Re: r7014 - in /1.3/sample_scripts: dasha.py diff_min.py generate_ri.py jw_mapping.py map.py palmer.py remap.py -- July 29, 2008 - 12:49

Hi,

Thanks for making all these fixes for the Boolean flags and the
cleaning up of the sample scripts.  There's quite a lot of old style
code that needs this kind of clean up in the 1.3 line.  In the case of
the heteronucleus, one other important change that has happened in the
redesign is that this variable is spin system specific.  This is to
allow different types of spins to be analysed simultaneously.
Therefore this user function should be executed only after the
molecule-residue-spin sequence has been loaded.  I might make these
changes another day (if they haven't already been fixed ;).

Cheers,

Edward


On Mon, Jul 28, 2008 at 10:44 PM,  <sebastien.morin.1@xxxxxxxxx> wrote:
> Author: semor
> Date: Mon Jul 28 22:44:16 2008
> New Revision: 7014
>
> URL: http://svn.gna.org/viewcvs/relax?rev=7014&view=rev
> Log:
> Changed the setting of the heteronuclei to the new design.
>
>
> Modified:
>    1.3/sample_scripts/dasha.py
>    1.3/sample_scripts/diff_min.py
>    1.3/sample_scripts/generate_ri.py
>    1.3/sample_scripts/jw_mapping.py
>    1.3/sample_scripts/map.py
>    1.3/sample_scripts/palmer.py
>    1.3/sample_scripts/remap.py
>
> Modified: 1.3/sample_scripts/dasha.py
> URL: 
> http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/dasha.py?rev=7014&r1=7013&r2=7014&view=diff
> ==============================================================================
> --- 1.3/sample_scripts/dasha.py (original)
> +++ 1.3/sample_scripts/dasha.py Mon Jul 28 22:44:16 2008
> @@ -5,7 +5,7 @@
>  pipes = ['m1', 'm2', 'm3', 'm4', 'm5']
>
>  # Nuclei type
> -nuclei('N')
> +value.set('15N', 'heteronucleus')
>
>  # Loop over the pipes.
>  for name in pipes:
>
> Modified: 1.3/sample_scripts/diff_min.py
> URL: 
> http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/diff_min.py?rev=7014&r1=7013&r2=7014&view=diff
> ==============================================================================
> --- 1.3/sample_scripts/diff_min.py (original)
> +++ 1.3/sample_scripts/diff_min.py Mon Jul 28 22:44:16 2008
> @@ -5,7 +5,7 @@
>  pipes = ['m1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
>
>  # Nuclei type
> -nuclei('N')
> +value.set('15N', 'heteronucleus')
>
>  # Minimise the model-free parameters.
>  print "\n\n\n\n\n"
>
> Modified: 1.3/sample_scripts/generate_ri.py
> URL: 
> http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/generate_ri.py?rev=7014&r1=7013&r2=7014&view=diff
> ==============================================================================
> --- 1.3/sample_scripts/generate_ri.py (original)
> +++ 1.3/sample_scripts/generate_ri.py Mon Jul 28 22:44:16 2008
> @@ -53,7 +53,7 @@
>  pipe.create('test', 'mf')
>
>  # Set the nucleus type to nitrogen.
> -nuclei('N')
> +value.set('15N', 'heteronucleus')
>
>  # Set the diffusion tensor to isotropic with tm set to 10 ns.
>  diffusion_tensor.init(10e-9)
>
> Modified: 1.3/sample_scripts/jw_mapping.py
> URL: 
> http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/jw_mapping.py?rev=7014&r1=7013&r2=7014&view=diff
> ==============================================================================
> --- 1.3/sample_scripts/jw_mapping.py (original)
> +++ 1.3/sample_scripts/jw_mapping.py Mon Jul 28 22:44:16 2008
> @@ -5,7 +5,7 @@
>  pipe.create(name, 'jw')
>
>  # Nuclei type
> -nuclei('N')
> +value.set('15N', 'heteronucleus')
>
>  # Load the sequence.
>  sequence.read(name, 'noe.600.out')
>
> Modified: 1.3/sample_scripts/map.py
> URL: 
> http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/map.py?rev=7014&r1=7013&r2=7014&view=diff
> ==============================================================================
> --- 1.3/sample_scripts/map.py (original)
> +++ 1.3/sample_scripts/map.py Mon Jul 28 22:44:16 2008
> @@ -5,7 +5,7 @@
>  pipe.create(name, 'mf')
>
>  # Nuclei type
> -nuclei('N')
> +value.set('15N', 'heteronucleus')
>
>  # Load the sequence.
>  sequence.read(name, 'noe.500.out')
>
> Modified: 1.3/sample_scripts/palmer.py
> URL: 
> http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/palmer.py?rev=7014&r1=7013&r2=7014&view=diff
> ==============================================================================
> --- 1.3/sample_scripts/palmer.py (original)
> +++ 1.3/sample_scripts/palmer.py Mon Jul 28 22:44:16 2008
> @@ -123,7 +123,7 @@
>  #############################
>
>  # Nuclei type.
> -nuclei('N')
> +value.set('15N', 'heteronucleus')
>
>  # Set the run name (also the name of a preset model-free model).
>  runs = ['m1', 'm2', 'm3', 'm4', 'm5']
>
> Modified: 1.3/sample_scripts/remap.py
> URL: 
> http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/remap.py?rev=7014&r1=7013&r2=7014&view=diff
> ==============================================================================
> --- 1.3/sample_scripts/remap.py (original)
> +++ 1.3/sample_scripts/remap.py Mon Jul 28 22:44:16 2008
> @@ -26,7 +26,7 @@
>  name = 'm5'
>
>  # Nuclei type
> -nuclei('N')
> +value.set('15N', 'heteronucleus')
>
>  # Create the run 'name'.
>  pipe.create(name, 'mf')
>
>
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