CYANA Command: enoe twospin: Difference between revisions

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== Parameters ==
== Parameters ==
; b0field =''real'': (required)
; time =''real'', coma separated list: (required)


; b0field =''real'': (required)
; tauc =''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 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 '''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 parameter '''b0field''' is the field strength [MHz].
The parameter '''labil''' is to specify atoms considered labil.
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).

Latest revision as of 16:02, 11 September 2019

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Parameters

b0field =real
(required)
time =real, coma separated list
(required)


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

Description

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 * read pdb.

The parameter b0field is the field strength [MHz]. 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 parameter labil is to specify atoms considered labil.

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