[IMP-users] IMP issue regarding examples in web-ste: this is probably an expert level issue

["Adhikari, Badri (MU-Student)" <>]

Hello IMP users and experts,

 

IMP looks attractive to us. Thank you for all the active support.

 

I am using IMP available at http://salilab.org/imp/get.php?pkg=1.0/download/imp-1.0.tar.gz

 

Two interesting questions:

1.       The example code at http://salilab.org/imp/nightly/doc/html/atom_examples.html#charmm_forcefield_verbose and the example at PREFIX/modules/atom/examples/charmm_forcefield.py are supposed to do the same thing, but the code are not exactly same. The web code uses functions that my IMP does not understand. Is this some IMP version issue?

2.       The first example, access dope, in http://salilab.org/imp/nightly/doc/html/atom_examples.html tries to pick up  1fdx.B99990001.pdb which I don’t find anywhere in any of the folders. So, how is this example supposed to run? Looks like this has something to do with my issues as well.

 

Most importantly, please, help me find a version of code for http://salilab.org/imp/nightly/doc/html/atom_examples.html#structure_from_sequence that is similar to the examples provided in the installation package. It looks like my version of IMP does not have functions like IMP.atom.get_all_atom_CHARMM_parameters(). I am not familiar enough with IMP’s language to convert the code myself.

 

I am desperately working on trying to generate some models from sequences.

 

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In case you think that it is some installation issues, here are the details:

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My IMP installation log is at http://web.missouri.edu/~bap54/IMPinstall.log

 

I have installed IMP in two of our servers. I don’t have root access in these machines. IMP seems to be working well for normal use because I can run almost all of the examples and test files. The list of programs that I can run are attached as list_of_programs_that_run_smoothly.txt

However, I get error while executing some programs. The list is attached in programs_that_throw_error.txt

Also, I cannot run examples at http://salilab.org/imp/nightly/doc/html/atom_examples.html#structure_from_sequence. The errors that I receive are attached in errors_in_the_website_examples.txt

 

The most important example that I need to run is http://salilab.org/imp/nightly/doc/html/atom_examples.html#structure_from_sequence. And the error that I get while trying to run this example is:

$python structure_from_sequence.py

Traceback (most recent call last):

  File "../imp_examples/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'

 

·         I have already tried in 3 different machines with different configurations, with no luck at all. In one virtual machine, I installed with root access as well. I get the same error everywhere. The interesting thing is: once installed nothing is written to share/doc/imp, so I need to manually copy the example files needed (like example_protein.pdb) to run the examples.

·         All required tools are installed properly. I worked hard to install all boost libraries. All the required programs are installed correctly. This can be seen in the IMPinstall.log at http://web.missouri.edu/~bap54/IMPinstall.log

·         I have single copy of IMP installed. No multiple copies.

 

Sincerely,

Badri Adhikari

CS Graduate Student,

University of Missouri-Columbia,

Columbia, Missouri

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Atom Example files
------------------------------------------------------------------
python charmm_forcefield.py
python load_protein_restrain_bonds.py
python molecular_hierarchy.py

Core Example files
------------------------------------------------------------------
python connectivity_restraint.py
python cover_particles.py
python excluded_volume.py
python pair_restraint.py
python restrain_diameter.py
python rigid_bodies.py
python rigid_collisions.py
python XYZ_Decorator.py
python XYZR_Decorator.py

Atom Test files
------------------------------------------------------------------
python test_bd.py
python test_bd_singleton_score.py
python test_bond_decorator_particle_pair_container.py
python test_bond_refiner.py
python test_bonds.py
python test_charged_decorator.py
python test_charmm_atom.py
python test_charmm_parameters.py
python test_charmm_topology.py
python test_clone.py
python test_coulomb.py
python test_cover_bond.py
python test_create_protein.py
python test_distance.py
python test_element.py
python test_estimates.py
python test_force_switch.py
python test_fragment.py
python test_get_residue.py
python test_hierarchy.py
python test_lennard_jones_decorator.py
python test_lennard_jones_pair_score.py
python test_md_optimizer.py
python test_mol2.py
python test_pdb.py
python test_pdb_string.py
python test_protein_ligand_score.py
python test_ref_optimizer_states.py
python test_rmsd_and_no.py
python test_simplify.py
python test_stereo_pair_filter.py

Core Test files
------------------------------------------------------------------
python test_angle.py				
python test_box.py                  
python test_centroid.py             
python test_cg_optimizer.py         
python test_children.py             
python test_close_pair_finders.py   
python test_close_pairs_ps.py       
python test_connectivity.py         
python test_cosine.py               
python test_cover.py                
python test_cover_refiner.py        
python test_diameter.py             
python test_dihedral.py             
python test_distance.py             
python test_ev_restraint.py         
python test_harmonic.py             
python test_hierarchy.py            
python test_linear.py               
python test_mccg.py                 
python test_mc_rigid_bodies.py      
python test_particles.py            
python test_refcount.py             
python test_refined_pairs_ps.py     
python test_ref_states.py           
python test_rigid_bodies.py         
python test_rigid_distance.py       
python test_sd_optimizer.py         
python test_splines.py              
python test_table.py                
python test_to_from_refined.py      
python test_transform_particles.py  
python test_transform.py            
python test_truncated_harmonic.py   
python test_typed_pair_score.py     
python test_volume.py               
python test_xyzr.py 

$ python fragments/custom_hierarchy.py 
	Traceback (most recent call last):
	  File "fragments/custom_hierarchy.py", line 1, in ?
		tr= IMP.core.HierarchyTraits("my hierarchy")
	NameError: name 'IMP' is not defined

$ python fragments/randomize_rigid_body.py 
	Traceback (most recent call last):
	  File "fragments/randomize_rigid_body.py", line 2, in ?
		rbd= IMP.core.RigidBody(p)
	NameError: name 'IMP' is not defined

$ python test_mc.py 
	EEE
	======================================================================
	ERROR: test montecarlo 1
	----------------------------------------------------------------------
	Traceback (most recent call last):
	  File "test_mc.py", line 46, in test_c1
		(model, opt)= self._setup_opt()
	  File "test_mc.py", line 71, in _setup_opt
		ls= IMP.container.ListSingletonContainer(model.get_particles())
	AttributeError: 'module' object has no attribute 'container'

	======================================================================
	ERROR: test montecarlo 2
	----------------------------------------------------------------------
	Traceback (most recent call last):
	  File "test_mc.py", line 52, in test_c2
		(model, opt)= self._setup_opt()
	  File "test_mc.py", line 71, in _setup_opt
		ls= IMP.container.ListSingletonContainer(model.get_particles())
	AttributeError: 'module' object has no attribute 'container'

	======================================================================
	ERROR: test montecarlo 3
	----------------------------------------------------------------------
	Traceback (most recent call last):
	  File "test_mc.py", line 58, in test_c3
		(model, opt)= self._setup_opt()
	  File "test_mc.py", line 71, in _setup_opt
		ls= IMP.container.ListSingletonContainer(model.get_particles())
	AttributeError: 'module' object has no attribute 'container'

$ python ../imp_examples/structure_from_sequence.py 
	Traceback (most recent call last):
	  File "../imp_examples/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'

$ 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'