Brief description of philosophy, commands, and functions of NMRPipe: Difference between revisions

From NESG Wiki
Jump to navigation Jump to search
No edit summary
No edit summary
Line 1: Line 1:
&nbsp;<span class="Apple-style-span" style="font-family: Cambria; font-size: 14px; line-height: normal; font-weight: bold; ">NMR Data Processing &gt;&nbsp; Overview</span>
&nbsp;NMR Data Processing &gt;&nbsp; Overview <br>  
<br>


===== '''Brief Description''' =====
===== '''Brief Description''' =====


There are many softwares available today for processing NMR data and this task usually involves processing the time domain signal to frequency domain spectrum via Fourier transform along with different mathematical functions (see section 1.4 of this article for brief description of commonly used functions) to adjust the spectrum.&nbsp; The NMRPipe data processing program consists of a number of functions that are linked together via UNIX pipes and it is widely used in the scientific community.&nbsp; A second program called ‘nmrDraw’ (part of the NMRPipe package) is used to visualize and inspect the processed NMR data.&nbsp; The nmrDraw program provides basic functions such as drawing contours, vertical or horizontal traces, peak picking, integration, and etc.&nbsp; The NMR data processing methods described in this TWiki are the routine procedures commonly used in the NESG community.&nbsp; For more detailed information on the functionality of NMRPipe, please visit the manual pages of NMRPipe. &nbsp; The general workflow of NMRPipe is as follows:
There are many softwares available today for processing NMR data and this task usually involves processing the time domain signal to frequency domain spectrum via Fourier transform along with different mathematical functions (see section 1.4 of this article for brief description of commonly used functions) to adjust the spectrum.&nbsp; The NMRPipe data processing program consists of a number of functions that are linked together via UNIX pipes and it is widely used in the scientific community.&nbsp; A second program called ‘nmrDraw’ (part of the NMRPipe package) is used to visualize and inspect the processed NMR data.&nbsp; The nmrDraw program provides basic functions such as drawing contours, vertical or horizontal traces, peak picking, integration, and etc.&nbsp; The NMR data processing methods described in this TWiki are the routine procedures commonly used in the NESG community.&nbsp; For more detailed information on the functionality of NMRPipe, please visit the manual pages of NMRPipe. &nbsp; The general workflow of NMRPipe is as follows:  


<br>
<br>  


Step 1: Converting the data from spectrometer format to NMRPipe format
Step 1: Converting the data from spectrometer format to NMRPipe format  


Step 2: Time domain data inspection using nmrDraw
Step 2: Time domain data inspection using nmrDraw  


Step 3: Trial processing for initial phasing and applying mathematical functions&nbsp;
Step 3: Trial processing for initial phasing and applying mathematical functions&nbsp;  


Step 4: Inspection of the trial processed spectrum via nmrDraw
Step 4: Inspection of the trial processed spectrum via nmrDraw  


Step 5: Final processing
Step 5: Final processing  


Step 6: Spectra format conversion to Sparky, CARA, XEASY or NMRViewJ
Step 6: Spectra format conversion to Sparky, CARA, XEASY or NMRViewJ  


&nbsp;&nbsp;
&nbsp;&nbsp;  


===== '''Software Information'''<br>  =====
===== '''Software Information'''<br>  =====
Line 32: Line 31:
Brief descriptions of specific functions are accessible via nmrPipe –  
Brief descriptions of specific functions are accessible via nmrPipe –  


‘nmrPipe –help’ will list most functions
‘nmrPipe –help’ will list most functions  


‘nmrPipe –fn GM –help’ will give description of the GM function.  
‘nmrPipe –fn GM –help’ will give description of the GM function.  
Line 52: Line 51:
<br>  
<br>  


<br>  
===== '''Commonly Used Processing Functions in NMRPipe<br>''' =====


<br>


===== '''Commonly Used Processing Functions in NMRPipe<br> =====
<span style="font: 12.0px Times New Roman"><span class="Apple-tab-span" style="white-space:pre"> </span></span>The processing functions describe here are the most commonly used for processing NMR spectra of protein.&nbsp; For the advance features, please visit the help pages of NMRPipe.


<span style="font: 12.0px Times New Roman"><span class="Apple-tab-span" style="white-space:pre"> </span></span>The processing functions describe here are the most commonly used for processing NMR spectra of protein.&nbsp; For the advance features, please visit the help pages of NMRPipe.
<br>  


<br>
'''Solvent Suppression:''' removes residual solvent.


