CYANA Command: enoe twospin - Revision history

Dean at 15:02, 11 September 2019

2019-09-11T15:02:51Z

← Older revision		Revision as of 17:02, 11 September 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 '''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.		The exception to this is for single mixing time calculations.

	The parameter '''labil''' is to specify atoms considered labil.		The parameter '''labil''' is to specify atoms considered labil.

Dean: /* Parameters */

2019-09-11T15:02:26Z

Parameters

← Older revision		Revision as of 17:02, 11 September 2019
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	== Parameters ==		== Parameters ==
	; b0field =''real'': (required)		; b0field =''real'': (required)
	~~; tauc =''real'': (required)~~
	; time =''real'', coma separated list: (required)		; time =''real'', coma separated list: (required)

Dean: /* Description */

2019-04-01T15:12:29Z

Description

← Older revision		Revision as of 17:12, 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.		The exception to this is for single mixing time calculations.

	The parameter '''labil''' is to specify atoms considered labil.		The parameter '''labil''' is to specify atoms considered labil.

Dean at 15:12, 1 April 2019

2019-04-01T15:12:01Z

← Older revision		Revision as of 17:12, 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)

Dean at 12:46, 1 April 2019

2019-04-01T12:46:18Z

← Older revision		Revision as of 14:46, 1 April 2019
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	This command calculates expected two-spin intensities for NOE measurements (direct magnetization transfer, no spin diffusion contributions).		This command calculates expected two-spin intensities for NOE measurements (direct magnetization transfer, no spin diffusion contributions).

	The calculation needs a pdb file with at least one conformer (if multiple conformers are provided, the average values are calculated for the two-spin intensities). The pdb file is read before executing 'enoe twospin', see		The calculation needs a pdb file with at least one conformer (if multiple conformers are provided, the average values are calculated for the two-spin intensities). The pdb file is read before executing 'enoe twospin', see * [[CYANA Command: read pdb\|read pdb]].

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

Dean: /* Description */

2019-04-01T12:44:23Z

Description

← Older revision		Revision as of 14:44, 1 April 2019
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	This command calculates expected two-spin intensities for NOE measurements (direct magnetization transfer, no spin diffusion contributions).		This command calculates expected two-spin intensities for NOE measurements (direct magnetization transfer, no spin diffusion contributions).

	The calculation needs a pdb file with at least one conformer (if multiple conformers are provided, the average values are calculated for the two-spin intensities). The pdb file is read before executing "'enoe twospin'", see		The calculation needs a pdb file with at least one conformer (if multiple conformers are provided, the average values are calculated for the two-spin intensities). The pdb file is read before executing 'enoe twospin', see

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

Dean: /* Description */

2019-04-01T12:43:35Z

Description

← Older revision		Revision as of 14:43, 1 April 2019
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	This command calculates expected two-spin intensities for NOE measurements (direct magnetization transfer, no spin diffusion contributions).		This command calculates expected two-spin intensities for NOE measurements (direct magnetization transfer, no spin diffusion contributions).

	The calculation needs a pdb file with at least on conformer (if multiple conformers are provided, the average values are calculated for the two-spin intensities). The pdb file is read before executing "'enoe twospin'", see		The calculation needs a pdb file with at least one conformer (if multiple conformers are provided, the average values are calculated for the two-spin intensities). The pdb file is read before executing "'enoe twospin'", see

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

Dean at 12:43, 1 April 2019

2019-04-01T12:43:16Z

← Older revision		Revision as of 14:43, 1 April 2019
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	== Parameters ==		== Parameters ==


	; b0field =''real'': (required)		; b0field =''real'': (required)
	; tauc =''real'': (required)		; tauc =''real'': (required)
			; time =''real'': (required)


	; labilatom=''[[atom selection]]'':(default: "HE @ARG + HD2 @ASP + HG @CYS + HE2 @GLU + HE2 @HIS + HG @SER + HG1 @THR + HH @TYR")		; labilatom=''[[atom selection]]'':(default: "HE @ARG + HD2 @ASP + HG @CYS + HE2 @GLU + HE2 @HIS + HG @SER + HG1 @THR + HH @TYR")
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	== Description ==		== Description ==

	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 calculates expected two-spin intensities for NOE measurements (direct magnetization transfer, no spin diffusion contributions).

	~~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

			The calculation needs a pdb file with at least on conformer (if multiple conformers are provided, the average values are calculated for the two-spin intensities). The pdb file is read before executing "'enoe twospin'", see

	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 '''labil''' is to specify atoms considered labil ~~(do not contribute to spin diffusion and will be excluded from pathways)~~.		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.

			The parameter '''labil''' is to specify atoms considered labil.

Dean at 12:31, 1 April 2019

2019-04-01T12:31:22Z

← Older revision		Revision as of 14:31, 1 April 2019
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	== Parameters ==		== Parameters ==

	~~;; mode =''integer'': (default: ''3'')~~

	; b0field =''real'': (required)		; b0field =''real'': (required)
	; tauc =''real'': (required)		; tauc =''real'': (required)
	~~; maxdist =''real'': (default: ''6.5A'')~~

	~~; rmode =''integer'': (default: ''1'')~~

	; labilatom=''[[atom selection]]'':(default: "HE @ARG + HD2 @ASP + HG @CYS + HE2 @GLU + HE2 @HIS + HG @SER + HG1 @THR + HH @TYR")		; labilatom=''[[atom selection]]'':(default: "HE @ARG + HD2 @ASP + HG @CYS + HE2 @GLU + HE2 @HIS + HG @SER + HG1 @THR + HH @TYR")
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	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 read, see

	~~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).

	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]].

	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].
	The parameter '''tauc''' is the overall correlation time [ns].		The parameter '''tauc''' is the overall correlation time [ns].
	~~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).


	~~The parameter '''rmode''' is used to specify if experimental or simulated auto-relaxation (rho) values are used (only TSS approach).~~


	~~The parameter info=full or info=debug may be used to print the simulated buildup values to screen.~~

Dean at 12:29, 1 April 2019

2019-04-01T12:29:33Z

← Older revision		Revision as of 14:29, 1 April 2019
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	== Parameters ==		== Parameters ==

	#; mode =''integer'': (default: ''3'')		;; mode =''integer'': (default: ''3'')

	; b0field =''real'': (required)		; b0field =''real'': (required)