Jmodulation Experiment RDC - Revision history

Kpederson at 20:51, 18 December 2013

2013-12-18T20:51:47Z

← Older revision		Revision as of 20:51, 18 December 2013
Line 120:		Line 120:
	<br>		<br>

	To calculate RDCs, ~~simply~~ take the difference between the measured scalar couplings for the isotropic and aligned samples. The sign of the residual dipolar coupling is dependent on the gyromagentic ratios of the coupled nuclei. For <sup>1</sup>H-<sup>15</sup>N couplings, a decrease in coupling upon alignment corresponds to a positive residual dipolar coupling.		To calculate RDCs, take the difference between the measured scalar couplings for the isotropic and aligned samples. The sign of the residual dipolar coupling is dependent on the gyromagentic ratios of the coupled nuclei. For <sup>1</sup>H-<sup>15</sup>N couplings, a decrease in observed coupling upon alignment corresponds to a positive residual dipolar coupling.

	Header to add to the isotropic peaklist: [[Media:Header-hsqc_ass.txt\|header-hsqc_ass.txt]] (Change extension to .tab to use)		Header to add to the isotropic peaklist: [[Media:Header-hsqc_ass.txt\|header-hsqc_ass.txt]] (Change extension to .tab to use)
Line 126:		Line 126:
	To calculate RDCs from isotropic and aligned coupling data: [[Media:I-jmod.txt\|i-jmod.txt]] (Change extension to .tcl to run)<br>		To calculate RDCs from isotropic and aligned coupling data: [[Media:I-jmod.txt\|i-jmod.txt]] (Change extension to .tcl to run)<br>

	<br>		<br>

	=== References ===		=== References ===

Kpederson at 20:47, 18 December 2013

2013-12-18T20:47:56Z

← Older revision		Revision as of 20:47, 18 December 2013
Line 78:		Line 78:

	To save the peak lists containing the intensities, do an “lt”. In “Options”, check “Data Height” so that the output contains the intensities for each peak.		To save the peak lists containing the intensities, do an “lt”. In “Options”, check “Data Height” so that the output contains the intensities for each peak.

	~~<br>~~

	<br>		<br>
Line 89:		Line 87:
	<br>		<br>

	#1<span class="Apple-tab-span~~" style="white-space:pre~~"> </span>0.001		#1<span style="white-space:pre" class="Apple-tab-span"> </span>0.001
	#2<span class="Apple-tab-span~~" style="white-space:pre~~"> </span>0.004		#2<span style="white-space:pre" class="Apple-tab-span"> </span>0.004
	#3<span class="Apple-tab-span~~" style="white-space:pre~~"> </span>0.007		#3<span style="white-space:pre" class="Apple-tab-span"> </span>0.007
	#4<span class="Apple-tab-span~~" style="white-space:pre~~"> </span>0.0124		#4<span style="white-space:pre" class="Apple-tab-span"> </span>0.0124
	#5<span class="Apple-tab-span~~" style="white-space:pre~~"> </span>0.0146		#5<span style="white-space:pre" class="Apple-tab-span"> </span>0.0146
	#6<span class="Apple-tab-span~~" style="white-space:pre~~"> </span>0.0168		#6<span style="white-space:pre" class="Apple-tab-span"> </span>0.0168
	#7<span class="Apple-tab-span~~" style="white-space:pre~~"> </span>0.025		#7<span style="white-space:pre" class="Apple-tab-span"> </span>0.025
	#8<span class="Apple-tab-span~~" style="white-space:pre~~"> </span>0.028		#8<span style="white-space:pre" class="Apple-tab-span"> </span>0.028

	<br>		<br>
Line 106:		Line 104:
	To measure the intensity of each peak click the “Measure All” button.  The graph to the right will show points indicative of a decaying cosine function. You can click through the peaks to see each peak using the up and down arrows.  Unfortunately, the equation to fit this type of data has not yet been placed in NMRViewJ, but it will be available in a future version.  For now, the data should be saved using the "Save Table" option and will be analyzed separately.		To measure the intensity of each peak click the “Measure All” button.  The graph to the right will show points indicative of a decaying cosine function. You can click through the peaks to see each peak using the up and down arrows.  Unfortunately, the equation to fit this type of data has not yet been placed in NMRViewJ, but it will be available in a future version.  For now, the data should be saved using the "Save Table" option and will be analyzed separately.

