CYANA Command: enoe twospin: Difference between revisions

From CYANA Wiki
Jump to navigation Jump to search
No edit summary
No edit summary
Line 2: Line 2:


== Parameters ==
== Parameters ==
; b0field =''real'': (required)
; b0field =''real'': (required)
; tauc =''real'': (required)
; tauc =''real'': (required)
; time =''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")
Line 11: Line 11:
== 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 on 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


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].  
The parameter '''labil''' is to specify atoms considered labil (do not contribute to spin diffusion and will be excluded from pathways).
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=0.02,0.03,0.04,0.05,0.06.
The exception to this is for single mixing time calculations.
 
The parameter '''labil''' is to specify atoms considered labil.

Revision as of 13:43, 1 April 2019

back to complete commands list

Parameters

b0field =real
(required)
tauc =real
(required)
time =real
(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 on 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

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=0.02,0.03,0.04,0.05,0.06. The exception to this is for single mixing time calculations.

The parameter labil is to specify atoms considered labil.

Retrieved from "https://cyana.org/w/index.php?title=CYANA_Command:_enoe_twospin&oldid=9003"