Hi,
On 19 October 2010 23:40, Michael Bieri<michael.bieri@xxxxxxxxxxxxx> wrote:
Hi Edward
...
Am 19.10.2010 22:46, schrieb Edward d'Auvergne:
Hi Micheal,
I've had a look at the PDC files, and there are 2 issues we need to
deal with (that I can see for now). Firstly Bruker is reporting T1s
and T2s. That in itself is not a problem as it is easy to convert to
R1 and R2 - an essential step in using the data. The problem is with
the errors, you can't simply invert them! There is no way to convert
these T1 and T2 errors into R1 and R2 errors that I know of. So I
would suggest that we need to recalculate the R1 and R2 and obtain the
errors by Monte Carlo simulations. This can be done easily as the PDC
files contain all that is needed. Maybe we need to talk to Bruker
about this.
I think the problem with the errors of T2 / R2 can be converted by
adding the error and subtracting the error to the mean value, invert
them and get the new error.
This works for linear relationships, but this is hyperbolic as you are
performing an inversion. Therefore there is no direct mapping of the
normal distribution equation of T2 errors to the normal distribution
of R2 errors. I think we really need to talk to Bruker so they might
reconsider this choice! None of the model-free programs - relax,
modelfree, dasha, or tensor - can use T1 and T2 values. That is
because Abragam's original equations are in terms of rates, and the
natural process is a rate. We should point the Bruker developers
behind the Bruker Dynamics Centre to these emails. This is very
important, T1 and T2 errors are totally useless to the field. They
can't even be used for spectral density mapping, SRLS, or anything!
Bruker is making a very silly mistake here!!! Do you know who the
person in charge is? Is Wolfgang involved?
The second is, how does Bruker calculate the errors? We will have to
ask them. For a data analysis, errors are just as important, or maybe
even more important than the data itself. So they need to be properly
estimated using the gold standard of Monte Carlo simulations - without
question. For the R1s and R2s, the errors is obviously come from the
duplicated spectra. But for the NOEs, it is totally unclear where the
errors come from. For the NOE, the error can be directly calculated -
no MC sims required - but where do they get their estimate of the
base-plane noise? We really need to be certain where the NOE errors
in the PDC file come from.
According to Bruker, the error originates from duplications and noise of
the spectra. In addition, they included a function, where the user can
specify the error themselves....
This sounds ok. Will have to give the software a try to see if they
can improve on their error estimates. These errors are incredibly
important, so this really needs to be done right.
Probably it makes sense to import the Bruker files and generate relax
parameter files. What do you think about this? I suggest to save those
files and the user will further analyse these data. In case of the GUI,
the files are placed in the model-free section.
If Bruker fixes the time vs. rate error problem, then all we need to
do is to modify relax_data.read() and read the R1, R2, and NOE
directly from the PDC files. Otherwise we are in trouble and will
have to perform the R1 and R2 exponential fitting again. We could
bootstrap the T1 errors to R2 errors, but it would be easier to
re-perform the curve-fitting. As for the GUI, this could be just part
of loading the relaxation data files. If it is implemented in the
back end through relax_data.read(), as soon as the system test passes,
the GUI will also be fully able to use the PDC files.
If we can get rates in the PDC files, then reading peak intensities is
not needed. Users could do this anyway by removing all extra lines
from the PDC file and using sprectrum.read_intensities() as it
currently is. This would be useful to validate the performance of the
Bruker software.
Regards,
Edward
Cheers
Michael
Regards,
Edward
On 7 October 2010 07:35, Michael Bieri<NO-REPLY.INVALID-ADDRESS@xxxxxxx>
wrote:
URL:
<http://gna.org/task/?7180>
Summary: Import of BRUKER Protein Dynamic Center Protject
Project: relax
Submitted by: michaelbieri
Submitted on: Donnerstag 07.10.2010 um 16:35
Should Start On: Donnerstag 07.10.2010 um 00:00
Should be Finished on: Donnerstag 07.10.2010 um 00:00
Category: relax's source code
Priority: 1 - Later
Status: In Progress
Privacy: Public
Percent Complete: 0%
Assigned to: michaelbieri
Open/Closed: Open
Discussion Lock: Any
Effort: 0.00
_______________________________________________________
Details:
BRUKER is developing a Protein Dynamic Center (PDC). This program will have
an interface with relax, so data collected with TopSpin and NOE, T1 and T2
values calculated by PDC can be imported into relax and analyzed.
An import function has to be created for the prompt and GUI interface. In
addition, the PDC manual has to be corrected (see attachment chapter 8).
The manual, T1, T2 and NOE sample data are attached.
_______________________________________________________
File Attachments:
-------------------------------------------------------
Date: Donnerstag 07.10.2010 um 16:35 Name: testT1.txt Size: 23kB By:
michaelbieri
<http://gna.org/task/download.php?file_id=10640>
-------------------------------------------------------
Date: Donnerstag 07.10.2010 um 16:35 Name: testT2.txt Size: 23kB By:
michaelbieri
<http://gna.org/task/download.php?file_id=10641>
-------------------------------------------------------
Date: Donnerstag 07.10.2010 um 16:35 Name: testNOE.txt Size: 8kB By:
michaelbieri
<http://gna.org/task/download.php?file_id=10642>
_______________________________________________________
Reply to this item at:
<http://gna.org/task/?7180>
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Re: [task #7180] Import of BRUKER Protein Dynamic Center Protject