Re: [bug #11004] Model elimination -- March 21, 2008 - 14:18

Hi,

I've fixed this bug, although I think other issues will arise.  From
the attached 'tail_1000_lines_log_model_5' file, it looks pretty
obvious that the global correlation time of 6.7 ns used in the script
is an underestimation.  The result is all the ts values are absorbing
this underestimation causing them to shoot up to values slower than
the global tumbling.  Of course it could be another issue causing the
large ts values.   Anyway, I have a feeling that this issue may cause
other bugs to be uncovered in relax.  Seb, could you test to see if
the 1.2 line now works?

Cheers,

Edward



On Fri, Feb 8, 2008 at 1:31 AM, Sébastien Morin
<NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
>  URL:
>   <http://gna.org/bugs/?11004>
>
>                  Summary: Model elimination
>                  Project: relax
>             Submitted by: semor
>             Submitted on: Thursday 02/07/2008 at 19:31
>                 Category: relax's source code
>                 Severity: 3 - Normal
>                 Priority: 5 - Normal
>                   Status: None
>                  Privacy: Public
>              Assigned to: None
>          Originator Name:
>         Originator Email:
>              Open/Closed: Open
>          Discussion Lock: Any
>                  Release: Repository: 1.2 line
>         Operating System: GNU/Linux
>
>     _______________________________________________________
>
>  Details:
>
>  Hi,
>
>  I recently got into a small problem related to model elimination, I think.
>
>  The relax version used was 1.2 from the repository (r4938).
>
>  The script used consisted of minimizing one model-free model, doing Monte
>  Carlo simulations, eliminating bad simulations and calculating errors (just
>  as in the sample script on page 30, section 6.2.1, of the manual, v1.2.11,
>  see attached file for an example with model 5).
>
>  R1s, R2s and NOEs were available from 2 magnetic fields for most residues,
>  some of which only had data from 1 magnetic field. For some models 
> (5,6,7,8),
>  model elimination eliminated lots of simulations... When reaching the
>  'monte_carlo.error_analysis' call, relax crashed (the saved state just 
> after
>  the eliminate() call, just before relax crashing, is available at :
>  http://maple.rsvs.ulaval.ca/users/semor/tmp/save_after_eliminate.bz2) with
>  the following error :
>
>  ==============================================================
>  relax> monte_carlo.error_analysis(run='m5', prune=0.0)
>  Traceback (most recent call last):
>   File "/home/semor/packages/relax-1.2/relax", line 454, in ?
>     Relax()
>   File "/home/semor/packages/relax-1.2/relax", line 166, in __init__
>     self.interpreter.run()
>   File "/home/semor/packages/relax-1.2/prompt/interpreter.py", line 216, in
>  run
>     run_script(intro=self.relax.intro_string, local=self.local,
>  script_file=self.relax.script_file, quit=1)
>   File "/home/semor/packages/relax-1.2/prompt/interpreter.py", line 391, in
>  run_script
>     console.interact(intro, local, script_file, quit)
>   File "/home/semor/packages/relax-1.2/prompt/interpreter.py", line 343, in
>  interact_script
>     execfile(script_file, local)
>   File "./model_5.py", line 43, in ?
>     monte_carlo.error_analysis(name)
>   File "/home/semor/packages/relax-1.2/prompt/monte_carlo.py", line 145, in
>  error_analysis
>     self.__relax__.generic.monte_carlo.error_analysis(run=run, prune=prune)
>   File "/home/semor/packages/relax-1.2/generic_fns/monte_carlo.py", line 
> 220,
>  in error_analysis
>     Xav = Xsum / float(n)
>  ZeroDivisionError: float division
>  ==============================================================
>
>  It seems 'n' was zero for at least one residue...
>
>  Thanks for help with this !
>
>
>  Séb
>
>
>
>
>     _______________________________________________________
>
>  File Attachments:
>
>
>  -------------------------------------------------------
>  Date: Thursday 02/07/2008 at 19:31  Name: model_5.py  Size: 1kB   By: semor
>
>  <http://gna.org/bugs/download.php?file_id=3760>
>
>     _______________________________________________________
>
>  Reply to this item at:
>
>   <http://gna.org/bugs/?11004>
>
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