HSQCTROSY RDC Measurement - Revision history

Hlee at 19:35, 17 August 2011

2011-08-17T19:35:59Z

← Older revision		Revision as of 19:35, 17 August 2011
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	Download: [[Media:I-hsqctrosy_step5.tcl\|I-hsqctrosy_step5.tcl]]		Download: [[Media:I-hsqctrosy_step5.tcl\|I-hsqctrosy_step5.tcl]]
	<~~div~~><~~/div~~>		<br>
			<br>
			<br>
			Updated by Hsiau-Wei Lee, 2011

Hlee at 19:34, 17 August 2011

2011-08-17T19:34:32Z

← Older revision		Revision as of 19:34, 17 August 2011
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	===== '''Fourier Transformation of Converted HSQC and TROSY spectra''' =====		===== '''Fourier Transformation of Converted HSQC and TROSY spectra''' =====

	~~<span style="font: 8.0px Courier">'''<span class="Apple-tab-span" style="white-space:pre"> </span>'''</span>~~The following script contains some data specific parameters including phasing parameters and convolution functions that will need to be optimized for each specific set.		The following script contains some data specific parameters including phasing parameters and convolution functions that will need to be optimized for each specific set.
			<pre>#!/bin/csh
	<~~nowiki~~>#!/bin/csh~~</nowiki>~~		#This script is to process one of the TROSY/
			\| nmrPipe -in hsqc.fid \
	~~<nowiki>~~#This script is to process one of the TROSY/~~</nowiki>~~		\| nmrPipe -fn SOL \
			\| nmrPipe -fn SP -off 0.5 -end 0.99 -pow 2 -c 0.5 \
	\| nmrPipe~~ ~~ -in hsqc.fid~~             ~~ \		\| nmrPipe -fn ZF -auto \
			\| nmrPipe -fn FT \
	\| nmrPipe -fn SOL ~~ ~~ \		\| nmrPipe -fn PS -p0 -61.6 -p1 -4.6 -di \
			\| nmrPipe -fn EXT -x1 6.00ppm -xn 11.50ppm -verb 2 -sw \
	\| nmrPipe~~ ~~ -fn SP -off 0.5 -end 0.99 -pow 2 -c 0.5~~ ~~ \		\| nmrPipe -fn TP \
			\| nmrPipe -fn LP -x1 1 -xn 256 -pred 256 -after -verb \
	\| nmrPipe~~ ~~ -fn ZF -auto~~                   ~~ \		\| nmrPipe -fn SP -off 0.5 -end 0.99 -pow 2 -c 1.0 \
			\| nmrPipe -fn ZF -auto \
	\| nmrPipe~~ ~~ -fn FT ~~                   ~~ \		\| nmrPipe -fn FT \
			\| nmrPipe -fn PS -p0 -91.8 -p1 7.0 -di \
	\| nmrPipe -fn PS -p0 -61.6 -p1 -4.6~~ ~~ -di~~   ~~ \		\| nmrPipe -fn TP \
			\| nmrPipe -fn EXT -y1 100.00ppm -yn 138.00ppm -sw \
	\| nmrPipe~~ ~~ -fn EXT -x1 6.00ppm -xn 11.50ppm -verb 2 -sw~~ ~~ \		\| nmrPipe -out hsqc.ft2 -verb 2 -ov
			</pre>
	\| nmrPipe -fn TP~~                     ~~ \

	\| nmrPipe -fn LP -x1 1 -xn 256 -pred 256 -after -verb ~~ ~~ \

	\| nmrPipe -fn SP -off 0.5 -end 0.99 -pow 2 -c 1.0~~ ~~ \

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

	\| nmrPipe -fn FT ~~                 ~~ \

	\| nmrPipe -fn PS -p0 -91.8 -p1 7.0 ~~ ~~ -di ~~   ~~ \

	\| nmrPipe -fn TP~~       ~~ \

	\| nmrPipe -fn EXT -y1 100.00ppm -yn~~   ~~ 138.00ppm -sw \

	\| nmrPipe -out hsqc.ft2 -verb 2 -ov

	<~~br>~~

	~~<br~~>

	===== '''RDC Assignment and Calculation''' =====		===== '''RDC Assignment and Calculation''' =====

