CYANA Command: enoe spindiff - Revision history

Dean: /* Description */

2020-02-19T11:51:40Z

Description

← Older revision		Revision as of 13:51, 19 February 2020
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	For the full relaxation matrix approach to spin-diffusion approximation we use the multi-spin Solomon equation to express the mixing time-dependence of the NOESY intensities. In the FRM approach, the buildup intensities containing spin-diffusion are calculated for all spins within the spheres centered at spins i and j (Orts et al. 2012).		For the full relaxation matrix approach to spin-diffusion approximation we use the multi-spin Solomon equation to express the mixing time-dependence of the NOESY intensities. In the FRM approach, the buildup intensities containing spin-diffusion are calculated for all spins within the spheres centered at spins i and j (Orts et al. 2012).

	The parameter '''mode''' set to perform an independent FRM calculation (FRM: mode=3) calculates NOE intensities for a single mixing time specified, for purposes other than spin diffusion calculations, i.e. to write out a peak list with intensities obtained from FMR calculations, see *[[CYANA Command: enoe ~~intensities~~\|enoe ~~intensities~~]].		The parameter '''mode''' set to perform an independent FRM calculation (FRM: mode=3) calculates NOE intensities for a single mixing time specified, for purposes other than spin diffusion calculations, i.e. to write out a peak list with intensities obtained from FMR calculations, see *[[CYANA Command: enoe vaslues\|enoe values]].

	With the three-spin system (TSS, mode=2) approach, we follow a strategy in which spin-diffusion contributions are obtained from the summed contributions of the exact solutions of three-spin systems ijk (Vögeli et al. 2010) for all neighboring spins k within the cross section of the spheres centered at spin i and j. Importantly, scaling the contribution to spin-diffusion from spin k by its protonation level allows the setting of individual, spin specific deuteration levels in sample specific manner corresponding i.e. to methyl-group specific labeling schemes, see *[[CYANA Command: atoms set\|atoms set]].		With the three-spin system (TSS, mode=2) approach, we follow a strategy in which spin-diffusion contributions are obtained from the summed contributions of the exact solutions of three-spin systems ijk (Vögeli et al. 2010) for all neighboring spins k within the cross section of the spheres centered at spin i and j. Importantly, scaling the contribution to spin-diffusion from spin k by its protonation level allows the setting of individual, spin specific deuteration levels in sample specific manner corresponding i.e. to methyl-group specific labeling schemes, see *[[CYANA Command: atoms set\|atoms set]].

Dean: /* Parameters */

2019-09-11T14:54:52Z

Parameters

← Older revision		Revision as of 16:54, 11 September 2019
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	; b0field =''real'': (required)		; b0field =''real'': (required)
	~~; tauc =''real'': (required)~~
	; time =''real'', coma separated list: (required)		; time =''real'', coma separated list: (required)
	; maxdist =''real'': (default: ''6.5A'')		; maxdist =''real'': (default: ''6.5A'')

Dean: /* Description */

2019-04-01T15:25:38Z

Description

← Older revision		Revision as of 17:25, 1 April 2019
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	This command performs the spin diffusion calculations within the eNORA routine (with mode=1 or 2, see below) or performs an independent (mode=3) full relaxation matrix (FRM) calculation to be used for purposes other than spin diffusion calculations within the eNORA routine (see below).		This command performs the spin diffusion calculations within the eNORA routine (with mode=1 or 2, see below) or performs an independent (mode=3) full relaxation matrix (FRM) calculation to be used for purposes other than spin diffusion calculations within the eNORA routine (see below).

	There are two different approaches to determine spin-diffusion contributions to cross-peak buildups, both of which require PDB coordinates of a previously determined structure (a conventional NMR structure or an X-ray structure). Usually the lowest energy model of structure bundles is used for spin-diffusion calculation; however, averaging of spin-diffusion over individual conformers is possible, depending on how many structures were ~~read~~, see		There are two different approaches to determine spin-diffusion contributions to cross-peak buildups, both of which require PDB coordinates of a previously determined structure (a conventional NMR structure or an X-ray structure). Usually the lowest energy model of structure bundles is used for spin-diffusion calculation; however, averaging of spin-diffusion over individual conformers is possible, depending on how many structures were selected, see * [[CYANA Command: structures select\|structures select]].

	The parameter '''mode''' is used to select the spin diffusion correction method (FRM: mode=1, TSS: mode=2).		The parameter '''mode''' is used to select the spin diffusion correction method (FRM: mode=1, TSS: mode=2).

