Re: Using | nmrPipe -fn REV \ for processing CPMG dispersiong experiments
Hi Troels, The -fn REV part is needed for certain acquisition modes. I copied the script contents for one such spectrum. This option can be removed for most 2D experiments though. Looking closely at the script I have noticed that there are a few things wrong with it or at least not ideal for a relaxation analysis. For example the extract function should be performed at the very end. In this case it does not matter as a polynomial baseline correction is not performed in the indirect dimension but, if it were to be added, performing the data trimming after a polynomial correction results in a better baseline. I must have copied the wrong script. I'll look into this and change the script contents to one of the scripts I use for processing spectra for standard R1, R2 or NOE spectra from back in my PhD days. Cheers, Edward On 25 August 2013 18:45, Troels Emtekær Linnet tlin...@gmail.com wrote: Hi. I was looking the in the manual, at page: 52 5.2.2 Spectral processing There is an example of processing script for NMRPipe. It mentions the line: | nmrPipe -fn REV \ which is for reversing the spectrum, since the CPMG element in a pulse sequence will make the magnetization end up negative. According to the manual: http://spin.niddk.nih.gov/NMRPipe/ref/nmrpipe/rev.html The recommendation is to do a negative Fourier Transform | nmrPipe -fn FT -neg \ Is there a special reason for | nmrPipe -fn REV \ Best Troels Emtekær Linnet ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org 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@gna.org 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
Running scripts inside relax
What is the correct way to run script commands ?
If I start relax, and I want to run a script with basic setup and then
spin commands.
Would the correct way be:
execfile('./relax_ini.py')
execfile('./spectrometer_data_processed/relax_spins.py')
Or is there a better way for relax?
Troels Emtekær Linnet
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Re: Running scripts inside relax
If I run:
relax_disp relax_1_ini.py
relax runs through the script and exit.
Is there a way to stop after reading?
Best
Troels Emtekær Linnet
2013/8/26 Edward d'Auvergne edw...@nmr-relax.com:
Hi Troels,
You should find the answer you are after in the following link:
http://www.nmr-relax.com/manual/Scripting.html
There is also the 'script' user function which you might find useful,
but this is not how relax scripts are made to be run. This is mainly
so you can run a script in the GUI, especially the Mac OS X
application where command line arguments are not possible.
Regards,
Edward
On 26 August 2013 15:56, Troels Emtekær Linnet tlin...@gmail.com wrote:
What is the correct way to run script commands ?
If I start relax, and I want to run a script with basic setup and then
spin commands.
Would the correct way be:
execfile('./relax_ini.py')
execfile('./spectrometer_data_processed/relax_spins.py')
Or is there a better way for relax?
Troels Emtekær Linnet
___
relax (http://www.nmr-relax.com)
This is the relax-users mailing list
relax-users@gna.org
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)
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relax-users@gna.org
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
