CYANA Command: enoe spindiff: Difference between revisions
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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 | 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]]. | ||
Latest revision as of 13:51, 19 February 2020
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Parameters
- mode =integer
- (default: 1)
- b0field =real
- (required)
- time =real, coma separated list
- (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")
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).
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 * structures select.
The parameter mode is used to select the spin diffusion correction method (FRM: mode=1, TSS: mode=2). 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 *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 *atoms set.
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 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 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.