]) AttributeError: 'module' object has no attribute 'Selection' $ python molecular_hierarchy.py residue #16 of name "LYS"Added particle for 0...1 Traceback (most recent call last): File "molecular_hierarchy.py", line 30, in ? mp1t= IMP.atom.get_hierarchy_tree(mp1) AttributeError: 'module' object has no attribute 'get_hierarchy_tree' $ python score_protein_with_legand.py Traceback (most recent call last): File "score_protein_with_legand.py", line 5, in ? protein= IMP.atom.read_pdb(IMP.atom.get_example_path('1d3d-protein.pdb'), m) _IMP.IOException: Unable to find example file 1d3d-protein.pdb at /rose/space1/integratedModelling/share/doc/imp/examples/atom/1d3d-protein.pdb. IMP is not installed or set up correctly. [bap54@protein imp_examples]$ python structure_from_sequence.py Traceback (most recent call last): File "structure_from_sequence.py", line 4, in ? topology = IMP.atom.CHARMMTopology(IMP.atom.get_all_atom_CHARMM_parameters()) AttributeError: 'module' object has no attribute 'get_all_atom_CHARMM_parameters'