Re: Hybrid model and writing of results -- April 09, 2008 - 15:48

Hi,

relax will calculate the AIC value for the hybrid models but will not
store it in a results file (it will store it in a saved state though).
 AIC values just sum, so this can be done by hand from the individual
results files if desired.  Note though that for other model-selection
techniques such as BIC, the values do not sum.  Also, relax will allow
2 or more hybrids to be compared.  For model selection you can have
any mixture of data pipes (runs), including model-free data pipes,
hybrid data pipes, or SRLS data pipes (if this gets coded one day).
The only requirement is that the data pipes contain the same sequence.
 You can even hybridise hybrid data pipes together with other data
pipes if you wish - because of relax's flexibility, anything is
possible.

Regards,

Edward


On Wed, Apr 9, 2008 at 3:17 PM, Sébastien Morin
<sebastien.morin.1@xxxxxxxxx> wrote:
>  Hi Ed,
>
>  I understand.
>
>  However, I would like to know if it is possible to calculate the AIC for a
> given hybrid... and possibly compare different hybrids together within
> relax...
>
>  Thanks !
>
>  Have a nice day !
>
>
>  Séb  :)
>
>
>
>
>
>
>  Edward d'Auvergne wrote:
>  Hi,
>
> This problem has quite a simple answer. There is no results writing
> code in relax for the hybrid models. The two runs (or data pipes if
> using 1.3 - I'll keep using this terminology here anyway) can be saved
> individually, but the hybrid itself cannot. Hence the message:
>
> RelaxError: The columnar format is not currently supported for hybrid
> models.
>
> or:
>
> RelaxError: The XML format is not currently supported for hybrid models.
>
> Also by saving the relax program state using the state.save() user
> function, then the hybrid information can be preserved. This save
> state should remain compatible with the 1.2 relax releases. Note that
> the hybrid data pipe is essentially an empty pipe which bundles a
> number of other data pipes together. It's own data content is very
> minimal, simply bing the information about which other pipes it
> encompases.
>
> The current format of the model-free results file is not flexible
> enough to handle these hybrid data pipes, but for the BMRB deposition
> code (a STAR formatted output) that I'll be adding to the 1.3
> development line, I will need to design a new format which can handle
> this. For example it will need to specify that subsets of spins are
> associated with one diffusion tensor (and that there can be many
> diffusion tensors for different spins, or no diffusion tenor for some
> spins)). This code will not make it to the 1.2 relax versions though.
>
> Regards,
>
> Edward
>
>
> On Fri, Apr 4, 2008 at 10:14 PM, Sébastien Morin
> <sebastien.morin.1@xxxxxxxxx> wrote:
>
>
>  Hi,
>
>  I encountered an error with the results.write() function concerning the
>  format when trying to work with an hybrid model.
>
>  In the default format (columnar) :
>
>  =========================
>
>  Traceback (most recent call last):
>  File "./hybrid.py", line 41, in ?
>  results.write(run=CORE_hybrid, file='results', dir=CORE_hybrid,
>  format='columnar', force=1)
>  File "/usr/local/packages/relax/prompt/results.py", line 201, in write
>  self.__relax__.generic.results.write(run=run, file=file,
>  directory=dir, force=force, format=format, compress_type=compress_type)
>  File "/usr/local/packages/relax/generic_fns/results.py", line 160, in
>  write
>  raise RelaxError, "The " + format + " format is not currently
>  supported for " + self.relax.specific_setup.get_string(function_type) + "."
>  RelaxError: RelaxError: The columnar format is not currently supported
>  for hybrid models.
>
>  =========================
>
>
>  Or in the XML format :
>
>  =========================
>
>  Traceback (most recent call last):
>  File "./hybrid.py", line 41, in ?
>  results.write(run=CORE_hybrid, file='results', dir=CORE_hybrid,
>  format='xml', force=1)
>  File "/usr/local/packages/relax/prompt/results.py", line 201, in write
>  self.__relax__.generic.results.write(run=run, file=file,
>  directory=dir, force=force, format=format, compress_type=compress_type)
>  File "/usr/local/packages/relax/generic_fns/results.py", line 160, in
>  write
>  raise RelaxError, "The " + format + " format is not currently
>  supported for " + self.relax.specific_setup.get_string(function_type) + "."
>  RelaxError: RelaxError: The XML format is not currently supported for
>  hybrid models.
>
>  =========================
>
>  Am I doing something wrong ?
>
>  Is it possible to write results from an hybrid model ?
>
>  Thanks !
>
>
>  Séb :)
>
>
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