Re: Stage 2 of palmer.py -- January 08, 2013 - 08:32

Hello Edward,

Thanks a lot for your reply and sorry for the delayed response.

1. You guessed absolutely correctly that I don't have data for the second magnetic field yet. Having said that, I do have access to the 500 MHz magnet except that my data with the 600 Mhz machine (with cryoprobe) was not too great. I am worried about the quality of data from the 500 MHz non cryoprobe spec.

2. I am indeed running the latest version of relax (2.1.2). The stage 2 of palmer.py keeps failing as I reported in my original email. I believe it might have something to do with the naming of the spin ids. it is just a hunch though. I am using only residue numbers as yet instead of actual residue names.

3. I got the farthest by running mf_multimodel.py followed by modsel.py. I am confused though about the diffusion tensor optimization part. If I run the script, how will the script know about the model selection and and elimination process that has already taken place. Is there a way I can tell that to the diff_min.py to not worry about selection and elimination but use the results from modsel.py ? Can I load the results ?

4. I am certainly hoping to find a way to get an automated script or set of scripts that perfectly handle the data at single magnetic field although quite rightly data from two magnetic fields ought to be used whenever possible. If I can do that, I will love to make it available as a part of the relax sample scripts.

Forgive me if some of my queries sound too beginner level but any help at this stage will be highly appreciated. 

Thanks,

Shantanu S. Bhattacharyya

On 7 January 2013 05:29, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:

Hi Shantanu,

I was wondering which version of relax you are using?  The bug looks
quite familiar and if you are not using relax 2.1.2, I would recommend
updating to the newer version and testing if the bug is still present
(http://www.nmr-relax.com/download.html).  I have checked the
diff_min.py sample script and noticed that it was designed back in
2003 in the very early days of relax development.  Today the script is
useless!  I have updated it in the relax subversion repository so you
can use this version instead
(http://svn.gna.org/viewcvs/relax/trunk/sample_scripts/model_free/diff_min.py?view=markup).

I am guessing that you are reverting to the 2 decade old analysis
methodology because you do not have data at two field strengths yet.
Note that you will have to do a lot of work writing and debugging
scripts to implement the old analysis types (even when using Art
Palmer's Modelfree4), and I will not have much time to help you.  If
you do implement them, would you could consider contributing them to
relax to be added to the sample script directory?  You should be able
to use Python's object oriented design to create one script
implementing the entirety of the algorithm of Mandel et al., 1995 (the
whole iterative process of the figure in
http://www.nmr-relax.com/manual/methodology_Mandel_et_al_1995.html).
I would recommend using the old data published by the Palmer group
using this methodology to test that your super-script produces the
expected results - such a test is essential to be sure that the full
protocol is producing the correct results.

If you are designing an entirely new model-free protocol to handle
single-field strength data (or even if you are implementing the full
Mandel et al., 1995 protocol), then it might be worth considering
becoming a relax developer and implementing the protocol in the
auto_analysis directory of relax.  The front end script can be very
similar to the dauvergne_protocol.py script, but the back end quite
different.  In such a case, you should create a set of test models of
synthetic data and implement a relax system test before starting with
the algorithm.  Once you algorithm is complete and fully debugged,
then the system test will pass.  This should all be developed in a
special relax branch.

Cheers,

Edward


P. S.  Do you intend on collecting data at a second field strength?





On 6 January 2013 19:54, Shantanu S. Bhattacharyya Mr
<ssbhatta@xxxxxxxxxxxxxx> wrote:
> Shantanu