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
