CYANA Command: enoe spindiff: Difference between revisions
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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 correlation time [ | 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 '''maxdist''' is the size of the spheres centered at spin i and j. | ||
Revision as of 16:45, 17 January 2019
Parameters
- mode =integer
- (default: 1)
- b0field =real
- (default: none)
- tauc =real
- (default: none)
- maxdist =real
- (default: 6.5A)
- rmode =integer
- (default: 1)
Description
This command performs the spin diffusion calculations within the eNORA routine.
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:1, TSS: 2). 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).
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.