Hi Edward,
On 05.06.2012, at 14:32, Edward d'Auvergne wrote: > I would recommend reading Sebastien Morin's paper about the > consistency testing to understand how to interpret the plots. He also > gives the relevant references for the different parts of the tests > where you will find more details. I would recommend it. Yes, of course I read the paper. But since the SH3 is such a small protein with a correlation time far less then the 5 ns mentioned in the paper, I'm not sure about the reliability of the results. From the interpretation of the correlation plots and the "J(0)-test" the data seem to be consistent. > As for the > model elimination, this is completely explained in my 2006 paper on > model-free model elimination > (http://dx.doi.org/10.1007/s10858-006-9007-z). Thank you for the hint. I should have just printed out and read each and every paper of yours. > Now that I looked more carefully at > the results file, I can see the exact problem. I would recommend > multiplying your proton frequencies by 1e6, as they should be in Hz ;) Great news! :D Thank you so much for the hint. I'll start relax once more with correct frequency values. Something that's bugging me anyway, and I should probably file a bug report for: There is no convenient or obvious way how to edit the relaxation data loaded into the MF auto-analysis. Also, deleting NOE data sets is failing here: relax> relax_data.delete(ri_id='noe.600') Traceback (most recent call last): File "/usr/local/relax/gui/interpreter.py", line 311, in run apply(fn, args, kwds) File "/usr/local/relax/prompt/relax_data.py", line 128, in delete relax_data.delete(ri_id=ri_id) File "/usr/local/relax/generic_fns/relax_data.py", line 484, in delete del spin.ri_data[ri_id] KeyError: 'noe.600' I guess this is some kind of bug. The error message is not telling so much. You can try for yourself by opening the "mf_state.bz2" file in the dropbox folder. Cheers Martin > I think I'll add some checks to relax for the input frequency. > > Regards, > > Edward > > > On 5 June 2012 13:35, Martin Ballaschk <[email protected]> wrote: >> 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 <[email protected]> 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 >> -- Martin Ballaschk AG Schmieder Leibniz-Institut für Molekulare Pharmakologie Robert-Rössle-Str. 10 13125 Berlin [email protected] Tel.: +49-30-94793-234/315 Büro: A 1.26 Labor: C 1.10 _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