	<br>		<br>

	=== '''Curve Fitting and RDC Calculation''' ===		=== '''Curve Fitting and RDC Calculation''' ===

Kpederson at 20:37, 18 December 2013

2013-12-18T20:37:59Z

← Older revision		Revision as of 20:37, 18 December 2013
Line 14:		Line 14:
	#Insufficient modulation points (at least 3, but >5 is suggested)		#Insufficient modulation points (at least 3, but >5 is suggested)
	#Incorrect setting of Delta step size (should NOT be around 5ms)		#Incorrect setting of Delta step size (should NOT be around 5ms)
	#Incomplete modulation curve. (at least two zero crossings are required)		#Incomplete modulation curve. (at least two zero crossings are required)<br>




			<br>

	==== Considerations for best use of acquisition time<br> ====		==== Considerations for best use of acquisition time<br> ====
Line 28:		Line 26:
	<br> 2. number of modulation points vs. nt <br>		<br> 2. number of modulation points vs. nt <br>

	Our simulation shows that these two are equivalent, i.e., one can choose to spend more time averaging each spectrum, or one can use to the time to acquire more modulation points. The errors in both cases are comparable.<br>		Our simulation shows that these two are equivalent, i.e., one can choose to spend more time averaging each spectrum, or one can use to the time to acquire more modulation points. The errors in both cases are comparable.<br>


	=== '''Data Processing''' ===		=== '''Data Processing''' ===
Line 90:		Line 89:
	<br>		<br>

	#1<span style="white-space:pre~~" class="Apple-tab-span~~"> </span>0.001		#1<span class="Apple-tab-span" style="white-space:pre"> </span>0.001
	#2<span style="white-space:pre~~" class="Apple-tab-span~~"> </span>0.004		#2<span class="Apple-tab-span" style="white-space:pre"> </span>0.004
	#3<span style="white-space:pre~~" class="Apple-tab-span~~"> </span>0.007		#3<span class="Apple-tab-span" style="white-space:pre"> </span>0.007
	#4<span style="white-space:pre~~" class="Apple-tab-span~~"> </span>0.0124		#4<span class="Apple-tab-span" style="white-space:pre"> </span>0.0124
	#5<span style="white-space:pre~~" class="Apple-tab-span~~"> </span>0.0146		#5<span class="Apple-tab-span" style="white-space:pre"> </span>0.0146
	#6<span style="white-space:pre~~" class="Apple-tab-span~~"> </span>0.0168		#6<span class="Apple-tab-span" style="white-space:pre"> </span>0.0168
	#7<span style="white-space:pre~~" class="Apple-tab-span~~"> </span>0.025		#7<span class="Apple-tab-span" style="white-space:pre"> </span>0.025
	#8<span style="white-space:pre~~" class="Apple-tab-span~~"> </span>0.028		#8<span class="Apple-tab-span" style="white-space:pre"> </span>0.028

	<br>		<br>

Kpederson at 20:37, 18 December 2013

2013-12-18T20:37:31Z

← Older revision		Revision as of 20:37, 18 December 2013
Line 9:		Line 9:
	[[Image:Vnmrj-Jmod.png\|Vnmrj-Jmod.png]]		[[Image:Vnmrj-Jmod.png\|Vnmrj-Jmod.png]]

