Re: [bug #19717] relax_fit.py: write.grace, deselect.read parameters -- May 09, 2012 - 09:20

Hi Martin,

Actually, I now know what you meant by res_num_col argument.  In the
revision r16127 I have added all of the column arguments to the sample
script (http://www.mail-archive.com/relax-commits@xxxxxxx/msg13830.html).

Cheers,

Edward


On 9 May 2012 09:12, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> Hi Martin,
>
> Thanks for the feedback!  I've been trying to find the 'int' verses
> 'intensity' problem and it looks like you have a sample script from
> relax 1.3.13 or earlier.  At 1.3.14, the grace.write user function
> lines in the sample_scripts/relax_fit.py file changed from:
>
> grace.write(x_data_type='relax_times', y_data_type='int',
> file='intensities.agr', force=True)
>
> to:
>
> grace.write(x_data_type='relax_times', y_data_type='intensities',
> file='intensities.agr', force=True)
>
> Therefore this is only a problem of using old scripts.  One idea for a
> solution I had a long time ago was to have a special script (in the
> scripts directory) which can convert or upgrade scripts from one relax
> version to the next.  However this proved to be too expensive for me,
> time-wise, to implement and most uses just use the docs fix as needed.
>  Such a conversion can be quite complex when a user has a 1000 line
> script.
>
> As for deselect.read needing the res_num_col argument set, this is
> definitely the case in proteins and RNA/DNA.  But for small organic
> molecules where there are no residues, this column would be
> meaningless.  I am making the error messages a bit clearer, but I
> can't think of a solution.  Would you have any ideas?
>
> Cheers,
>
> Edward
>
>
>
> On 7 May 2012 11:19, Martin Ballaschk <NO-REPLY.INVALID-ADDRESS@xxxxxxx> 
> wrote:
> > URL:
> >  <http://gna.org/bugs/?19717>
> >
> >                 Summary: relax_fit.py: write.grace, deselect.read 
> > parameters
> >                 Project: relax
> >            Submitted by: mab
> >            Submitted on: Mon 07 May 2012 09:19:50 AM GMT
> >                Category: relax sample scripts
> >                Severity: 3 - Normal
> >                Priority: 5 - Normal
> >                  Status: None
> >                 Privacy: Public
> >             Assigned to: None
> >         Originator Name:
> >        Originator Email:
> >             Open/Closed: Open
> >         Discussion Lock: Any
> >                 Release: 1.3.15
> >        Operating System: Mac OS X (Intel)
> >
> >    _______________________________________________________
> >
> > Details:
> >
> > I noticed that in the sample script relax_fit.py some parameters need to be
> > updated:
> >
> > * in write.grace: y_data_type needs to be 'intensities' instead of 'int',
> > otherwise relax complains
> > * deselect.read needs the res_num_col specified, otherwise relax complains:
> > "RelaxError: The identifier '' corresponds to more than a single spin in 
> > the
> > 'rx' data pipe."
> >
> > All of this can be found via the help function however.
> >
> >
> >
> >
> >    _______________________________________________________
> >
> > Reply to this item at:
> >
> >  <http://gna.org/bugs/?19717>
> >
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