CYANA Command: enoe reff - Revision history

Dean: /* Description */

2019-09-11T15:01:15Z

Description

← Older revision		Revision as of 17:01, 11 September 2019
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	== Description ==		== Description ==

	This command ~~fits the experimental buildups to obtain~~ the cross-relaxation ~~rates and converts the~~ rates to distances~~. If spin diffusion correction was calculated, the correction is applied to the experimental buildups before fitting the cross-correlation rates~~.		This command converts the cross-relaxation rates to distances.

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

Dean: /* Description */

2019-09-11T14:59:59Z

Description

← Older revision		Revision as of 16:59, 11 September 2019
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	This command fits the experimental buildups to obtain the cross-relaxation rates and converts the rates to distances. If spin diffusion correction was calculated, the correction is applied to the experimental buildups before fitting the cross-correlation rates.		This command fits the experimental buildups to obtain the cross-relaxation rates and converts the rates to distances. If spin diffusion correction was calculated, the correction is applied to the experimental buildups before fitting the cross-correlation rates.

	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~~].

Dean: /* Parameters */

2019-09-11T14:56:33Z

Parameters

← Older revision		Revision as of 16:56, 11 September 2019
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	; b0field =''real'': (required)		; b0field =''real'': (required)
	~~; tauc =''real'': (required)~~

	== Description ==		== Description ==

Dean at 11:40, 21 January 2019

2019-01-21T11:40:46Z

← Older revision		Revision as of 13:40, 21 January 2019
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			[[CYANA Commands\|back to complete commands list]]

	== Parameters ==		== Parameters ==

Dean at 15:04, 17 January 2019

2019-01-17T15:04:59Z

← Older revision		Revision as of 17:04, 17 January 2019
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	== Parameters ==		== Parameters ==

	; b0field =''real'': (~~default: ''none''~~)		; b0field =''real'': (required)
	; tauc =''real'': (~~default: ''none''~~)		; tauc =''real'': (required)

	== Description ==		== Description ==

Dean at 14:51, 17 January 2019

2019-01-17T14:51:30Z

← Older revision		Revision as of 16:51, 17 January 2019
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	== Description ==		== Description ==

	This converts the calculated cross-correlation rates ~~to distances~~.		This command fits the experimental buildups to obtain the cross-relaxation rates and converts the rates to distances. If spin diffusion correction was calculated, the correction is applied to the experimental buildups before fitting the cross-correlation rates.

	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].

Dean at 14:48, 17 January 2019

2019-01-17T14:48:14Z

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 This converts the calculated cross-correlation rates to distances.
 The parameter '''b0field''' is the field strength [MHz].
 The parameter '''tauc''' is the overall correlation time [ns].

Dean at 14:47, 17 January 2019

2019-01-17T14:47:55Z

← Older revision		Revision as of 16:47, 17 January 2019
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	== Parameters ==		== Parameters ==

	; ~~normalize~~=''~~integer'': (default: ''none'')~~		; b0field =''real'': (default: ''none'')
	~~; normed =''integer~~'': (default: ''none'')		; tauc =''real'': (default: ''none'')
	; ~~rhoavg~~ =''real~~'': (default: ''none'')~~
	~~; time =''string~~'': (default: ''none'')

	== Description ==		== Description ==

	This ~~command initializes~~ the ~~eNORA routine, fits the diagonal decays~~ to ~~obtain the auto-relaxation (rho) values and I(0), normalizes the cross peak intensities and fits the experimental buildups~~.		This converts the calculated cross-correlation rates to distances.

	~~The diagonal peak~~ to ~~use for normalization is specified by the parameter '''normalize''', using the integers 1 or 2, with the integers referring~~ to ~~the proton dimension in the~~ peak ~~list.~~		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 '''normed''' specifies~~, ~~if one wants to keep non-normalizable peaks~~ (0) or ~~only peaks that are properly normalized (1~~).

	~~In practice, many diagonal peak decays cannot be fitted (due to spectral overlap, artifacts, etc.):~~		The parameter '''mode''' is used to select the spin diffusion correction method (FRM:1, TSS: 2).
	The parameter '''~~rhoavg~~''' ~~allows~~ the ~~input of an average auto~~-~~relaxation values~~ to ~~be used non specifically [s~~-1].		For the full-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).

	~~A spin-type specific value may be calculated to be read in a file containing spin type specific auto-relaxation values, the same file may be used to read spin-type specific I(0) values,~~
	~~see * [[CYANA Command: read rho\|read rho]].~~

	The parameter '''~~time~~''' ~~specifies~~ the ~~measured NOE mixing times in ascending order~~ [s]. The ~~NOE mixing times are given as a coma separated list,~~ i.e. ~~time~~=~~"0.02,0.04,0~~.~~06"~~		In the TSS (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

			The parameter '''b0field''' is the field strength [MHz].
			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 '''rmode''' is used to specify if experimental or simulated auto-relaxation (rho) values are used.


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

Dean: Created page with " == Parameters == ; normalize=''integer'': (default: ''none'') ; normed =''integer'': (default: ''none'') ; rhoavg =''real'': (default: ''none'') ; time =''string'': (default..."

2019-01-17T14:46:03Z

Created page with " == Parameters == ; normalize=''integer'': (default: ''none'') ; normed =''integer'': (default: ''none'') ; rhoavg =''real'': (default: ''none'') ; time =''string'': (default..."

New page

== Parameters ==

; normalize=''integer'': (default: ''none'')
; normed =''integer'': (default: ''none'')
; rhoavg =''real'': (default: ''none'')
; time =''string'': (default: ''none'')

== Description ==

This command initializes the eNORA routine, fits the diagonal decays to obtain the auto-relaxation (rho) values and I(0), normalizes the cross peak intensities and fits the experimental buildups.

The diagonal peak to use for normalization is specified by the parameter '''normalize''', using the integers 1 or 2, with the integers referring to the proton dimension in the peak list.
The parameter '''normed''' specifies, if one wants to keep non-normalizable peaks (0) or only peaks that are properly normalized (1).

In practice, many diagonal peak decays cannot be fitted (due to spectral overlap, artifacts, etc.):
The parameter '''rhoavg''' allows the input of an average auto-relaxation values to be used non specifically [s-1].

A spin-type specific value may be calculated to be read in a file containing spin type specific auto-relaxation values, the same file may be used to read spin-type specific I(0) values,
see * [[CYANA Command: read rho|read rho]].

The parameter '''time''' specifies the measured NOE mixing times in ascending order [s]. The NOE mixing times are given as a coma separated list, i.e. time="0.02,0.04,0.06"