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 <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
--
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
Re: SH3, model-free failed (relax GUI)