URL:
<http://gna.org/bugs/?12487>
Summary: Problem reading PDB file from full_analysis.py
Project: relax
Submitted by: None
Submitted on: Wednesday 10/22/2008 at 14:47 CEST
Category: relax's source code
Severity: 4 - Important
Priority: 5 - Normal
Status: None
Privacy: Public
Assigned to: None
Originator Name: Tyler Reddy
Originator Email: treddy@xxxxxx
Open/Closed: Open
Discussion Lock: Any
Release: 1.3.2
Operating System: Mac OS X
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Details:
Similar output for DIFF_MODEL = 'prolate', 'oblate', or 'ellipsoid'
Output:
relax> pipe.create(pipe_name='ellipsoid', pipe_type='mf')
relax> results.read(file='results', dir='local_tm/aic')
Opening the file 'local_tm/aic/results.bz2' for reading.
relax> model_free.remove_tm(spin_id=None)
relax> structure.read_pdb(file='PDB_file.pdb', dir=None, model=None,
parser='scientific')
Scientific Python PDB parser.
Loading all structures from the PDB file.
Structure('PDB_file.pdb', model=1):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=2):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=3):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=4):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=5):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=6):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=7):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=8):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=9):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=10):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=11):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=12):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=13):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=14):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=15):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=16):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=17):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=18):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=19):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=20):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=21):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=22):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=23):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=24):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=25):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=26):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=27):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=28):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=29):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=30):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=31):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=32):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=33):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=34):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=35):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=36):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=37):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=38):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=39):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=40):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=41):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=42):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=43):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=44):
Peptide chain A of length 27
Structure('PDB_file.pdb', model=45):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=46):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=47):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=48):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=49):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=50):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=51):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=52):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=53):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=54):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=55):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=56):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=57):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=58):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=59):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=60):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=61):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=62):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=63):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=64):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=65):
Peptide chain A of length 27
1 NH2 molecule
Structure('PDB_file.pdb', model=66):
Peptide chain A of length 27
1 NH2 molecule
relax> structure.vectors(attached='H', spin_id=None, struct_index=None,
verbosity=1, ave=True, unit=True)
Extracting vectors for all 66 structures.
Averaging all vectors.
Calculating the unit vectors.
The attached atom is a proton.
RelaxWarning: Either the spin number or name must be set for the spin ':254'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':258'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':261'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':264'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':268'
to identify the corresponding atom in the structure.
RelaxWarning: Either the spin number or name must be set for the spin ':273'
to identify the corresponding atom in the structure.
relax> diffusion_tensor.init(params=(1e-08, 0, 0, 0, 0, 0), time_scale=1.0,
d_scale=1.0, angle_units='deg', param_types=0, spheroid_type=None,
fixed=False)
relax> fix(element='all_spins', fixed=True)
relax> grid_search(lower=None, upper=None, inc=6, constraints=True,
verbosity=1)
Only diffusion tensor parameters will be used.
Unconstrained grid search size: 46656 (constraints may decrease this size).
Grid search
~~~~~~~~~~~
Searching the grid.
Traceback (most recent call last):
File "/Applications/relax-1.3.1/relax-1.3/relax", line 408, in <module>
Relax()
File "/Applications/relax-1.3.1/relax-1.3/relax", line 125, in __init__
self.interpreter.run(self.script_file)
File "/Applications/relax-1.3.1/relax-1.3/prompt/interpreter.py", line 270,
in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
File "/Applications/relax-1.3.1/relax-1.3/prompt/interpreter.py", line 531,
in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/Applications/relax-1.3.1/relax-1.3/prompt/interpreter.py", line 427,
in interact_script
execfile(script_file, local)
File "full_analysis.py", line 673, in <module>
Main(self.relax)
File "full_analysis.py", line 284, in __init__
grid_search(inc=inc)
File "/Applications/relax-1.3.1/relax-1.3/prompt/minimisation.py", line
152, in grid_search
minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File "/Applications/relax-1.3.1/relax-1.3/generic_fns/minimise.py", line
185, in grid_search
grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
verbosity=verbosity)
File
"/Applications/relax-1.3.1/relax-1.3/specific_fns/model_free/mf_minimise.py",
line 479, in grid_search
self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File
"/Applications/relax-1.3.1/relax-1.3/specific_fns/model_free/mf_minimise.py",
line 987, in minimise
results = generic_minimise(func=self.mf.func, dfunc=self.mf.dfunc,
d2func=self.mf.d2func, args=(), x0=param_vector, min_algor=min_algor,
min_options=min_options, func_tol=func_tol, grad_tol=grad_tol,
maxiter=max_iterations, A=A, b=b, full_ou
erbosity)
File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/minfx/generic.py",
line 319, in generic_minimise
xk, fk, k = grid(func=func, args=args, grid_ops=min_options, A=A, b=b,
l=l, u=u, c=c, print_flag=print_flag)
File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/minfx/grid.py",
line 129, in grid
f = func(*(params,)+args)
File "/Applications/relax-1.3.1/relax-1.3/maths_fns/mf.py", line 506, in
func_diff
self.diff_data.calc_di(data, self.diff_data)
File "/Applications/relax-1.3.1/relax-1.3/maths_fns/direction_cosine.py",
line 233, in calc_ellipsoid_di
data.dx = dot(data.xh_unit_vector, diff_data.dx)
TypeError: unsupported operand type(s) for *: 'NoneType' and 'float'
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[bug #12487] Problem reading PDB file from full_analysis.py