Re: latex script on final results -- November 12, 2008 - 20:35

This result will have to be checked carefully.  Maybe a comparsion
with the Bacteriorhodopsin fragment analysis of:

Orekhov, V. Y., Korzhnev, D. M., Diercks, T., Kessler, H., and
Arseniev, A. S. (1999a). H-1-N-15 NMR dynamic study of an isolated
alpha-helical peptide (1-36)- bacteriorhodopsin reveals the
equilibrium helix-coil transitions. J. Biomol. NMR, 14(4), 345–356.

would be useful.  The data and results need to be carefully checked.

Regards,

Edward


On Wed, Nov 12, 2008 at 1:48 PM, Tyler Reddy <TREDDY@xxxxxx> wrote:
> In terms of the low order parameters, I do observe the values in the results
> file in the 'final' directory, and not just in the .tex file table.
>
> Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
>
> > On Tue, Nov 11, 2008 at 11:59 AM, Tyler Reddy <TREDDY@xxxxxx> wrote:
> > > > Tyler, would you know what fixed the first traceback issue?  I'd like
> > > > to try to fix that in relax as any traceback message in relax is
> > > > considered a bug.
> > >
> > > I think it's just my python ignorance on this one. Here's how I produced
> > > the
> > > traceback in latex_mf_table.py:
> > >
> > > RESULTS_FILE = 'final/results.bz2'
> > > results.read(RESULTS_FILE, dir=None)
> > >
> > > I was proceeding on the assumption that specifying a directory at the
> > > location
> > > of the file name would be equivalent to specifying the same information
> > > to
> > > the
> > > dir argument of results.read
> > >
> > > However, by setting dir='final' and removing the directory argument from
> > > the
> > > file name itself, which I think is what was intended, the script works
> > > alright
> > > (except for the RelaxError discussed below).
> >
> > Hi,
> >
> > This actually shouldn't be a problem and relax will work if you use:
> >
> > results.read('final/results.bz2', dir=None)
> >
> > At worst relax should throw a clean RelaxError, but I'm pretty sure
> > relax will fully understand what you are trying to do there.  And from
> > the error message, the command was in fact:
> >
> > relax> results.read(file='results', dir=None)
> >
> > So the error message is caused by some other issue/bug, probably the
> > restoring of the 3D structural data from the results file.
> >
> >
> > > > The only errors that don't count as bugs are the
> > > > RelaxError messages.  This one seems like a directory issue within the
> > > > structure section of the results file.  Could you possibly cut and
> > > > paste the results files lines corresponding to the loaded structure?
> > > > I would suggest submitting a bug report as well - and I think I might
> > > > be able to reproduce it with all the mol, res, and spin entries
> > > > deleted.  If I can get the test suite to reproduce this, I should be
> > > > able to easily fix this.
> > >
> > > I'll try to get on this today. Would this influence my final values? All
> > > of
> > > my
> > > S^2 values are <0.05 which is disturbing, and Sf^2 values are all <0.5.
> > > I'm
> > > just reading these manually from the .tex file (assuming all this TeX
> > > coding
> > > basically just means value|error for the successive column elements
> > > listed).
> >
> > Strange.  Can you see these values in the results file as well?  You
> > only need to check one or two spins for that.  As for the TypeError
> > message, if you could help me fix this bug it would be appreciated as
> > if would help others as well.
> >
> > Regards,
> >
> > Edward
> >
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