Hlee at 19:33, 17 August 2011

2011-08-17T19:33:08Z

← Older revision		Revision as of 19:33, 17 August 2011
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	===== '''Bruker to NMRPipe Data Conversion''' =====		===== '''Bruker to NMRPipe Data Conversion''' =====

	The conversion of data collected on most Bruker spectrometers can be accomplished with the following script. ~~(insert script)~~		The conversion of data collected on most Bruker spectrometers can be accomplished with the following script.

	~~<br>~~		(insert script)

	===== '''Fourier Transformation of Converted HSQC and TROSY spectra''' =====		===== '''Fourier Transformation of Converted HSQC and TROSY spectra''' =====

Hlee at 19:32, 17 August 2011

2011-08-17T19:32:34Z

← Older revision		Revision as of 19:32, 17 August 2011
Line 72:		Line 72:
	===== '''Bruker to NMRPipe Data Conversion''' =====		===== '''Bruker to NMRPipe Data Conversion''' =====

	~~<span style="font: 12.0px Times New Roman"><span class="Apple-tab-span" style="white-space:pre"> </span></span>~~The conversion of data collected on most Bruker spectrometers can be accomplished with the following script.~~  The same precautions pertain?~~		The conversion of data collected on most Bruker spectrometers can be accomplished with the following script. (insert script)

	~~(insert script)~~		<br>

	<br>

	===== '''Fourier Transformation of Converted HSQC and TROSY spectra''' =====		===== '''Fourier Transformation of Converted HSQC and TROSY spectra''' =====

Hlee at 19:29, 17 August 2011

2011-08-17T19:29:46Z

@@ Line 41: / Line 41: @@
 ===== '''Varian to NMRPipe Data Conversion'''  =====
-<nowiki>#!/bin/csh</nowiki>
+var2pipe -in ./fid \
+  -xN           2048    -yN      1024   \
-<nowiki>##conversion of varian 2d fids into nmrPipe format for a TROSY/hsqc data set</nowiki>
+   -xT           1024    -yT      256   \
+   -xMODE     Complex    -yMODE   Rance-Kay  \
-<nowiki>##with array= ‘(TROSY, dm2),phase’</nowiki>
+   -xSW       10000.00   -ySW     2800.00  \
+   -xOBS      599.520    -yOBS      60.756   \
-var2pipe -in ./fid \
+   -xCAR         4.773    -yCAR    118.262   \
+   -xLAB           HN    -yLAB         N   \
-&nbsp;&nbsp; -xN &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 2048&nbsp; &nbsp; -yN&nbsp; &nbsp; &nbsp; 1024 &nbsp; \
+   -ndim            2    -aq2D    States   \
+   | nmrPipe -fn QMIX -ic 4 -oc 2 -cList 0 0 0 0 1 0 0 1   \
-&nbsp;&nbsp; -xT &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 1024&nbsp; &nbsp; -yT&nbsp; &nbsp; &nbsp; 256 &nbsp; \
+   -out hsqc.fid -verb –ov
+</pre>
-&nbsp;&nbsp; -xMODE &nbsp; &nbsp; Complex&nbsp; &nbsp; -yMODE &nbsp; Rance-Kay&nbsp; \
+'''Cautions:''' The usual Varian to NMRPipe macros will read in experimental parameters, but will not be able to perform data conversion since both the HSQC and TROSY spectra are collected in a interleaved manner and are stored in a single FID data file.&nbsp; The above script includes the QMIX function to separate fids.
 ===== '''Bruker to NMRPipe Data Conversion'''  =====