'''Solvent Suppression:''' removes residual solvent.
<br>


<br>
‘SOL’ solvent filter


‘SOL’ solvent filter
‘POLY –time’ time-domain correction for solvent subtraction <br>


‘POLY –time’ time-domain correction for solvent subtraction
'''Baseline correction:''' removes dc offsets and baseline imperfection due to tilting, bowing, or rolling.
<br>


'''Baseline correction:''' removes dc offsets and baseline imperfection due to tilting, bowing, or rolling.
<br>


<br>
‘CBF’ DC correction


‘CBF’ DC correction
‘POLY –auto’ automatically generate a polynomial baseline correction  


‘POLY –auto’ automatically generate a polynomial baseline correction
<br>


<br>
'''Apodization: '''removes artifact and improve S/N


'''Apodization: '''removes artifact and improve S/N
<br>


<br>
‘em –lb 1.0’ exponential line broadening


‘em –lb 1.0’ exponential line broadening
‘SP –off 0.5’ sine bell (offset by 90 degree, equivalent to cosine)


‘SP –off 0.5’ sine bell (offset by 90 degree, equivalent to cosine)
<br>


<br>
'''Zero fill the data:''' One can add zeros to the end of the fid so that there are more points in the final Fourier transformed spectrum. &nbsp; This will smooth the data and increase the resolution to some degree.


'''Zero fill the data:''' One can add zeros to the end of the fid so that there are more points in the final Fourier transformed spectrum. &nbsp; This will smooth the data and increase the resolution to some degree.
<br>


<br>
‘zf –auto’ round up the number of points to the nearest power of 2


‘zf –auto’ round up the number of points to the nearest power of 2
‘zf –size 16384’ zero fills up to 16384 points  


‘zf –size 16384’ zero fills up to 16384 points
<br>


<br>
'''Linear prediction:''' instead of adding zeros, one can calculate additional points based on a mathematical analysis of the existing fid.


'''Linear prediction:''' instead of adding zeros, one can calculate additional points based on a mathematical analysis of the existing fid.
<br>


<br>
‘lp –fb’ uses&nbsp; default values and doubles the size of the fid to increase digital resolution.


‘lp –fb’ uses&nbsp; default values and doubles the size of the fid to increase digital resolution.
<br>


<br>
<br>  


<br>
<br>  


<br>
<br>  
 
<br>


<br>
<br>

Revision as of 23:42, 2 December 2009

 NMR Data Processing >  Overview

Brief Description

There are many softwares available today for processing NMR data and this task usually involves processing the time domain signal to frequency domain spectrum via Fourier transform along with different mathematical functions (see section 1.4 of this article for brief description of commonly used functions) to adjust the spectrum.  The NMRPipe data processing program consists of a number of functions that are linked together via UNIX pipes and it is widely used in the scientific community.  A second program called ‘nmrDraw’ (part of the NMRPipe package) is used to visualize and inspect the processed NMR data.  The nmrDraw program provides basic functions such as drawing contours, vertical or horizontal traces, peak picking, integration, and etc.  The NMR data processing methods described in this TWiki are the routine procedures commonly used in the NESG community.  For more detailed information on the functionality of NMRPipe, please visit the manual pages of NMRPipe.   The general workflow of NMRPipe is as follows:


Step 1: Converting the data from spectrometer format to NMRPipe format

Step 2: Time domain data inspection using nmrDraw

Step 3: Trial processing for initial phasing and applying mathematical functions 

Step 4: Inspection of the trial processed spectrum via nmrDraw

Step 5: Final processing

Step 6: Spectra format conversion to Sparky, CARA, XEASY or NMRViewJ

  

Software Information

NMRPipe (download information and user manual)

http://spin.niddk.nih.gov/NMRPipe/

Brief descriptions of specific functions are accessible via nmrPipe –

‘nmrPipe –help’ will list most functions

‘nmrPipe –fn GM –help’ will give description of the GM function.


Supported Platform

Linux (RedHat Linux/Fedora) 

Mac OS X (10.3.4 and up)

SGI Irix  (6.2 and up)

Sparc Solaris (2 and up)

Windows XP Pro with Microsoft Services for UNIX (SFU 3.5).


Commonly Used Processing Functions in NMRPipe

The processing functions describe here are the most commonly used for processing NMR spectra of protein.  For the advance features, please visit the help pages of NMRPipe.


Solvent Suppression: removes residual solvent.


‘SOL’ solvent filter

‘POLY –time’ time-domain correction for solvent subtraction

Baseline correction: removes dc offsets and baseline imperfection due to tilting, bowing, or rolling.


‘CBF’ DC correction

‘POLY –auto’ automatically generate a polynomial baseline correction


Apodization: removes artifact and improve S/N


‘em –lb 1.0’ exponential line broadening

‘SP –off 0.5’ sine bell (offset by 90 degree, equivalent to cosine)


Zero fill the data: One can add zeros to the end of the fid so that there are more points in the final Fourier transformed spectrum.   This will smooth the data and increase the resolution to some degree.


‘zf –auto’ round up the number of points to the nearest power of 2

‘zf –size 16384’ zero fills up to 16384 points


Linear prediction: instead of adding zeros, one can calculate additional points based on a mathematical analysis of the existing fid.


‘lp –fb’ uses  default values and doubles the size of the fid to increase digital resolution.






Retrieved from "https://nesgwiki.chem.buffalo.edu/index.php?title=Brief_description_of_philosophy,_commands,_and_functions_of_NMRPipe&oldid=2925"