Hi,
I'm now back from holidays. Please see below:
On 28 October 2010 23:51, Michael Bieri <michael.bieri@xxxxxxxxxxxxx> wrote:
Hi Edward
I was in contact with Bruker about the conversion of the errors of T1/T2
to R1/R2. I was not aware of the 'Propagation of Uncertainty'.
He was recalculating his fits of T1/T2 for R1/R2 and compared the
errors. They were exact for 5 decimal places.
This should be accurate enough. A percentage error would be nicer to
have though. Though I don't understand why they want or need T1/T2
times and not relaxation rates, as all the fundamental NMR theory uses
rates. It would be horrible if half the protein NMR people started
publishing graphs in papers of Tx values rather than Rx, while the
rest continue with Rx values!!! This would be an absolute nightmare.
So we could simply calculate the error of R1/R2 as follows:
Rx = 1/Tx
errRx = R * errTx/T
Did Peter give this equation? This seems a little strange as R/T =
R^2, so then errRx = R^2*errTx or errRx = errTx/T^2. Would you know
if there is an error in this equation? Is there a reference for this
equation?
This should be simple to implement!
If the equations are correct, we should be able to read the rates and
errors in directly with the relax_data.read() user function, and then
perform model-free analysis as normal. For the next version of the
GUI, maybe we can implement the relax_data.read() user function as
wizard type GUI element where:
1) ri_label, frq_label, and frq are first given.
2) The file is then selected. This would perform the automatic file
type detection.
3) The *_col and sep args can then be supplied for the generically
columnar formatted input files (a bit like the Excel CSV file import
dialog). This would be skipped for PDC or other specially formatted
files.
For non-GUI related operation, Bruker have the option of controlling
relax automatically. Though I don't know if they would be interested
in this as it would require installing Python, all the necessary
python modules, bmrblib (https://gna.org/projects/bmrblib/), minfx
(http://gna.org/projects/minfx/), and relax. Although this could be
bundled all together and be part of the Protein Dynamic Center without
the users having to do any work. If we implement the PDC file
handling, they could provide the model-free related GUI elements
needed (i.e. something similar to your GUI) and use the automatic
protocol (http://www.nmr-relax.com/refs.html under "The new model-free
analysis protocol"). I don't know how Bruker would like the idea of
the 1-2 weeks computation time required for a complete high precision
model-free analysis. The GUI would also remove some of the
flexibility currently in relax for having multiple diffusion tensors,
or parts of the molecule having local_tm parameters while other parts
have a common diffusion tensor. But they have the option of further
integration of relax and PDC via this path, and could in the end have
the full model-free results within the PDC and even have the ability
to submit results to the BMRB. From our point of view though, this is
not ideal as users might forget that relax is doing all the work
behind the scenes and we may not get citations. And it would
duplicate and make redundant your GUI currently going into relax.
Regards,
Edward
P.S. Maybe you could forward this message to Peter and the other
Bruker people behind the PDC? It would be good to get them involved
in these discussions. Cheers.
Cheers
Michael
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.
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.
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