[bug #7224] Test Suite Check: Angles.py -- September 28, 2006 - 15:04

URL:
  <http://gna.org/bugs/?7224>

                 Summary: Test Suite Check:  Angles.py
                 Project: relax
            Submitted by: viochemist
            Submitted on: Thursday 09/28/2006 at 13:04
                Category: None
                Priority: 5 - Normal
                Severity: 3 - Normal
                  Status: None
                 Privacy: Public
             Assigned to: None
         Originator Name: 
        Originator Email: 
             Open/Closed: Open
                 Release: Repository: 1.3 line
        Operating System: GNU/Linux

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Details:

Please see https://mail.gna.org/public/relax-users/2006-09/msg00031.html
for a complete post.

 angles.py is short and relatively straight forward ...
 Ap4Aase_new_3.pdb doesn't exist in the directory, so I change that line to
test.pdb

$ python relax angles.py
-- I need to include python because my python directory isn't
/usr/bin/python

Everything seems to work, but I get some warnings:

RelaxWarning: The atom H could not be found for residue 1

RelaxWarning: The atom H could not be found for residue 2

RelaxWarning: The atom H could not be found for residue 9

RelaxWarning: The atom H could not be found for residue 10


Calculating the unit XH vectors from the structure.

relax> diffusion_tensor.init(run='spheroid', params=(16980000.0, 14170000.0,
67.174000000000007, -83.718000000000004), time_scale=1.0, d_scale=1.0,
angle_units='deg', param_types=0, spheroid_type=None, fixed=1)
RelaxError: The tm value of 16980000.0 should be between zero and one
microsecond.

The default param_types for diffusion_tensor.init is (tm, Da, theta, phe),
so I change that line to:

diffusion_tensor.init(name, (1.698e7, 1.417e7, 67.174, -83.718),
param_types=3)
-- the first two look like D// and Dperp to me

$ python relax angles.py

And I get something like I had before with full_analysis.py at the end:

relax> diffusion_tensor.init(run='spheroid', params=(16980000.0, 14170000.0,
67.174000000000007, -83.718000000000004), time_scale=1.0, d_scale=1.0,
angle_units='deg', param_types=3, spheroid_type=None, fixed=1)

relax> angles(run='spheroid')
Traceback (most recent call last):
 File "relax", line 458, in ?
   Relax()
 File "relax", line 170, in __init__
   self.interpreter.run()
 File "/local/home/viochem/relax/prompt/interpreter.py", line 213, in run
   run_script(intro=self.relax.intro_string, local=self.local, script_file=
self.relax.script_file, quit=1)
 File "/local/home/viochem/relax/prompt/interpreter.py", line 388, in
run_script
   console.interact(intro, local, script_file, quit)
 File "/local/home/viochem/relax/prompt/interpreter.py", line 340, in
interact_script
   execfile(script_file, local)
 File "angles.py", line 5, in ?
   angles(name)
 File "/local/home/viochem/relax/prompt/angles.py", line 64, in angles
   self.relax.generic.angles.angles(run=run)
 File "/local/home/viochem/relax/generic_fns/angles.py", line 62, in angles
   self.spheroid_frame()
 File "/local/home/viochem/relax/generic_fns/angles.py", line 106, in
spheroid_frame
   for i in xrange(len(self.relax.data.res[self.run])):
KeyError






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