CYANA Command: enoe init: Difference between revisions

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== Parameters ==
== Parameters ==


; normalize=''integer'': (default: ''none'')
; normalize=''integer'': (default: ''1'')
; normed =''integer'': (default: ''none'')
; normed =''integer'': (default: ''1'')
; rhoavg =''real'': (default: ''none'')
; time =''real'', coma separated list: (required)
; time =''string'': (default: ''none'')


== Description ==
== Description ==


Sets new names for the residues, dihedral angles, and atoms in the residue library that are matched by the given atom and/or angle ''selection''.
This command initializes the eNORA routine, fits the diagonal decays to obtain the auto-relaxation (rho) values  and back-predicted diagonal intensities, I(0) values. The routine then normalizes the cross peak intensities with the fitted or user supplied I(0) values and fits the experimental buildups using the fitted or user supplied rho values (see below and *[[CYANA Command: read rho|read rho]]). As input the module requires as many peak-lists (one per mixing time) as there are mixing times specified (see below, parameter: time).
The new names for residues, dihedral angles and atoms are defined by the parameters '''residue''', '''angle''' and '''atom''', respectively. A new residue name is applied to all residue entries for which at least one atom has been selected.
 
The parameters '''residue''', '''angle''' and '''atom''' can take the special value “'''*'''” to reset the corresponding name to the original name that was read from the library file.
The diagonal peak to use for normalization is specified by the parameter '''normalize'''; using the normalize=1 or normalize=2, with the integers referring to the proton dimension in the peak list.
The parameter '''normed''' specifies, if one wants to keep non-normalizable peaks (normed=0) or only peaks that are properly normalized (normed=1).  
 
A spin-type specific value may be calculated to be read in a file containing spin type specific auto-relaxation values, the same file may be used to read spin-type specific I(0) values,  see * [[CYANA Command: read rho|read rho]].
 
The parameter '''time''' specifies the measured NOE mixing times in ascending order [s]. The NOE mixing times are given as a coma separated list, i.e. time=0.02,0.03,0.04,0.05.

Latest revision as of 15:58, 11 September 2019

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Parameters

normalize=integer
(default: 1)
normed =integer
(default: 1)
time =real, coma separated list
(required)

Description

This command initializes the eNORA routine, fits the diagonal decays to obtain the auto-relaxation (rho) values and back-predicted diagonal intensities, I(0) values. The routine then normalizes the cross peak intensities with the fitted or user supplied I(0) values and fits the experimental buildups using the fitted or user supplied rho values (see below and *read rho). As input the module requires as many peak-lists (one per mixing time) as there are mixing times specified (see below, parameter: time).

The diagonal peak to use for normalization is specified by the parameter normalize; using the normalize=1 or normalize=2, with the integers referring to the proton dimension in the peak list. The parameter normed specifies, if one wants to keep non-normalizable peaks (normed=0) or only peaks that are properly normalized (normed=1).

A spin-type specific value may be calculated to be read in a file containing spin type specific auto-relaxation values, the same file may be used to read spin-type specific I(0) values, see * read rho.

The parameter time specifies the measured NOE mixing times in ascending order [s]. The NOE mixing times are given as a coma separated list, i.e. time=0.02,0.03,0.04,0.05.

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