Re: Precision with ModelFree (palmer.py) -- January 15, 2008

Hi Ed,

I checked and ModelFree accepts the higher precision gyromagnetic value 
(-2.7126
instead of -2.713). Giving the higher precision value doesn't cause any error 
or
warning and the value is already with 4 decimals in the mfout file.

I tried two runs with the palmer.py script a the three stages. The 
optimization
is indeed slightly different.

I used an isotropic diffusion tensor with 5 residues, doing 100 Monte Carlo
simulations. You'll see in the attached file that differences are small.

The modification in the 'create_mfpar' method of the generic_fns.palmer module
was changing line 382 (in the repository version of the 1.2 line) from :

file.write('%-8.3f' % (self.relax.data.gx / 1e7))

to :

file.write('%-8.4f' % (self.relax.data.gx / 1e7))

I think that this change should go in the 1.3 line.

Do you think we need more tests ?

Cheers,


Séb  :)






Selon Edward d'Auvergne <edward.dauvergne@xxxxxxxxx>, 14.01.2008:

Hi,

The reason for the rounding is because I was mimicking the example of
the 'mfpar' file in the Modelfree manual

(http://www.cumc.columbia.edu/dept/gsas/biochem/labs/palmer/software/modelfree_manual.pdf).

 There the numbers are given to 3 decimal places.  This may make a bit
of a difference in the optimisation, but I don't know if Modelfree
will accept higher precision numbers.  To increase this number, it
will have to be thoroughly tested using Modelfree.  It will involve
modifying the 'create_mfpar' method in the generic_fns.palmer module
(I'll be changing this one day soon from a class method to a module
function).  This change, if it doesn't cause problems with Modelfree,
should go into the 1.3 line after approval.

Cheers,

Edward


On Jan 11, 2008 6:54 PM, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> 
wrote:

Hi,

I used the palmer.py script to run ModelFree from within relax 1.2
(repository).

The value for the 15N gyromagnetic ratio in the file
'generic_fns/nuclei.py' is -2.7126e7.

However, in the 'mfpar' file created by the script 'palmer.py', the
value specified is rounded up (-2.713).

Is it something intended or should this be changed ?

Cheers


Séb

--
Sebastien Morin
Etudiant au PhD en biochimie
Laboratoire de resonance magnetique nucleaire
Dr Stephane Gagne
CREFSIP (Universite Laval, Quebec, CANADA)
1-418-656-2131 #4530



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------------------------
Sébastien Morin
Étudiant M.Sc. Biochimie
Laboratoire S. Gagné
3252 Pav. Marchand (Université Laval)
Tél : (418) 656-2131 #4530
Fax : (418) 656-7176
e-mail : sebastien.morin.1@xxxxxxxxx

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Re: Precision with ModelFree (palmer.py)

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