Hi Martin, Do you have information about which version of relax you are using? The only place a RelaxFault can occur in relax is with the creation of the Molmol and PyMOL macros, specifically when creating the representation for the amplitude of motion for fast motions. I'm surprised that no one, apart from yourself, has ever seen this problem! This code path (see specific_fns/model_free/macro_base.py at line ~242) has probably been executed thousands of times without failure. Anyway, it would be appreciated if you could submit a bug report for this (https://gna.org/bugs/?func=additem&group=relax).
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. This is essentially a massive relax script which implements the special model-free protocol I came with in my 2007 and 2008 papers (http://dx.doi.org/10.1039/b702202f, http://dx.doi.org/10.1007/s10858-007-9213-3). It originally was a relax script, but was converted into an auto-analysis as my protocol should not be changed by a user and then the results published as being the result of my protocol. The exact failure point would be the lines: self.interpreter.pymol.macro_write(data_type='amp_fast', dir=dir, force=True) or: self.interpreter.molmol.macro_write(data_type='amp_fast', dir=dir, force=True) If you have a look at what is after this, you'll see which parts of this analysis have not executed. This includes the diffusion tensor PDB representation in the write_results() method and then if you follow the code you'll see that nothing else happens before falling off the end of the analysis. This means that you have the results for the completed analysis sitting on your computer! If you would like the PDB representation of the diffusion tensor for a figure, or just to play with, you can execute that user function directly from the menus. You might be able work out the name of this user function from auto_analyses/dauvergne_protocol.py file. Anyway, the RelaxFault is nothing to worry about, but a bug report would be very useful so I can then make sure no one ever sees this problem again. Cheers, Edward 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
