Dear Keith,
I'm sorry for the late response, I've only just come back from the ENC
conference. The software relax can operate without problem using
single field strength data and should be able to replicate all
published model-free results (after significantly decreasing its
precision and ignoring published results which are due to program
bugs). For example see the sample scripts 'mf_multimodel.py' and
'modsel.py'. In these two scripts, you will need to remove any models
with more than 3 parameters.
As for using single field strength data with the new model-free
optimisation protocol (full_analysis.py), this question has already
been asked by Clare-Louise Evans
(https://mail.gna.org/public/relax-users/2007-04/msg00006.html). My
response continues at
https://mail.gna.org/public/relax-users/2007-05/msg00003.html,
although what you are after is probably found later on in the thread
at https://mail.gna.org/public/relax-users/2007-05/msg00009.html.
Essentially, single field strength data is very problematic for the
theory of this new model-free approach (see
http://dx.doi.org/10.1039/b702202f for the problems) and I would never
recommend it. From the fitting of the local tm models, you could look
at the tm values and if they are the same (within errors) for all
residues, then you could conclude that you have isotropic tumbling.
This is highly unlikely though. As the more complex 2 time scale
model cannot be used, the all internal correlation times will be
absorbed into the tm value causing it to decrease from its true value.
Finally, the analysis of methyl 2H relaxation data can be added to
relax. The 1.3 development line is being made flexible enough to add
this type of analysis (and to look at this simultaneously with all
other relaxation data). The relevant spectral density functions will
need to be added to the program, as well as the deuterium gyromagnetic
ratio, and then the rest should be trivial. The quadrupolar
relaxation means that current relax versions cannot handle this data
yet.
Regards,
Edward
On Fri, Mar 14, 2008 at 7:58 PM, Keith L Constantine
<keith.constantine@xxxxxxx> wrote:
Dear relax users:
I have a couple of questions regarding the relax program.
First, the example scripts for model-free selection and optimization
described in the relax manual utilize 15N relaxation data recorded at two
fields. Does anyone have advice/experience in using relax to fit T1, T2 and
NOE data recorded at only one field, particularly to models that include
anisotropic global motion?
Idealy, I would like to follow a local tm approach to model-free model
selection and optimization, as recently described [d'Auvergne and Gooley
(2008) J. Biomol. NMR 40, 107-119; ibid., 121-133], rather than a "diffusion
seeded" approach. With data at one field, this analysis would be limted to
models tm0 through tm3, and tm9. Are there relax scripts available for this
type of an analysis with data at one field? Also, again using data from only
one field, could one readily discern from the results of a local tm analysis
if isotropic diffusion models are adequate? If adequate, this would allow
fitting the data to models m0 through m5, and m9.
A final question - have any facilites been added to relax (or planned) for
fitting methyl 2H relaxation data?
Thank you very much for your consideration. Any suggestions would be
greatly appreciated.
Keith Constantine
Re: relax: data at one field, 2H relaxation