Hi Edward,
I would be very glad to help out with that.
My input data format is sparky peak lists (I export them from ccpnmr, but
that doesn't make a difference))
The other part of the input data is a sequence file. I have problems loading
a cyana generated structure. Not sure how it would behave with a structure
outputted from ccpnmr or other programs. The structure is not in the pdb yet.
I have two spin systems in there, but for testing, we can throw out the NHe
from my tryptophan indole rings.
For my test set, I can even calculate rates for inversion recovery and
saturation recovery in ccpnmr. The reason that I changed to relax is, that
the ccpnmr fitting routine is not robust enough for other sets.
I'm very happy to send you real peak lists, or do they have to be synthetic
for some reason? I could make real peak lists without tryptophan NHes if that
helps. For synthetic peak lists, I have no experience in making those. But I
think I could figure that out.
I am attaching one set of relax that I did on this system with inversion
recovery to the task and if this is what you are looking for, then I can also
send you R1 values for inversion and saturation recovery fitting of this set
in ccpnmr.
I did have a problem with the experiment that I ran on relax though. It does
converge and produces beautiful values, but the Rx values are negative. Which
doesn't make any sense to me. The pattern is exactly as it should be, but the
values are simply wrong. Do you have an idea what could be going on there?
Best regards,
Andras
________________________________________
From: edward.dauvergne@xxxxxxxxx [edward.dauvergne@xxxxxxxxx] On Behalf Of
Edward d'Auvergne [edward@xxxxxxxxxxxxx]
Sent: Wednesday, November 26, 2014 1:04 PM
To: Andras Boeszoermenyi
Cc: Boeszoermenyi, Andras; relax-devel@xxxxxxx
Subject: Re: [sr #3195] Fitting of saturation recovery experiment
Hi Andras,
I was wondering if you were interested in helping out with the
inversion-recovery task at https://gna.org/task/index.php?7415 ? What
is your input data format, i.e. which peak list format are you using?
Would it be possible to create synthetic peak lists containing with a
single spin system whereby you have calculated what the peak
intensities are based on your equation and some I0 and Rx parameter
values? If this could be done, it could be added to the relax test
suite directories and form the basis of an implementation. It could
easily then be used to create a system test which checks that the
fitting occurs as expected. Then implementing this should be easy.
Cheers,
Edward
On 26 November 2014 at 16:59, Andras Boeszoermenyi
<NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
URL:
<http://gna.org/support/?3195>
Summary: Fitting of saturation recovery experiment
Project: relax
Submitted by: andras
Submitted on: Wed 26 Nov 2014 03:59:50 PM UTC
Category: Feature request
Priority: 5 - Normal
Severity: 3 - Normal
Status: None
Assigned to: None
Originator Email:
Open/Closed: Open
Discussion Lock: Any
Operating System: Mac OS
_______________________________________________________
Details:
Hi,
would it be possible to add an option to fit saturation recovery experiments
to the existing 'exp' and 'inv' options in relax_fit?
The formula should look like this:
I(t) = I0*(1 - exp(−R1*t))
Best regards,
Andras Boeszoermenyi
_______________________________________________________
Reply to this item at:
<http://gna.org/support/?3195>
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RE: [sr #3195] Fitting of saturation recovery experiment