Dear Edward,
I attached 3 files to the link
(https://gna.org/task/?7180)
you had sent me, it seems that everything worked.
Regarding the T1, T2 files I added the columns you suggested and also
supplied more digits. Please
have a look a it.
As you suggested most recently and as was also a result of some discussions
here, we keep the
confidence limit stuff since indeed other users not working in the area of
relaxation data modelling
have a different view on this. As I mentioned earlier the PDC will later
become a part of a more
general Dynamics Center (DC) that also offers T1, T2 etc but also for 1D
data and small molecules
and furthermore topics like kinetics, diffusion, Redor etc. The wish is
here a uniform handling of
all these methods. In the area of Export we have the option to become
specific, adding Rx to an output
that so far contained Tx for example is ok. Providing more details in the
documentation is also
no problem preferably by just giving references to books, papers or links.
The Monte Carlo issue is still in discussion I do not expect a decision
before the end of next week.
If the basic stuff is sorted out we should at some time also compare our
model-free analysis results.
Of course there I expect differences since your implementations are much
more advanced. Nevertheless
the differences should be explainable and not too large.
Best regards,
Peter
On 2/24/2011 10:32 AM, Edward d'Auvergne wrote:
Dear Peter,
Please see below:
On 23 February 2011 19:33, Neidig, Klaus-Peter
<Klaus-Peter.Neidig@xxxxxxxxxxxxxxxxx> wrote:
Dear Edward,
in short:
the first 2 fit options (by fit, by weighted fit) both use the covariance
technique. The difference is that
the first option applies an additional internal scaling by: final
chi/number of degrees of freedom
This means that when doing modelling of (NOE, T1, T2) with (M1-M5, TM1-TM5)
it cannot be used if these
triples of number are only available at one field and the model contains 3
parameters.
Could such details be given to the user? Many will know about the
covariance matrix error estimation method (those that don't really
should).
But in
in that area the PDC user does not have a selection of fit methods anyway,
we internally use a combination
of simplex and marquardt. But this is another area and should be done by
relax anyway.
For model-free, simplex is better than Marquardt. The problem with
Levenberg-Marquardt is in the fine print. This method works well for
most cases. But there is one situation where it totally fails, the
fine print says that is when the internally used matrix is singular.
At that point it cannot be inverted and the algorithm is forced to
terminate. Unfortunately this happens a lot in model-free analysis,
and it happens when a parameter is undefined. For example when S2 is
perfectly 1 or 0. Then te can be anything - it falls out of the
equations. This is the reason why there is much published data with
order parameters of exactly 1. It is not because the residue is
rigid, but because the optimisation came to a screaming halt.
I pick up your statements about the confidence stuff. Indeed you are right
that everything would be
much simpler if the PDC did just output Rx instead of Tx and corresponding
error. Whether keep the
confidence stuff at all is then a question, in the mean I think I follow
your opinion and would rather
give it up. But this I have to discuss internally here. It might be that
I'm not allowed to just give it up
then I would have to increase the output with more columns or a further
section which you could read
instead of the current section.
I think the confidence limit values have worth, some users will
appreciated it. I would simply consider adding the additional
information so that the user need not perform the conversion
themselves. It would simply be an augmentation of the PDC output.
There will be absolutely no new information in it as it is already in
the file.
I also have to say that my developments on the PDC must end by April (ENC)
and this includes
updating the manul, release procedure and some internal developments. So
there is not too much
time left. The PDC release number will then go up to 1.2. After April I can
still maintenance work
but no major changes, at least until someone decides something else.
The simple solution would be some quick code adding a few columns.
Additional columns should be no problem for parsers, as long as the
original columns remain in place. The key for downstream analysis
would be the R(1/2) value and standard deviation columns that the user
can directly feed into the other software.
Cheers,
Edward
.
--
Dr. Klaus-Peter Neidig
Software Development / Head of Analysis Group
Bruker BioSpin GmbH
Silberstreifen
76287 Rheinstetten, Germany
Phone: +49 721 5161-6447
Fax: +49 721 5161-6480
Peter.Neidig@xxxxxxxxxxxxxxxxx
www.bruker.com
________________________________
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Re: Addition of PDC support to relax 1.3.10 and an inconsistency in the error calculation.