Dean: /* Description */

2019-04-01T15:24:17Z

Description

← Older revision		Revision as of 17:24, 1 April 2019
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	The parameter '''tauc''' is the overall correlation time [ns].		The parameter '''tauc''' is the overall correlation time [ns].
	The parameter '''time''' is the mixing time [s], usually given as a coma separated vector with mixing time's sorted in ascending order, i.e. time=0.02,0.03,0.04,0.05.		The parameter '''time''' is the mixing time [s], usually given as a coma separated vector with mixing time's sorted in ascending order, i.e. time=0.02,0.03,0.04,0.05.
	~~The exception to this is for single mixing time calculations performed with mode=3.~~

	The parameter '''maxdist''' is the size of the spheres centered at spin i and j.		The parameter '''maxdist''' is the size of the spheres centered at spin i and j.

Dean: /* Description */

2019-04-01T15:23:15Z

Description

← Older revision		Revision as of 17:23, 1 April 2019
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	The parameter '''mode''' is used to select the spin diffusion correction method (FRM: mode=1, TSS: mode=2).		The parameter '''mode''' is used to select the spin diffusion correction method (FRM: mode=1, TSS: mode=2).
	For the full relaxation matrix ~~(FRM, mode=1)~~ approach to spin-diffusion approximation we use the multi-spin Solomon equation to express the mixing time-dependence of the NOESY intensities. In the FRM approach, the buildup intensities containing spin-diffusion are calculated for all spins within the spheres centered at spins i and j (Orts et al. 2012).		For the full relaxation matrix approach to spin-diffusion approximation we use the multi-spin Solomon equation to express the mixing time-dependence of the NOESY intensities. In the FRM approach, the buildup intensities containing spin-diffusion are calculated for all spins within the spheres centered at spins i and j (Orts et al. 2012).

	The parameter '''mode''' set to perform an independent FRM calculation (FRM: mode=3) calculates NOE intensities for a single mixing time specified, for purposes other than spin diffusion calculations, i.e. to write out a peak list with intensities obtained from FMR calculations, see *[[CYANA Command: enoe intensities\|enoe intensities]].		The parameter '''mode''' set to perform an independent FRM calculation (FRM: mode=3) calculates NOE intensities for a single mixing time specified, for purposes other than spin diffusion calculations, i.e. to write out a peak list with intensities obtained from FMR calculations, see *[[CYANA Command: enoe intensities\|enoe intensities]].

Dean: /* Description */

2019-04-01T15:22:22Z

Description

← Older revision		Revision as of 17:22, 1 April 2019
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	The parameter '''mode''' set to perform an independent FRM calculation (FRM: mode=3) calculates NOE intensities for a single mixing time specified, for purposes other than spin diffusion calculations, i.e. to write out a peak list with intensities obtained from FMR calculations, see *[[CYANA Command: enoe intensities\|enoe intensities]].		The parameter '''mode''' set to perform an independent FRM calculation (FRM: mode=3) calculates NOE intensities for a single mixing time specified, for purposes other than spin diffusion calculations, i.e. to write out a peak list with intensities obtained from FMR calculations, see *[[CYANA Command: enoe intensities\|enoe intensities]].

	With the three-spin system (TSS, mode=2) approach, we follow a strategy in which spin-diffusion contributions are obtained from the summed contributions of the exact solutions of three-spin systems ijk (Vögeli et al. 2010) for all neighboring spins k within the cross section of the spheres centered at spin i and j. Importantly, scaling the contribution to spin-diffusion from spin k by its protonation level allows the setting of individual, spin specific deuteration levels in sample specific manner corresponding i.e. to methyl-group specific labeling schemes, see [[CYANA Command: atoms set\|atoms set]].		With the three-spin system (TSS, mode=2) approach, we follow a strategy in which spin-diffusion contributions are obtained from the summed contributions of the exact solutions of three-spin systems ijk (Vögeli et al. 2010) for all neighboring spins k within the cross section of the spheres centered at spin i and j. Importantly, scaling the contribution to spin-diffusion from spin k by its protonation level allows the setting of individual, spin specific deuteration levels in sample specific manner corresponding i.e. to methyl-group specific labeling schemes, see *[[CYANA Command: atoms set\|atoms set]].

	The parameter '''b0field''' is the field strength [MHz].		The parameter '''b0field''' is the field strength [MHz].

Dean: /* Description */

2019-04-01T15:13:42Z

Description

← Older revision		Revision as of 17:13, 1 April 2019
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	The parameter '''b0field''' is the field strength [MHz].		The parameter '''b0field''' is the field strength [MHz].
	The parameter '''tauc''' is the overall correlation time [ns].		The parameter '''tauc''' is the overall correlation time [ns].
	The parameter '''time''' is the mixing time [s], usually given as a coma separated vector with mixing time's sorted in ascending order, i.e. time=0.02,0.03,0.04,0.05~~,0.06~~.		The parameter '''time''' is the mixing time [s], usually given as a coma separated vector with mixing time's sorted in ascending order, i.e. time=0.02,0.03,0.04,0.05.
	The exception to this is for single mixing time calculations performed with mode=3.		The exception to this is for single mixing time calculations performed with mode=3.

