Routine 2D Experiment - Revision history

Hlee at 13:50, 19 August 2011

2011-08-19T13:50:18Z

← Older revision		Revision as of 13:50, 19 August 2011
Line 75:		Line 75:
	<br>		<br>

	[[Image:NMRPipe-Macro-Editors.png]]		[[Image:NMRPipe-Macro-Editors.png\|900px\|Left]]

	<br>		<br>

Hlee at 19:23, 17 August 2011

2011-08-17T19:23:43Z

← Older revision		Revision as of 19:23, 17 August 2011
Line 82:		Line 82:

	<br>		<br>
			<pre>\|nmrPipe -in test.fid \
	<~~nowiki~~>~~#!/bin/csh</nowiki>~~		\| nmrPipe -fn SOL \ ## Solvent suppresion
			\| nmrPipe -fn SP -off 0.5 -end 1.00 -pow 2 -c 0.5 \ ## Apodization
	nmrPipe~~ ~~ -in test.fid ~~                                           ~~\		\| nmrPipe -fn ZF -auto \ ## Zero fill
			\| nmrPipe -fn FT -auto \ ## Fourier transformation
	\| nmrPipe -fn SOL ~~                                             ~~ \ ## Solvent suppresion		\| nmrPipe -fn PS -p0 13.6 -p1 0.0 -di \ ## Phase correction
			\| nmrPipe -fn EXT –left –sw \ # Extract spectrum
	\| nmrPipe~~ ~~ -fn SP -off 0.5 -end 1.00 -pow 2 -c 0.5 ~~ ~~\ ## Apodization		\| nmrPipe -fn TP \ ## Transpose to the y-axis
			\| nmrPipe -fn LP -fb \ ## Add liner prediction
	\| nmrPipe~~ ~~ -fn ZF -auto ~~                                       ~~\ ## Zero fill		\| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 1.0 \
			\| nmrPipe -fn ZF -auto \
	\| nmrPipe~~ ~~ -fn FT -auto ~~                                       ~~\ ## Fourier transformation		\| nmrPipe -fn FT -auto \
			\| nmrPipe -fn PS -p0 -90.0 -p1 180.0 -di \
	\| nmrPipe -fn PS -p0 13.6 -p1 0.0~~ ~~ -di ~~                   ~~\ ## Phase correction		\| nmrPipe -fn TP \
			\| nmrPipe –out test.ft2 -verb 2 -ov
	\| nmrPipe~~ ~~ -fn EXT –left –sw ~~                               ~~\ # Extract spectrum		</pre>

	\| nmrPipe -fn TP ~~                                               ~~ \ ## Transpose to the y-axis

	\| nmrPipe -fn LP -fb ~~                                           ~~ \ ## Add liner prediction

	\| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 1.0 ~~   ~~\

	\| nmrPipe -fn ZF -auto ~~                                         ~~\

	\| nmrPipe -fn FT -auto ~~                                         ~~\

	\| nmrPipe -fn PS -p0 -90.0 -p1 180.0 ~~ ~~ -di ~~             ~~ \

	\| nmrPipe -fn TP ~~                                                 ~~\

	\| nmrPipe –out test.ft2~~ ~~ -verb 2 -ov

	<br>		<br>

Hlee at 18:16, 17 August 2011

2011-08-17T18:16:59Z

← Older revision		Revision as of 18:16, 17 August 2011
Line 135:		Line 135:
	<br>		<br>

	Step 4: Convert the processed data to the format of graphical NMR assignment program.		Step 4: Convert the processed data to the format of graphical NMR assignment program. <br> <br> <br> Updated by Hsiau-Wei Lee, 2011
	<~~div~~><~~/div~~>

Hlee at 00:59, 7 December 2009

2009-12-07T00:59:41Z

← Older revision		Revision as of 00:59, 7 December 2009
Line 83:		Line 83:
	<br>		<br>

	#!/bin/csh		<nowiki>#!/bin/csh</nowiki>

	nmrPipe  -in test.fid                                            \		nmrPipe  -in test.fid                                            \

