Re: Hybrid model and writing of results -- April 08, 2008 - 19:46

Hi again,

I realized I didn't supply my script for hybridization... If it can be 
of any help, here it is :

========================================
###################################
# Code for running a hybrid model #
###################################

# The core diffusion model to hybridize with the C-terminus.
CORE = 'sphere'
CORE_hybrid = 'sphere_hybrid'

# The PDB file.
PDB_FILE = 'PROT.pdb'

# The file containing the sequence.
SEQUENCE = 'PROT.seq'

# The optimisation technique.
MIN_ALGOR = 'newton'

# The number of Monte Carlo simulations to be used for error analysis.
MC_NUM = 500


#############
# Main code #
#############

# Create the hybrid run
run.create(CORE, 'mf')
run.create('C-terminus', 'mf')

# Load the runs.
results.read(CORE, 'results', CORE)
results.read('C-terminus', 'results', 'C-terminus')

# Create the hybridized model.
run.hybridise(hybrid=CORE_hybrid, runs=[CORE, 'C-terminus'])

# Load the sequence
sequence.read(CORE_hybrid, SEQUENCE)

# Write the final results.
results.write(run=CORE_hybrid, file='results', dir=CORE_hybrid, 
format='columnar', force=1)
========================================


I can't find how to make this script work without crashing at the 
results writing step.

Can anyone help me ?

Thanks !


Séb  :)





Sébastien Morin 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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