	~~<br>~~		====  General considerations ====

			#Poor signal to noise (too few scans)
			#Insufficient modulation points (at least 3, but >5 is suggested)
			#Incorrect setting of Delta step size (should NOT be around 5ms)
			#Incomplete modulation curve. (at least two zero crossings are required)





	==== Considerations for best use of acquisition time<br> ====		==== Considerations for best use of acquisition time<br> ====
Line 19:		Line 28:
	<br> 2. number of modulation points vs. nt <br>		<br> 2. number of modulation points vs. nt <br>

	Our simulation shows that these two are equivalent, i.e., one can choose to spend more time averaging each spectrum, or one can use to the time to acquire more modulation points. The errors in both cases are comparable.<br>		Our simulation shows that these two are equivalent, i.e., one can choose to spend more time averaging each spectrum, or one can use to the time to acquire more modulation points. The errors in both cases are comparable.<br>

	~~==== Other general considerations ====~~

	~~#Poor signal to noise (too few scans)~~
	~~#Insufficient modulation points (at least 3, but >5 is suggested)~~
	~~#Incorrect setting of Delta step size (should NOT be around 5ms)~~
	~~#Incomplete modulation curve. (at least two zero crossings are required)~~


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

Kpederson at 20:35, 18 December 2013

2013-12-18T20:35:14Z

← Older revision		Revision as of 20:35, 18 December 2013
Line 27:		Line 27:
	#Incorrect setting of Delta step size (should NOT be around 5ms)		#Incorrect setting of Delta step size (should NOT be around 5ms)
	#Incomplete modulation curve. (at least two zero crossings are required)		#Incomplete modulation curve. (at least two zero crossings are required)


	=== '''Data Processing''' ===		=== '''Data Processing''' ===
Line 88:		Line 89:
	<br>		<br>

	#1<span class="Apple-tab-span~~" style="white-space:pre~~"> </span>0.001		#1<span style="white-space:pre" class="Apple-tab-span"> </span>0.001
	#2<span class="Apple-tab-span~~" style="white-space:pre~~"> </span>0.004		#2<span style="white-space:pre" class="Apple-tab-span"> </span>0.004
	#3<span class="Apple-tab-span~~" style="white-space:pre~~"> </span>0.007		#3<span style="white-space:pre" class="Apple-tab-span"> </span>0.007
	#4<span class="Apple-tab-span~~" style="white-space:pre~~"> </span>0.0124		#4<span style="white-space:pre" class="Apple-tab-span"> </span>0.0124
	#5<span class="Apple-tab-span~~" style="white-space:pre~~"> </span>0.0146		#5<span style="white-space:pre" class="Apple-tab-span"> </span>0.0146
	#6<span class="Apple-tab-span~~" style="white-space:pre~~"> </span>0.0168		#6<span style="white-space:pre" class="Apple-tab-span"> </span>0.0168
	#7<span class="Apple-tab-span~~" style="white-space:pre~~"> </span>0.025		#7<span style="white-space:pre" class="Apple-tab-span"> </span>0.025
	#8<span class="Apple-tab-span~~" style="white-space:pre~~"> </span>0.028		#8<span style="white-space:pre" class="Apple-tab-span"> </span>0.028

	<br>		<br>
Line 127:		Line 128:
	To calculate RDCs from isotropic and aligned coupling data: [[Media:I-jmod.txt\|i-jmod.txt]] (Change extension to .tcl to run)<br>		To calculate RDCs from isotropic and aligned coupling data: [[Media:I-jmod.txt\|i-jmod.txt]] (Change extension to .tcl to run)<br>

			<br>

			=== References ===

	~~=== References ===~~		<references />

	<references />

	<br> <br> <br> Updated by Hsiau-Wei Lee, 2011		<br> <br> <br> Updated by Hsiau-Wei Lee, 2011

	Updated by Kari Pederson, 2013		Updated by Kari Pederson, 2013

Kpederson: /* Pulse Sequence (J H-N) */

2013-12-18T20:34:22Z

Pulse Sequence (J H-N)

