I did not used relax to get r1,r2,noe -- November 26, 2012 - 12:20

Ok, i answer your question now.

Values are S2 values just for a sample.

I did not use relax to get r1,r2 and noe but used NMRDraw text output, so all data is in text.

I copied dauvergne protocol and modified it with my own data set and then on "gui", just followed each step, no problems with "gui" following.

Rex values seem to correlate a bit with Palmers modelfree4 i executed perfectly but relax is more robust and can perform complete anisotropic which modelfree from Palmer cannot. so i used relax to gain more understanding. Relax result of Rex values also correlates with cpmg results but i want to gain more information how to extract data for presentation like i want to know distribution of residues per model. my structure looks "prolate" but how to tell with relax? i saw it chooses "prolate" for which am happy.

---

From: Edward d'Auvergne <edward@xxxxxxxxxxxxx>
To: Kozo Keisho <crystalrlx@xxxxxxxxxxx>
Cc: "relax-users@xxxxxxx" <relax-users@xxxxxxx>
Sent: Monday, 26 November 2012, 18:30
Subject: Re: Relax finished with this message

Hello Kozo,

Would you be able to submit a bug report for this?  The link is
http://www.nmr-relax.com/manual/Reporting_bugs.html.  Cheers.  It
would be useful if you could describe what you have done.  The more
information the better.  If you have used a script, you can attach the
script to the bug report.  Otherwise describe all the steps you
performed in the GUI or prompt modes.  The RelaxFault you have
encountered really should never be reached.  The only way this can
happen is if the S2f order parameter is optimised to the value of
None, or the optimisation is skipped entirely.  But relax should have
stopped you long before reaching this point, clearly explaining what
went wrong.

Also the output you show is totally unidentifiable.  I could guess
that these are some sort of order parameters, but it could be chemical
exchange or possibly even internal correlation times.  Therefore I
cannot tell you why you have no values for residues 6-9.  Also because
there is zero information about how you reached the RelaxFault, that
also makes it beyond impossible to determine the problem.  If you can
provide more information, this would considerably help me in
identifying what went wrong.

Cheers,

Edward


P. S.  I was wondering if you have followed my graphical tutorials in
how to use the relax GUI for a model-free analysis
(http://www.nmr-relax.com/manual/new_protocol_in_GUI.html, in the
model-free chapter of the user manual
http://www.nmr-relax.com/manual/Model_free_analysis.html)?  And did
you use relax to determine the R1, R2, and NOE values?

On 20 November 2012 15:16, Kozo Keisho <crystalrlx@xxxxxxxxxxx> wrote:
> Traceback (most recent call last):
>  File "gui/analyses/execute.pyc", line 87, in run
>  File "gui/analyses/auto_model_free.pyc", line 808, in run_analysis
>  File "auto_analyses/dauvergne_protocol.pyc", line 234, in __init__
>  File "auto_analyses/dauvergne_protocol.pyc", line 735, in execute
>  File "auto_analyses/dauvergne_protocol.pyc", line 901, in write_results
>  File "prompt/uf_objects.pyc", line 219, in __call__
>  File "generic_fns/pymol_control.pyc", line 504, in macro_write
>  File "generic_fns/pymol_control.pyc", line 358, in create_macro
>  File "specific_fns/model_free/macro_base.pyc", line 499, in create_macro
>  File "specific_fns/model_free/macro_base.pyc", line 179, in classic_style
>
>
> Storing the relax state in the file 'relax_state_20121120_113729.bz2'.
>
>
> RelaxFault: RelaxError: Impossible to be here, please re-run relax with the
> '--debug' flag and summit a bug report at https://gna.org/projects/relax/.
>
>
> in viewer i get something like this
>
> # mol_name      res_num    res_name    spin_num    spin_name    value
> error
> Juk_relx_mol1    1          ALA        20          N
> 0.7657749408593296        0.04038631865475668
> Juk_relx_mol1    1          ALA        25          H            None
> None
> Juk_relx_mol1    2          MSE        30          N
> 0.8019303974275404        0.048612135756403115
> Juk_relx_mol1    2          MSE        38          H            None
> None
> Juk_relx_mol1    2          MSE        44          HE1          None
> None
> Juk_relx_mol1    6          TRP        90          N            None
> None
> Juk_relx_mol1    6          TRP        104        H            None
> None
> Juk_relx_mol1    6          TRP        100        NE1          None
> None
> Juk_relx_mol1    6          TRP        109        HE1          None
> None
> Juk_relx_mol1    7          ALA        114        N            None
> None
> Juk_relx_mol1    7          ALA        119        H            None
> None
> Juk_relx_mol1    8          GLU        124        N            None
> None
> Juk_relx_mol1    8          GLU        133        H            None
> None
> Juk_relx_mol1    9          ALA        139        N            None
> None
> Juk_relx_mol1    9          ALA        144        H            None
> None
>
> why i get no value for residues like 6, 7, 8 and 9?