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
ballaschk@xxxxxxxxxxxxx
Tel.: +49-30-94793-234/315
Büro: A 1.26
Labor: C 1.10
SH3, model-free failed (relax GUI)