Hi Edward,
thank you for the reply. I will file a bug report soon.
I'll answer below:
On 05.06.2012, at 11:41, Edward d'Auvergne wrote:
Do you have information about which version of relax you are using?
It's 1.3.16 – newly downloaded from the main page.
[...]
Note that this RelaxFault is not much of an issue. You can see the
exact failure point by looking into the
auto_analyses/dauvergne_protocol.py file.
The "relax controller" also showed me the point of failure. I copied the
last 100.000 lines of messages into this file:
https://www.dropbox.com/sh/ijah1ll37o9xmsy/le6rGRguU5/mf_firstrun_log.txt
That's the last lines:
relax> pymol.macro_write(data_type='amp_fast', style='classic',
colour_start=None, colour_end=None, colour_list=None, file=None,
dir='/faust/TENSOR/sh3_EdA/final/pymol', force=True)
Exception raised in thread.
Traceback (most recent call last):
File "/usr/local/relax/gui/analyses/execute.py", line 88, in run
self.run_analysis()
File "/usr/local/relax/gui/analyses/auto_model_free.py", line 765, in
run_analysis
dauvergne_protocol.dAuvergne_protocol(pipe_name=self.data.pipe_name,
results_dir=self.data.save_dir, diff_model=self.data.global_models,
mf_models=self.data.mf_models, local_tm_models=self.data.local_tm_models,
grid_inc=self.data.inc,
diff_tensor_grid_inc=self.data.diff_tensor_grid_inc,
mc_sim_num=self.data.mc_sim_num, max_iter=self.data.max_iter,
conv_loop=self.data.conv_loop)
File "/usr/local/relax/auto_analyses/dauvergne_protocol.py", line 223, in
__init__
self.execute()
File "/usr/local/relax/auto_analyses/dauvergne_protocol.py", line 710, in
execute
self.write_results()
File "/usr/local/relax/auto_analyses/dauvergne_protocol.py", line 858, in
write_results
self.interpreter.pymol.macro_write(data_type='amp_fast', dir=dir,
force=True)
File "/usr/local/relax/prompt/pymol_control.py", line 266, in macro_write
pymol_control.macro_write(data_type=data_type, style=style,
colour_start=colour_start, colour_end=colour_end, colour_list=colour_list,
file=file, dir=dir, force=force)
File "/usr/local/relax/generic_fns/pymol_control.py", line 458, in
macro_write
commands = create_macro(data_type=data_type, style=style,
colour_start=colour_start, colour_end=colour_end, colour_list=colour_list)
File "/usr/local/relax/generic_fns/pymol_control.py", line 352, in
create_macro
commands = macro(data_type, style, colour_start, colour_end,
colour_list)
File "/usr/local/relax/specific_fns/model_free/macro_base.py", line 551,
in create_macro
self.classic_style(data_type, colour_start, colour_end, colour_list,
spin_id)
File "/usr/local/relax/specific_fns/model_free/macro_base.py", line 242,
in classic_style
raise RelaxFault
Storing the relax state in the file 'relax_state_20120602_135951.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/.
[...] This means that you have the results for
the completed analysis sitting on your computer!
Yes, you're right. I can see the the final result files in the respective
directories ("./final"). Unfortunately, something is still wrong, and I
suspect it's my data.
relax obviously went for the ellipsoid model, but during the runs, most of
the spin systems got eliminated. That means, for most of the parameters I
don't have any values (see
https://www.dropbox.com/sh/ijah1ll37o9xmsy/UgQuNzBSwl/final ).
I don't really understand what exactly is tested against what when relax
tells me e.g.:
Data pipe 'm5': The ts value of 8.5026e-10 is greater than 6.377e-10,
eliminating spin system '#1aey-NMR_mol1:30&:ILE@410&@N'.
I'm sure that's described somewhere in the manual or the thesis, but I
couldn't find it.
***
So what can I do about this. The obviuos thing is to validate my data
(again) and finally do the temperature calibration at the 750 machine.
Isn't it odd that the R1, R2 methanol calibrations we did showed no
differences in ppm, regardless of the duration of the R2 measurements?
Is maybe the peak maximum searching in CCPN introducing systematic error
by picking positive noise on top of the peaks?
The NOE error calculation in CCPN is somewhat opaque and is based on
getting the spectrum noise. Could a under / overestimation of the NOE
errors lead to such a massive elimination of spin models?
I don't really know where to start looking for errors.
Cheers
Martin
On 5 June 2012 11:00, Martin Ballaschk <ballaschk@xxxxxxxxxxxxx> wrote:
Hello Edward, hello relax-users,
for five days relax calculated mf models for SH3 and then something went
wrong. It stopped with
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/
A look at the relax messages tells me that almost all spin got
eleminated. The "debugging run" is still running.
I will try to give a detailed description of what we've done to collect
the input data and maybe you can give me a hint what may be a problem;
if it's something with the sample, the measuring setup or the processing
workflow.
====
1.) Protein / sample
* SH3 from chicken alpha-spectrin, 62 residues (1AEY.pdb)
* 2H/13C/15N and metyhl-group labeled
* concentration: ~ .5 mM
* our "all-purpose model protein" for testing new stuff
2.) Data collection
* two fields: 600 MHz & 750 MHz (Bruker spectrometers with cryo probes)
* 600 machine:
http://www.fmp-berlin.de/schmieder/nmr_facility/av600sel.htm
* 750 machine:
http://www.fmp-berlin.de/schmieder/nmr_facility/av750.htm
* temperature: 300.1 K
o comparison between between T1 and T2 temperatures /w methanol
gave *no* differences in temperature at the 600 MHz machine (!)
o 750 MHz spectrometer needs still to be tested though
o temperature differences in HetNOE also need to be tested
* single-scan interleaved recording was performed for T1, T2 and HetNOE
measurements
* T1: delays between 12 and 1500 ms, 8 data points, 4 of them replicated
* T2: delays between 17 and 217 ms, 8 data points, 4 of them replicated
3.) Data processing
* processing of all spectra: Bruker TOPSPIN 3.1
* peak picking with CCPN 2.2.1:
o T1, T2 (pseudo-3D) picked with „Follow intensity changes“ function
o HetNOE (2D planes) picked with „Heteronuclear NOE“ function
* T1, T2 analysed with relax' fitting function
* consisteny testing performed with Sebastien Morins script
(although I'm not sure about the interpretation of the results,
also: the molecule is very small and tau_m < 5ns)
4.) Model-free analysis within relax GUI
* imported all relaxation data as described
* CSA, bond length values: default values taken
* unit vectors from 1AEY.pdb (averaged in relax)
All the relax data of this run including the results files and
consistency testing plots have been made publicly available:
https://www.dropbox.com/sh/ijah1ll37o9xmsy/OybJrGT13e
I would be very grateful if you could have a look at the data and tell
me: is it me or is it a bug?
Cheers
Martin
Re: SH3, model-free failed (relax GUI)