Hlee at 18:41, 4 December 2009

2009-12-04T18:41:41Z

← Older revision		Revision as of 18:41, 4 December 2009
Line 121:		Line 121:
	<br>		<br>

	Step 1: Generate the processing script with the appropriate commands and functions using the macro editor or ~~modified~~ existing script.  Set both the p0 and p1 phasing values of the direct dimension to 0.		Step 1: Generate the processing script with the appropriate commands and functions using the macro editor or modifying an existing script.  Set both the p0 and p1 phasing values of the direct dimension to 0.

	<br>		<br>

	Step 2: Execute the processing script in a UNIX terminal.  Load the spectrum into nmrDraw to perform phase correction and ~~optimizing~~ the applied functions.  A 1D horizontal trace can be activate by typing ‘h’ in the spectrum window and the phase of the dimension can be adjusting using the P0 and P1 slider bars.~~ ~~		Step 2: Execute the processing script in a UNIX terminal.  Load the spectrum into nmrDraw to perform phase correction and optimize the applied functions.  A 1D horizontal trace can be activate by typing ‘h’ in the spectrum window and the phase of the dimension can be adjusting using the P0 and P1 slider bars. To phase an indirect dimension, type 'v'. Now the P0 and P1 slider bars will change the phase of the indirectly-detected dimension.
	[[Image:NMRDraw-Phasing.png]]
			[[Image:NMRDraw-Phasing.png]]

	<br>		<br>

Hlee at 18:39, 4 December 2009

2009-12-04T18:39:07Z

← Older revision		Revision as of 18:39, 4 December 2009
Line 79:		Line 79:
	<br>		<br>

	An alternative way to create ~~these~~ processing script is to copy an existing one and edit it with a text editor.  An example of processing script for a 2D ~~15N~~ HSQC spectrum is shown below.  The script starts off by ~~read~~ in the time domain data ‘test.fid’ using the ‘nmrPipe –in’ command following by ‘\’ at the end of each line.  Each subsequent ‘nmrPipe –fn’ command line will begin with a unix ‘\|’ and end with ‘\’.   A solvent suppression filter SOL was first applied to removed residual solvent followed by a 90 degrees sine bell ~~square~~ apodization (equivalent to cosine) with scale factor for first point as 0.5.  The data is then zero<span style="font: 12.0px Times New Roman">-</span>filled to the nearest power of 2, Fourier transformed, phased, and the amide region of the spectrum (left half) extracted.  The TP functions transpose the data to the y-axis to apply linear prediction, apodization, zero fill, Fourier transform, phasing to the y-dimension, and output the finished file as ‘test.ft2’.  When the first point is collected at half dwell time (for Varian instrument, f1180=’y’), the phasing values in the indirect dimension is set to ‘-90 for p0 and 180 for p1’ and the first point multiplier set to 1.0<span style="font: 12.0px Times New Roman">.</span>		An alternative way to create a processing script is to copy an existing one and edit it with a text editor.  An example of processing script for a 2D <sup>15</sup>N HSQC spectrum is shown below.  The script starts off by reading in the time domain data ‘test.fid’ using the ‘nmrPipe –in’ command following by ‘\’ at the end of each line.  Each subsequent ‘nmrPipe –fn’ command line will begin with a unix ‘\|’ and end with ‘\’.   A solvent suppression filter SOL was first applied to removed residual solvent followed by a 90 degrees sine bell squared apodization (equivalent to cosine) with scale factor for first point as 0.5.  The data is then zero<span style="font: 12.0px Times New Roman">-</span>filled to the nearest power of 2, Fourier transformed, phased, and the amide region of the spectrum (left half) extracted.  The TP functions transpose the data to the y-axis to apply linear prediction, apodization, zero fill, Fourier transform, phasing to the y-dimension, and output the finished file as ‘test.ft2’.  When the first point is collected at a half dwell time (for a Varian instrument, f1180=’y’), the phasing values in the indirect dimension are set to ‘-90 for p0 and 180 for p1’ and the first point multiplier set to 1.0<span style="font: 12.0px Times New Roman">.</span>

