frustrated in michigan -- September 27, 2006 - 19:56

Hello,

I would first  like to apologize that this post is going to be painfully remedial and likely nothing more than spam to most, but I am really having trouble getting relax to work and I don't know if it's because of me, or if I don't have things installed correctly, or something else entirely.  I'm going to go through what I'm doing step-by-step and hopefully it will shed light on what I'm doing wrong.

The relax manual, I find, is very good at explaining what relax is, describing the theory, and describing functions, but is less helpful in the practical aspects of running relax, like a tutorial.  The understanding I came to from Chapter 2 is that relax is run by scripts, so my goal is to go through the sample scripts and 1) run the scripts, 2) read and understand each line comparing to Chapter 10, 3) modify the scripts for real data.  Unfortunately, my problems begin with step 1.

So, here's what I'm doing ...

Get the program)
============

$ svn co svn://svn.gna.org/svn/relax/1.3 relax
-- it downloads everything into the folder relax

At revision 2581

$ cd relax
-- every single step :)
$ cp sample_scripts/*  .
$ cp test_suite/data/model_free/S2_0.970_te_2048_Rex_0.149/*  .
$ cp test_suite/data/test.pdb .
-- just bringing everything I need to the directory where the relax program is

====================
Find a simple script to run) 
====================
   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

=============================================================
Angles didn't work, let's try palmer.py because I'll want to compare relax with modelfree4
=============================================================
-- the stage is set to 2 in palmer.py, so I change that to 1

$ python relax palmer.py

It fails with this at the end:

...
relax> palmer.execute(run='m1', dir=None, force=1, binary='modelfree4')
RelaxError: Execution of the program Modelfree4 has failed.

I figure it needs modelfree4 to be there so, I copy it from another directory into  the relax directory and try again

$ python relax palmer.py

...
relax> palmer.create(run='m1', dir=None, force=0, binary='modelfree4', diff_search='none', sims=0, sim_type='pred', trim=0, steps=20, constraints=1, nucleus='15N', atom1='N', atom2='H')
RelaxError: The file 'm1/mfin' already exists.  Set the force flag to 1 to overwrite.

Oh yeah, modelfree doesn't like writing over things ... try again with force = 1

$ python relax palmer.py

...
relax> palmer.execute(run='m1', dir=None, force=1, binary='modelfree4')
RelaxError: Execution of the program Modelfree4 has failed.

So now I'm stumped.

================
Let's try running relax
================

$ python relax model-free.py

-- Works perfectly!  Nice!

$ python relax mf_multimodel.py

-- Also, works flawlessly, I'm on a roll!

$ python relax modsel.py

-- No go ... I get the full_analysis.py error again.  It successfully reads stuff in, as far as I can tell but this at the end:

relax> eliminate(run=None, function=None, args=None)
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 "modsel.py", line 20, in ?
    eliminate()
  File "/local/home/viochem/relax/prompt/eliminate.py", line 97, in eliminate
    self.relax.generic.eliminate.eliminate(run=run, function=function, args=args)
  File "/local/home/viochem/relax/generic_fns/eliminate.py", line 69, in eliminate
    names = param_names(self.run, i)
  File "/local/home/viochem/relax/specific_fns/model_free.py", line 1448, in get_param_names
    if not self.relax.data.res[self.run][j].model:
AttributeError: Element instance has no attribute 'model'

======================================
So, last but not least, let's try full_analysis.py again
======================================

$ python relax full_analysis.py

-- oops, need to create a "unresolved" file. Try again ...

$ python relax full_analysis.py

- working .... working .... working .... fails:

relax> run.create(run='aic', run_type='mf')

relax> eliminate(run=None, function=None, args=None)

relax> model_selection(method='AIC', modsel_run='aic', runs=None)
AIC model selection.
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 "full_analysis.py", line 415, in ?
    Main()
  File "full_analysis.py", line 145, in __init__
    self.model_selection(run='aic', dir=self.base_dir + 'aic')
  File "full_analysis.py", line 352, in model_selection
    model_selection('AIC', run)
  File "/local/home/viochem/relax/prompt/model_selection.py", line 121, in model_selection
    self.relax.generic.model_selection.select(method=method, modsel_run=modsel_run, runs=runs)
  File "/local/home/viochem/relax/generic_fns/model_selection.py", line 162, in select
    for i in xrange(self.min_instances):
TypeError: an integer is required

=======================================================================

So that's what I've done so far.  Does any of this make sense?  Hopefully there's a simple reason why I'm not able to get things to work correctly.



Alex Hansen