Hlee at 19:27, 17 August 2011

2011-08-17T19:27:42Z

← Older revision		Revision as of 19:27, 17 August 2011
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	The data processing described below is specific for data collected on Varian spectrometers having the BioPack (version: 2009<span style="font: 12.0px Times New Roman">-0</span>9<span style="font: 12.0px Times New Roman">-0</span>3) sequence (gNhsqc.c) installed.  Or on Bruker spectrometers having the …….. It is applied to both isotropic and aligned HSQC-TROSY pairs.		The data processing described below is specific for data collected on Varian spectrometers having the BioPack (version: 2009<span style="font: 12.0px Times New Roman">-0</span>9<span style="font: 12.0px Times New Roman">-0</span>3) sequence (gNhsqc.c) installed.  Or on Bruker spectrometers having the …….. It is applied to both isotropic and aligned HSQC-TROSY pairs.

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

	NMRPipe (download information and user manual)		NMRPipe (download information and user manual) <br>[http://spin.niddk.nih.gov/NMRPipe/ http://spin.niddk.nih.gov/NMRPipe/] <br> <br> Brief descriptions of specific functions are accessible via nmrPipe –

	~~<span style="text-decoration~~: ~~underline">[http://%22 http~~:~~//spin.niddk.nih~~.~~gov/NMRPipe/]</span>~~		:‘nmrPipe –help’ will list most functions.
			:‘nmrPipe –fn GM –help’ will give description of the GM function.

	<~~span class="Apple-tab-span" style="white-space:pre"> </span~~>		<br> Supported Platforms

	~~Brief descriptions of specific functions are accessible via nmrPipe –~~		:Linux (RedHat Linux/Fedora)
			:Mac OS X (10.3.4 and up)
	~~<span style="font: 12.0px Times New Roman"><span class="Apple-tab-span" style="white-space:pre"> </span></span>‘nmrPipe –help’ will list most functions.~~		:SGI Irix  (6.2 and up)
			:Sparc Solaris (2 and up)
	~~<span class="Apple-tab-span" style="white-space~~:~~pre"> </span>‘nmrPipe –fn GM –help’ will give description of the GM function.~~		:Windows XP Pro with Microsoft Services for UNIX (SFU 3.5)

	~~<br>~~

	~~Supported Platforms~~

	Linux (RedHat Linux/Fedora)~~ ~~

	Mac OS X (10.3.4 and up)

	SGI Irix  (6.2 and up)

	~~ <span class="Apple-tab-span" style="white-space~~:~~pre"> </span>~~Sparc Solaris (2 and up)

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

	~~<br>~~

	~~<br>~~

	===== '''Varian to NMRPipe Data Conversion''' =====		===== '''Varian to NMRPipe Data Conversion''' =====

Hlee at 19:26, 17 August 2011

2011-08-17T19:26:57Z

← Older revision		Revision as of 19:26, 17 August 2011
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	===== '''Brief Experimental Description''' =====		===== '''Brief Experimental Description''' =====

	<span style="font: 12.0px Times New Roman">'''<span class="Apple-tab-span" style="white-space:pre"> </span>'''</span>HSQC-TROSY pairs provide one way of measuring RDCs.  The procedure is applicable to proteins of small and moderate size (10-30 kDa).  The acquisition time in the indirect t1 should be at least T2 of nitrogen.  The measurements are easily visualized as displacements of peaks in 2D frequency domain spectra.  The HSQC member of the pair gives a single peak at the center of the four peaks expected in a fully coupled HSQC experiment. The TROSY member gives only the sharpest component. The offset in either H or N direction is one half (J).  Procedures for collecting this pair of experiments are described elsewhere in this Twiki (Experimental setup for HSQC-TROSY). ~~ ~~		<span style="font: 12.0px Times New Roman">'''<span class="Apple-tab-span" style="white-space:pre"> </span>'''</span>HSQC-TROSY pairs provide one way of measuring RDCs.  The procedure is applicable to proteins of small and moderate size (10-30 kDa).  The acquisition time in the indirect t1 should be at least T2 of nitrogen.  The measurements are easily visualized as displacements of peaks in 2D frequency domain spectra.  The HSQC member of the pair gives a single peak at the center of the four peaks expected in a fully coupled HSQC experiment. The TROSY member gives only the sharpest component. The offset in either H or N direction is one half (J).  Procedures for collecting this pair of experiments are described elsewhere in this Twiki (Experimental setup for HSQC-TROSY).

