Re: [bug #12487] Problem reading PDB file from full_analysis.py -- October 22, 2008 - 16:47

PDB file (which is now attached to bug report) is from several rounds of
simulated annealing in XPLOR-NIH. The structure is already published but for
privacy I did delete all but 1 residue of 1 model and changed the residue and
atom #s. It produces an identical error output.

It might take me a bit longer to appropriately truncate/'modify' the results
file since those are a mess to read. I'll attach it as soon as I can change it
and test it as well.

Tyler

Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:

> Hi,
>
> Thanks for the bug report.  This will probably be quite helpful as the
> messages don't indicate any problems.  It could be because of the
> format of the PDB file.  Do you know which program created this file?
> For debugging it would be very useful if you could attach the PDB file
> you used with all but one model deleted.  If this is sensitive
> information, then please randomise the coordinates, preserving the PDB
> columns.  Additionally, the file 'local_tm/aic/results.bz2' would be
> very useful as well.  This can be randomised (and truncated) as well,
> as it contains all your relaxation data and everything else needed to
> perform a full model-free analysis of your system.  If you do
> randomise or truncate data, it would be useful if you tested if this
> error occurs on that data before it is attached to the bug report.
>
> Cheers,
>
> Edward
>
>
>
> On Wed, Oct 22, 2008 at 2:47 PM, anonymous
> <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
> > 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
> >
> >    _______________________________________________________
> >
> > 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'
> >
> >
> >
> >
> >
> >
> >    _______________________________________________________
> >
> > Reply to this item at:
> >
> >  <http://gna.org/bugs/?12487>
> >
> > _______________________________________________
> >  Message sent via/by Gna!
> >  http://gna.org/
> >
> >
> > _______________________________________________
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> >
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