Hi Sam,
For relax, you simply input the peak lists. Using the
spectrum.read_intensities user function
(http://www.nmr-relax.com/manual/spectrum_read_intensities.html), you
can load in peak intensities - either height or volumes - from many
different spectral software programs. This includes Sparky, XEasy,
NMRView, NMRPipe seriesTab, and a generic column formatted text file
(the Bruker Dynamics Centre format is also supported). relax is
designed so that users never have to perform format conversions to
input or output data. If a format conversion is necessary, I would
insist on a new support request being created and an example data file
attached to it. Then the support for the format can be quickly added
to relax (by first implementing system tests).
The problem with conversions is the chance of data loss or a mistake
being made. But the conversions in relax are all extensively and
repeatedly checked via the comprehensive test suite, so that you can
be sure that no mistakes are made:
$ relax --test-suite --time
But just with all other analysis software, you should always be on the
look out for problems, as all software contains bugs. So software can
be treated as a black box, but always be vigilant and sceptical of all
results. Oh, thanks to advances implemented by Troels, you can now
simultaneously load all peak lists with one spectrum.read_intensities
user function call. This is especially useful if you are using the
GUI.
Regards,
Edward
On 26 February 2015 at 23:58, Sze Chan <samuelsw.chan@xxxxxxxxxxxxxxxx> wrote:
Hello,
Currently, I'm collecting more NMR data so I haven't had much time to
analyze the data.
Usually, I extract the raw peak heights at each CPMG Hz for each residue
(assignments saved in my ccpnmr project) so I don't have a peaklist for my
CPMG data. The same is done for my fast time scale dynamics (T1/T2/NOE).
So I was wondering if there was a way to set up the files in a tabular
format by hand? (an example of such a table would be very helpful). I was
hoping if there was some way to fit my dispersion data just on a per
residue basis, similar to how another NMR program, NESSY, takes in data.
Thank you for your time and patience, as an undergrad a lot of the
information and navigation is quite overwhelming so its great to have some
help!
Regards,
Sam
________________________________________
From: edward.dauvergne@xxxxxxxxx <edward.dauvergne@xxxxxxxxx> on behalf of
Edward d'Auvergne <edward@xxxxxxxxxxxxx>
Sent: Thursday, February 26, 2015 12:32 PM
To: Troels Emtekær Linnet
Cc: Sze Chan; relax-users@xxxxxxx
Subject: Re: Help with setting up relax files
Hi Sam,
I was wondering if you still had problems with the loading of peak
heights for relaxation dispersion in relax? It should be pretty
flexible and handle most formats you throw at relax. If you have a
peak list format that is not supported, it would be appreciated if you
could create a support request (https://gna.org/support/?group=relax,
https://gna.org/support/?func=additem&group=relax). If you attach a
truncated peak list to the request, slightly randomised if you would
like to keep the data private, then that file could be used to quickly
implement support for the format.
Cheers,
Edward
On 15 February 2015 at 10:58, Troels Emtekær Linnet
<tlinnet@xxxxxxxxxxxxx> wrote:
Hi Sam.
Try to have a look on the wiki:
http://wiki.nmr-relax.com/Category:Tutorials
http://wiki.nmr-relax.com/Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved
Maybe you can figure out something.
If you need more help.
Make a suppert request
https://gna.org/support/?group=relax
Upload an example peak list for each CPMG frq.
Make a file, listing filename for peaklist and corresponding CPMG frq.
You need to determine the error of your experiments.
If you have peak heights which are replicate/triplicate, then this is fine.
Or else you need to measure RMSD of the noise in the spectrum.
What is also:
Relaxation dispersion CPMG constant time delay T (in s).
The NMR field strength of the spectrum. (750 MHz ?)
Best
Troels
2015-02-15 1:09 GMT+01:00 Sze Chan <samuelsw.chan@xxxxxxxxxxxxxxxx>:
Hello all,
I am an undergrad that is new to the field of NMR and I was hoping to get
some basic help in setting up my data for analysis.
For my CPMG relaxation dispersion experiments, I usually process my data
through NMR pipe and then extract the peak heights through ccpnmr with
each
plane as the CPMG frequency. In the end for each residue, I get the peak
height at various CPMG frequencies.
However, I'm not sure how to format my table or know what software I can
use to format my data so that I can input it into relax. If anyone has any
help, I'd greatly appreciate it since I'm very new to the field and all
the
analysis that comes with it.
Regards,
Sam
Department of Biochemistry - University of Toronto
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-users mailing list
relax-users@xxxxxxx
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-users
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-users mailing list
relax-users@xxxxxxx
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-users
Re: Help with setting up relax files