Re: [bug #20674] UnboundLocalError in consistency_tests.py -- April 02, 2013 - 16:18

Hi Edward,

Thank you very much. I am a little bit confused, the pdb file  
2QFK_MONOMERHabc5.pdb have been added H by software reduce, I also  
check the first residue GLY, which has 5 H atoms. Perhaps I  
misunderstand your meanings, do you mean the 2QFK_MONOMERHabc5.pdb  
file (I have submitted before)? Thank you.

Regards,

Mengjun


Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:

> Hi Mengjun,
>
> This bug has now been fixed.  The problem was with the very first
> residue, as the PDB file has no H atom for it.  Normally this is not
> an issue because the first atom should normally not be visible in a
> nitrogen HSQC.  So there are 3 ways of fixing the problem.  You could
> wait until a new version of relax is released, though this could take
> a while as the next version will be the first of a brand new 3.0
> release series.  Alternatively you can check out a copy of the relax
> trunk as described in the docs
> (http://www.nmr-relax.com/manual/Latest_sources_relax_repositories.html).
>  Or thirdly, you can deselect your first residue.
>
> Regards,
>
> Edward
>
>
>
> On 29 March 2013 18:03,  <mengjun.xue@xxxxxxxxxxxxxxxxxxxx> wrote:
> > Hi Edward,
> >
> > Thank you so much for your suggestions. I will read it carefully.
> >
> >
> > Regards,
> >
> > Mengjun
> >
> >
> > Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> >
> > > Hi,
> > >
> > > The best way would be to read the manual.  Sebastien Morin has written
> > > a nice guide with step-by-step instructions on what you need to do in
> > > the manual.  You will need to read this as there are some manual steps
> > > which relax does not automate for you which you should be aware of.
> > > You should also read Sebastien's paper on the subject
> > > (http://dx.doi.org/10.1007/s10858-009-9381-4).
> > >
> > > Regards,
> > >
> > > Edward
> > >
> > >
> > > On 28 March 2013 21:10,  <mengjun.xue@xxxxxxxxxxxxxxxxxxxx> wrote:
> > > > Hi Edward,
> > > >
> > > > Thanks. I have submitted the pdb file. I understand that the consistency
> > > > test is for 2 field nmr data, for example, by comparing the J(0) at 500
> > > > MHz
> > > > and J(0) at 700 MHz, so I loaded the two field data when using
> > > > consistency_tests.py. I am confused that if one field data is loaded in
> > > > consistency_tests.py, how can consistency_tests.py check the consistency
> > > > between NMR data at 500 MHz and NMR data at 700 MHz? Thank you.
> > > >
> > > > With best regards,
> > > >
> > > > Mengjun
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > > >
> > > > > Hi again,
> > > > >
> > > > > I was wondering if you have read the consistency testing part of the
> > > > > relax manual written by Sebastien Morin (the person who implemented
> > > > > this analysis).  Specifically this section:
> > > > >
> > > > >
> > > > >
> > > > > http://www.nmr-relax.com/manual/Consistency_testing_script_mode_relaxation_data_lo.html
> > > > >
> > > > > Note the text, "For this analysis, only data for a single field
> > > > > strength can be loaded".  This may possibly be the source of some of
> > > > > your problems.
> > > > >
> > > > > Regards,
> > > > >
> > > > > Edward
> > > > >
> > > > >
> > > > >
> > > > > On 28 March 2013 20:02, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> > > > > > Hi Mengjun,
> > > > > >
> > > > > > Could you also attach the PDB file?  I need it to be able to run the
> > > > > > script and replicate the problem.
> > > > > >
> > > > > > Cheers,
> > > > > >
> > > > > > Edward
> > > > > >
> > > > > >
> > > > > >
> > > > > > On 28 March 2013 16:39, anonymous <NO-REPLY.INVALID-ADDRESS@xxxxxxx>
> > > > > > wrote:
> > > > > > > Additional Item Attachment, bug #20674 (project relax):
> > > > > > >
> > > > > > > File name: T1 dhp 700.txt                 Size:74 KB
> > > > > > > File name: T2 dhp 500.txt                 Size:67 KB
> > > > > > > File name: T2 dhp 700.txt                 Size:68 KB
> > > > > > > File name: logconsistency                 Size:371 KB
> > > > > > >
> > > > > > >
> > > > > > >     _______________________________________________________
> > > > > > >
> > > > > > > Reply to this item at:
> > > > > > >
> > > > > > >   <http://gna.org/bugs/?20674>
> > > > > > >
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