← Older revision		Revision as of 20:34, 18 December 2013
Line 5:		Line 5:
	A series of 2D experiments should be acquired with the J modulation delay (Delta) set to different values, preferably in an interleaved fashion. (Note that “Delta” is half the total modulation delay.)  For example, in Vnmr, this can be realized by:		A series of 2D experiments should be acquired with the J modulation delay (Delta) set to different values, preferably in an interleaved fashion. (Note that “Delta” is half the total modulation delay.)  For example, in Vnmr, this can be realized by:
	<pre>Delta=(0.0005,0.002,0.0035,0.0062,0.0073,0.0084,0.0125,0.014)</pre>		<pre>Delta=(0.0005,0.002,0.0035,0.0062,0.0073,0.0084,0.0125,0.014)</pre>
	which sets Delta from 0.0005 to 0.014, corresponding to J modulating delays from 1 to 28 msec. At least 3 modulation points are needed to extract the coupling constant, along with <sup>15</sup>N T<sub>2</sub> and a parameter related to pulse imperfection. It is recommended to take more than 3 points to get an estimation of experimental error. The maximum delay (28 msec in this case) should be bigger than 3/(2J) ( ~16 msec in case of JNH) to make sure the modulation curve crosses zero at least twice~~.<ref>Tjandra N. et al., JACS (1996), 118, 6364-72</ref>~~ (Tjandra et al.). Our simulation shows that the modulation interval should not be close to 1/J (~10ms for JNH),  i.e. the stepsize for Delta should not be close to ~5 msec.  An example of the J-modulation experiment is shown below:		which sets Delta from 0.0005 to 0.014, corresponding to J modulating delays from 1 to 28 msec. At least 3 modulation points are needed to extract the coupling constant, along with <sup>15</sup>N T<sub>2</sub> and a parameter related to pulse imperfection. It is recommended to take more than 3 points to get an estimation of experimental error. The maximum delay (28 msec in this case) should be bigger than 3/(2J) ( ~16 msec in case of JNH) to make sure the modulation curve crosses zero at least twice (Tjandra et al.). Our simulation shows that the modulation interval should not be close to 1/J (~10ms for JNH),  i.e. the stepsize for Delta should not be close to ~5 msec.  An example of the J-modulation experiment is shown below:

	[[Image:Vnmrj-Jmod.png\|Vnmrj-Jmod.png]]		[[Image:Vnmrj-Jmod.png\|Vnmrj-Jmod.png]]

Kpederson: /* Pulse Sequence (J H-N) */

2013-12-18T20:33:52Z

Pulse Sequence (J H-N)

← Older revision		Revision as of 20:33, 18 December 2013
Line 5:		Line 5:
	A series of 2D experiments should be acquired with the J modulation delay (Delta) set to different values, preferably in an interleaved fashion. (Note that “Delta” is half the total modulation delay.)  For example, in Vnmr, this can be realized by:		A series of 2D experiments should be acquired with the J modulation delay (Delta) set to different values, preferably in an interleaved fashion. (Note that “Delta” is half the total modulation delay.)  For example, in Vnmr, this can be realized by:
	<pre>Delta=(0.0005,0.002,0.0035,0.0062,0.0073,0.0084,0.0125,0.014)</pre>		<pre>Delta=(0.0005,0.002,0.0035,0.0062,0.0073,0.0084,0.0125,0.014)</pre>
	which sets Delta from 0.0005 to 0.014, corresponding to J modulating delays from 1 to 28 msec. At least 3 modulation points are needed to extract the coupling constant, along with <sup>15</sup>N T<sub>2</sub> and a parameter related to pulse imperfection. It is recommended to take more than 3 points to get an estimation of experimental error. The maximum delay (28 msec in this case) should be bigger than 3/(2J) ( ~16 msec in case of JNH) to make sure the modulation curve crosses zero at least twice (Tjandra et al.). Our simulation shows that the modulation interval should not be close to 1/J (~10ms for JNH),  i.e. the stepsize for Delta should not be close to ~5 msec.  An example of the J-modulation experiment is shown below:		which sets Delta from 0.0005 to 0.014, corresponding to J modulating delays from 1 to 28 msec. At least 3 modulation points are needed to extract the coupling constant, along with <sup>15</sup>N T<sub>2</sub> and a parameter related to pulse imperfection. It is recommended to take more than 3 points to get an estimation of experimental error. The maximum delay (28 msec in this case) should be bigger than 3/(2J) ( ~16 msec in case of JNH) to make sure the modulation curve crosses zero at least twice.<ref>Tjandra N. et al., JACS (1996), 118, 6364-72</ref> (Tjandra et al.). Our simulation shows that the modulation interval should not be close to 1/J (~10ms for JNH),  i.e. the stepsize for Delta should not be close to ~5 msec.  An example of the J-modulation experiment is shown below:

	[[Image:Vnmrj-Jmod.png\|Vnmrj-Jmod.png]]		[[Image:Vnmrj-Jmod.png\|Vnmrj-Jmod.png]]

Kpederson at 20:33, 18 December 2013

2013-12-18T20:33:01Z

← Older revision		Revision as of 20:33, 18 December 2013
Line 1:		Line 1:
	=== '''Pulse Sequence (J H-N)''' ===		=== '''Pulse Sequence (J H-N)''' ===

	The sequence is modified from the fast HSQC sequence (gNfhsqc) in Varian BioPack).<ref>Tjandra N. et al, JACS (1996), 118, 6364-72</ref><br>		The sequence is modified from the fast HSQC sequence (gNfhsqc) in Varian BioPack).<ref>Tjandra N. et al., JACS (1996), 118, 6364-72</ref><br>

	A series of 2D experiments should be acquired with the J modulation delay (Delta) set to different values, preferably in an interleaved fashion. (Note that “Delta” is half the total modulation delay.)  For example, in Vnmr, this can be realized by:		A series of 2D experiments should be acquired with the J modulation delay (Delta) set to different values, preferably in an interleaved fashion. (Note that “Delta” is half the total modulation delay.)  For example, in Vnmr, this can be realized by:

Kpederson at 20:31, 18 December 2013

2013-12-18T20:31:54Z

← Older revision		Revision as of 20:31, 18 December 2013
Line 1:		Line 1:
	=== '''Pulse Sequence (J H-N)''' ===		=== '''Pulse Sequence (J H-N)''' ===

	The sequence is modified from the fast HSQC sequence (gNfhsqc) in Varian BioPack).<ref>Tjandra N. et al, JACS (1996), 118, 6364-72</ref><br>		The sequence is modified from the fast HSQC sequence (gNfhsqc) in Varian BioPack).<ref>Tjandra N. et al, JACS (1996), 118, 6364-72</ref><br>

	A series of 2D experiments should be acquired with the J modulation delay (Delta) set to different values, preferably in an interleaved fashion. (Note that “Delta” is half the total modulation delay.)  For example, in Vnmr, this can be realized by:		A series of 2D experiments should be acquired with the J modulation delay (Delta) set to different values, preferably in an interleaved fashion. (Note that “Delta” is half the total modulation delay.)  For example, in Vnmr, this can be realized by:
Line 88:		Line 88:
	<br>		<br>