Dean: /* Parameters */

2019-04-01T15:11:27Z

Parameters

← Older revision		Revision as of 17:11, 1 April 2019
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	; b0field =''real'': (required)		; b0field =''real'': (required)
	; tauc =''real'': (required)		; tauc =''real'': (required)
	; time =''real'': (required)		; time =''real'', coma separated list: (required)
	; maxdist =''real'': (default: ''6.5A'')		; maxdist =''real'': (default: ''6.5A'')

Dean at 12:36, 1 April 2019

2019-04-01T12:36:31Z

← Older revision		Revision as of 14:36, 1 April 2019
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	For the full relaxation matrix (FRM, mode=1) approach to spin-diffusion approximation we use the multi-spin Solomon equation to express the mixing time-dependence of the NOESY intensities. In the FRM approach, the buildup intensities containing spin-diffusion are calculated for all spins within the spheres centered at spins i and j (Orts et al. 2012).		For the full relaxation matrix (FRM, mode=1) approach to spin-diffusion approximation we use the multi-spin Solomon equation to express the mixing time-dependence of the NOESY intensities. In the FRM approach, the buildup intensities containing spin-diffusion are calculated for all spins within the spheres centered at spins i and j (Orts et al. 2012).

	The parameter '''mode''' set to perform an independent FRM calculation (FRM: mode=3) calculates NOE intensities ~~per~~ mixing time specified for purposes other than spin diffusion calculations, i.e. write out a peak list with intensities obtained from FMR calculations, see *[[CYANA Command: enoe intensities\|enoe intensities]].		The parameter '''mode''' set to perform an independent FRM calculation (FRM: mode=3) calculates NOE intensities for a single mixing time specified, for purposes other than spin diffusion calculations, i.e. to write out a peak list with intensities obtained from FMR calculations, see *[[CYANA Command: enoe intensities\|enoe intensities]].

	With the three-spin system (TSS, mode=2) approach, we follow a strategy in which spin-diffusion contributions are obtained from the summed contributions of the exact solutions of three-spin systems ijk (Vögeli et al. 2010) for all neighboring spins k within the cross section of the spheres centered at spin i and j. Importantly, scaling the contribution to spin-diffusion from spin k by its protonation level allows the setting of individual, spin specific deuteration levels in sample specific manner corresponding i.e. to methyl-group specific labeling schemes, see [[CYANA Command: atoms set\|atoms set]].		With the three-spin system (TSS, mode=2) approach, we follow a strategy in which spin-diffusion contributions are obtained from the summed contributions of the exact solutions of three-spin systems ijk (Vögeli et al. 2010) for all neighboring spins k within the cross section of the spheres centered at spin i and j. Importantly, scaling the contribution to spin-diffusion from spin k by its protonation level allows the setting of individual, spin specific deuteration levels in sample specific manner corresponding i.e. to methyl-group specific labeling schemes, see [[CYANA Command: atoms set\|atoms set]].
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	The parameter '''b0field''' is the field strength [MHz].		The parameter '''b0field''' is the field strength [MHz].
	The parameter '''tauc''' is the overall correlation time [ns].		The parameter '''tauc''' is the overall correlation time [ns].
			The parameter '''time''' is the mixing time [s], usually given as a coma separated vector with mixing time's sorted in ascending order, i.e. time=0.02,0.03,0.04,0.05,0.06.
			The exception to this is for single mixing time calculations performed with mode=3.

	The parameter '''maxdist''' is the size of the spheres centered at spin i and j.		The parameter '''maxdist''' is the size of the spheres centered at spin i and j.
	The parameter '''labil''' is to specify atoms considered labil (do not contribute to spin diffusion and will be excluded from pathways).		The parameter '''labil''' is to specify atoms considered labil (do not contribute to spin diffusion and will be excluded from pathways).

Dean at 12:32, 1 April 2019

2019-04-01T12:32:22Z

← Older revision		Revision as of 14:32, 1 April 2019
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	; b0field =''real'': (required)		; b0field =''real'': (required)
	; tauc =''real'': (required)		; tauc =''real'': (required)
			; time =''real'': (required)
	; maxdist =''real'': (default: ''6.5A'')		; maxdist =''real'': (default: ''6.5A'')