	~~<br>~~

	===== '''NMR Data Processing''' =====		===== '''NMR Data Processing''' =====

Hlee at 20:02, 10 January 2010

2010-01-10T20:02:56Z

← Older revision		Revision as of 20:02, 10 January 2010
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	<br>		<br>

	Download: i-hsqctrosy_step2.tcl		Download: [[Media:I-hsqctrosy_step2.tcl\|I-hsqctrosy_step2.tcl]]

	<br>		<br>
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	<br>		<br>

	Download: i-hsqctrosy_step3.tcl		Download: [[Media:I-hsqctrosy_step3.tcl\|I-hsqctrosy_step3.tcl]]

	<br>		<br>
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	<br>		<br>

	Download: i-hsqctrosy_step4.tcl		Download: [[Media:I-hsqctrosy_step4.tcl\|I-hsqctrosy_step4.tcl]]

	<br>		<br>
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	<br>		<br>

	Download: i-hsqctrosy_step5.tcl		Download: [[Media:I-hsqctrosy_step5.tcl\|I-hsqctrosy_step5.tcl]]
	<div></div>		<div></div>

Hlee at 18:17, 10 January 2010

2010-01-10T18:17:41Z

← Older revision		Revision as of 18:17, 10 January 2010
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	'''Command: '''		'''Command: '''
			<pre>./step1_hsqc_ass.tcl hsqc_ass.tab hsqc.tab</pre>
	./step1_hsqc_ass.tcl hsqc_ass.tab hsqc.tab

	Where “hsqc_ass.tab” is the output file and “hsqc.tab” is the input file to this script.		Where “hsqc_ass.tab” is the output file and “hsqc.tab” is the input file to this script.

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	'''Command: '''		'''Command: '''
			<pre>./i-hsqctrosy_step2.tcl</pre>
	./i-hsqctrosy_step2.tcl

	<br>		<br>

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	'''Command:'''		'''Command:'''
			<pre>./i-hsqctrosy_step3.tcl</pre>
	./i-hsqctrosy_step3.tcl

	<br>		<br>

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	'''Command:'''		'''Command:'''
			<pre>./i-hsqctrosy_step4.tcl</pre>
	./i-hsqctrosy_step4.tcl

	<br>		<br>

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	'''Command:'''		'''Command:'''
			<pre>./i-hsqctrosy_step5.tcl</pre>
	./i-hsqctrosy_step5.tcl

	<br>		<br>

	Download: i-hsqctrosy_step5.tcl		Download: i-hsqctrosy_step5.tcl
	<div></div>		<div></div>

Hlee at 01:05, 7 December 2009

2009-12-07T01:05:34Z

← Older revision		Revision as of 01:05, 7 December 2009
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	<span style="font: 8.0px Courier">'''<span class="Apple-tab-span" style="white-space:pre"> </span>'''</span>The following script contains some data specific parameters including phasing parameters and convolution functions that will need to be optimized for each specific set.		<span style="font: 8.0px Courier">'''<span class="Apple-tab-span" style="white-space:pre"> </span>'''</span>The following script contains some data specific parameters including phasing parameters and convolution functions that will need to be optimized for each specific set.

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

	#This script is to process one of the TROSY/		<nowiki>#This script is to process one of the TROSY/</nowiki>

	\| nmrPipe  -in hsqc.fid              \		\| nmrPipe  -in hsqc.fid              \
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	<br>		<br>

	<br>		<br>

	===== '''RDC Assignment and Calculation''' =====		===== '''RDC Assignment and Calculation''' =====