	#1<span style="white-space:pre~~" class="Apple-tab-span~~"> </span>0.001		#1<span class="Apple-tab-span" style="white-space:pre"> </span>0.001
	#2<span style="white-space:pre~~" class="Apple-tab-span~~"> </span>0.004		#2<span class="Apple-tab-span" style="white-space:pre"> </span>0.004
	#3<span style="white-space:pre~~" class="Apple-tab-span~~"> </span>0.007		#3<span class="Apple-tab-span" style="white-space:pre"> </span>0.007
	#4<span style="white-space:pre~~" class="Apple-tab-span~~"> </span>0.0124		#4<span class="Apple-tab-span" style="white-space:pre"> </span>0.0124
	#5<span style="white-space:pre~~" class="Apple-tab-span~~"> </span>0.0146		#5<span class="Apple-tab-span" style="white-space:pre"> </span>0.0146
	#6<span style="white-space:pre~~" class="Apple-tab-span~~"> </span>0.0168		#6<span class="Apple-tab-span" style="white-space:pre"> </span>0.0168
	#7<span style="white-space:pre~~" class="Apple-tab-span~~"> </span>0.025		#7<span class="Apple-tab-span" style="white-space:pre"> </span>0.025
	#8<span style="white-space:pre~~" class="Apple-tab-span~~"> </span>0.028		#8<span class="Apple-tab-span" style="white-space:pre"> </span>0.028

	<br>		<br>
Line 105:		Line 105:
	To measure the intensity of each peak click the “Measure All” button.  The graph to the right will show points indicative of a decaying cosine function. You can click through the peaks to see each peak using the up and down arrows.  Unfortunately, the equation to fit this type of data has not yet been placed in NMRViewJ, but it will be available in a future version.  For now, the data should be saved using the "Save Table" option and will be analyzed separately.		To measure the intensity of each peak click the “Measure All” button.  The graph to the right will show points indicative of a decaying cosine function. You can click through the peaks to see each peak using the up and down arrows.  Unfortunately, the equation to fit this type of data has not yet been placed in NMRViewJ, but it will be available in a future version.  For now, the data should be saved using the "Save Table" option and will be analyzed separately.

			<br>

	=== '''Curve Fitting and RDC Calculation''' ===		=== '''Curve Fitting and RDC Calculation''' ===
Line 125:		Line 126:

	To calculate RDCs from isotropic and aligned coupling data: [[Media:I-jmod.txt\|i-jmod.txt]] (Change extension to .tcl to run)<br>		To calculate RDCs from isotropic and aligned coupling data: [[Media:I-jmod.txt\|i-jmod.txt]] (Change extension to .tcl to run)<br>



			=== References ===

			<references />

	<br> <br> <br> Updated by Hsiau-Wei Lee, 2011		<br> <br> <br> Updated by Hsiau-Wei Lee, 2011

	Updated by Kari Pederson, 2013		Updated by Kari Pederson, 2013

Kpederson at 20:30, 18 December 2013

2013-12-18T20:30:15Z

← Older revision		Revision as of 20:30, 18 December 2013
Line 1:		Line 1:
	=== '''Pulse Sequence (J H-N)''' ===		=== '''Pulse Sequence (J H-N)''' ===

	The sequence is modified from the fast HSQC sequence (gNfhsqc) in Varian BioPack. ~~For details see~~ Tjandra N. et al, ''JACS ''(1996), 118, 6364-72~~.   ~~		The sequence is modified from the fast HSQC sequence (gNfhsqc) in Varian BioPack).<ref>Tjandra N. et al, JACS (1996), 118, 6364-72</ref><br>

	A series of 2D experiments should be acquired with the J modulation delay (Delta) set to different values, preferably in an interleaved fashion. (Note that “Delta” is half the total modulation delay.)  For example, in Vnmr, this can be realized by:		A series of 2D experiments should be acquired with the J modulation delay (Delta) set to different values, preferably in an interleaved fashion. (Note that “Delta” is half the total modulation delay.)  For example, in Vnmr, this can be realized by:
Line 27:		Line 27:
	#Incorrect setting of Delta step size (should NOT be around 5ms)		#Incorrect setting of Delta step size (should NOT be around 5ms)
	#Incomplete modulation curve. (at least two zero crossings are required)		#Incomplete modulation curve. (at least two zero crossings are required)


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