CYANA Command: enoe spindiff

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Parameters

mode =integer

(default: 1)

b0field =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")

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: 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).

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 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.

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