	<br>		<br>
Line 85:		Line 85:
	#!/bin/csh		#!/bin/csh

	nmrPipe  -in test.fid               \		nmrPipe  -in test.fid                                            \

	\| nmrPipe -fn SOL   \ ## Solvent suppresion		\| nmrPipe -fn SOL                                               \ ## Solvent suppresion

	\| nmrPipe  -fn SP -off 0.5 -end 1.00 -pow 2 -c 0.5  \ ## Apodization		\| nmrPipe  -fn SP -off 0.5 -end 1.00 -pow 2 -c 0.5  \ ## Apodization

	\| nmrPipe  -fn ZF -auto                   \ ## Zero fill		\| nmrPipe  -fn ZF -auto                                        \ ## Zero fill

	\| nmrPipe  -fn FT -auto                     \ ## Fourier transformation		\| nmrPipe  -fn FT -auto                                        \ ## Fourier transformation

	\| nmrPipe -fn PS -p0 13.6 -p1 0.0  -di    \ ## Phase correction		\| nmrPipe -fn PS -p0 13.6 -p1 0.0  -di                    \ ## Phase correction

	\| nmrPipe  -fn EXT –left –sw   \ # Extract spectrum		\| nmrPipe  -fn EXT –left –sw                                \ # Extract spectrum

	\| nmrPipe -fn TP                      \ ## Transpose to the y-axis		\| nmrPipe -fn TP                                                 \ ## Transpose to the y-axis

	\| nmrPipe -fn LP -fb         \ ## Add liner prediction		\| nmrPipe -fn LP -fb                                             \ ## Add liner prediction

	\| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 1.0  \		\| nmrPipe -fn SP -off 0.5 -end 0.98 -pow 2 -c 1.0    \

	\| nmrPipe -fn ZF -auto           \		\| nmrPipe -fn ZF -auto                                          \

	\| nmrPipe -fn FT -auto                  \		\| nmrPipe -fn FT -auto                                          \

	\| nmrPipe -fn PS -p0 -90.0 -p1 180.0   -di     \		\| nmrPipe -fn PS -p0 -90.0 -p1 180.0   -di               \

	\| nmrPipe -fn TP        \		\| nmrPipe -fn TP                                                  \

	\| nmrPipe –out test.ft2  -verb 2 -ov		\| nmrPipe –out test.ft2  -verb 2 -ov

Hlee at 18:35, 4 December 2009

2009-12-04T18:35:20Z

← Older revision		Revision as of 18:35, 4 December 2009
Line 43:		Line 43:
	===== '''Converting Spectrometer Data into NMRPipe Format''' =====		===== '''Converting Spectrometer Data into NMRPipe Format''' =====

	To convert data from spectrometer format to NMRPipe format is usually done using the build-in program called ‘varian’ for Varian dataset (bruker for Bruker dataset and delta for dataset from JEOL).   Brief summaries of the build-in ~~program~~ can be found here ~~(this is a link)~~.		To convert data from spectrometer format to NMRPipe format is usually done using the build-in program called ‘varian’ for a Varian dataset ('bruker' for a Bruker dataset and 'delta' for dataset from JEOL).   [[Brief_description_of_philosophy,_commands,_and_functions_of_NMRPipe\|Brief summaries of the build-in programs can be found here.]]

	<br>		<br>
Line 61:		Line 61:
	<br>		<br>

	The template shows parameters for two dimensions x and y.  The x dimension is the direct dimension and is always collected as complex data (quadrature detection) and the xMODE is set as complex.  The xN (real+imaginary points) parameter is twice the xT (complex points) parameter.  For the indirect dimension y, the yN parameter is twice the yT parameter (number of ~~increment~~, ni for Varian instrument)<span style="font: 12.0px Times New Roman">,</span> indicating that we are collecting ~~two datasets~~ to ~~allow~~ for ‘quadrature’ in the indirect dimension.  For the sensitivity enhanced ~~experiment~~ the yMODE will be set to “Rance-Kay”.  The frequency values can be modified using the pull down tab.  The center position ppm of each dimension (xCAR and yCAR) can be updated at this stage and it can also be update later.		The template shows parameters for two dimensions x and y.  The x dimension is the direct dimension and is always collected as complex data (quadrature detection) and the xMODE is set as complex.  The xN (real+imaginary points) parameter is twice the xT (complex points) parameter.  For the indirect dimension y, the yN parameter is twice the yT parameter (number of increments, ni for a Varian instrument)<span style="font: 12.0px Times New Roman">,</span> indicating that we are collecting complex dataset to account for ‘quadrature’ in the indirect dimension.  For the sensitivity-enhanced experiments the yMODE will be set to “Rance-Kay”.  The frequency values can be modified using the pull down tab.  The center position ppm of each dimension (xCAR and yCAR) can be updated at this stage and it can also be update later.

	<br>		<br>

Hlee at 18:31, 4 December 2009

2009-12-04T18:31:51Z

← Older revision		Revision as of 18:31, 4 December 2009
Line 5:		Line 5:
	===== '''Brief Description''' =====		===== '''Brief Description''' =====

	NMRPipe is designed for multidimensional NMR processing.  The preferred method of processing data is to compile the commands and functions into a script file.  The script file can be easily modified for different type of experiments and ~~used~~ as a record of how the data was processed.  An example of converting the 2D HSQC spectrometer data to NMRPipe format is shown along with processing and visualizing of the dataset.		NMRPipe is designed for multidimensional NMR processing.  The preferred method of processing data is to compile the commands and functions into a script file.  The script file can be easily modified for different type of experiments and serves as a record of how the data was processed.  An example of converting the 2D HSQC spectrometer data to NMRPipe format is shown along with processing and visualizing of the dataset.

	<br>		<br>

	===== '''Software Information''' =====		===== '''Software Information''' =====

Hlee at 06:06, 3 December 2009

2009-12-03T06:06:58Z

← Older revision		Revision as of 06:06, 3 December 2009
Line 51:		Line 51:
	<br>		<br>

	[[Image:Varian-utility-raw.png]] [[Image:Varian-~~utility~~-raw.png]]		[[Image:Varian-utility-raw.png]] [[Image:Varian-script-raw.png]]

	<br>		<br>
Line 57:		Line 57:
	Step 2: Click on the ‘Read Parameters’ button and the script will read the parameter file (‘procpar’) and update the parameters.		Step 2: Click on the ‘Read Parameters’ button and the script will read the parameter file (‘procpar’) and update the parameters.

	<br>		<br> [[Image:Varian-utility-readed.png]] [[Image:Varian-script-readed.png]] <br>
	[[Image:Varian-utility-readed.png]] [[Image:Varian-script-readed.png]]
	<br>

	<br>		<br>

Hlee at 00:20, 3 December 2009

2009-12-03T00:20:36Z

← Older revision		Revision as of 00:20, 3 December 2009
Line 119:		Line 119:
	<br>		<br>

	===== Suggested Workflow =====		===== Suggested Workflow =====

	<br>		<br>
Line 128:		Line 128:

	Step 2: Execute the processing script in a UNIX terminal.  Load the spectrum into nmrDraw to perform phase correction and optimizing the applied functions.  A 1D horizontal trace can be activate by typing ‘h’ in the spectrum window and the phase of the dimension can be adjusting using the P0 and P1 slider bars.		Step 2: Execute the processing script in a UNIX terminal.  Load the spectrum into nmrDraw to perform phase correction and optimizing the applied functions.  A 1D horizontal trace can be activate by typing ‘h’ in the spectrum window and the phase of the dimension can be adjusting using the P0 and P1 slider bars.
			[[Image:NMRDraw-Phasing.png]]

	<br>		<br>