NOE script mode - the NOE calculation

At this point the NOE can be calculated. The user function

[firstnumber=33]
# Calculate the NOEs.
minimise.calculate()

will calculate both the NOE and the errors. The NOE value will be calculated using the formula

NOE = $\displaystyle {\frac{{I_{sat}}}{{I_{ref}}}}$, (6.1)

where Isat is the intensity of the peak in the saturated spectrum and Iref is that of the reference spectrum. The error is calculated by

σNOE = $\displaystyle \sqrt{{\frac{(\sigma_{sat} \cdot I_{ref})^2 + (\sigma_{ref} \cdot I_{sat})^2}{I_{ref}}}}$, (6.2)

where σsat and σref are the peak intensity errors in the saturated and reference spectra respectively. To create a file of the NOEs the command

[firstnumber=36]
# Save the NOEs.
value.write(param='noe', file='noe.out', force=True)

will create a file called noe.out with the NOE values and errors. The force flag will cause any file with the same name to be overwritten. An example of the format of noe.out is

# mol_name          res_num  res_name  spin_num  spin_name  value                  error                   
Ap4Aase_new_3_mol1  1        GLY       1         N          None                   None                    
Ap4Aase_new_3_mol1  2        PRO       11        N          None                   None                    
Ap4Aase_new_3_mol1  3        LEU       28        N          None                   None                    
Ap4Aase_new_3_mol1  4        GLY       51        N          -0.038921946984531344  0.019031770246176943    
Ap4Aase_new_3_mol1  5        SER       59        N          -0.312404225679127     0.018596937298386886    
Ap4Aase_new_3_mol1  6        MET       71        N          -0.42850831873249773   0.02525856323041225     
Ap4Aase_new_3_mol1  7        ASP       91        N          -0.5305492810313481    0.027990623144176396    
Ap4Aase_new_3_mol1  8        SER       104       N          -0.5652842977581912    0.021706121467731133    
Ap4Aase_new_3_mol1  9        PRO       116       N          None                   None                    
Ap4Aase_new_3_mol1  10       PRO       133       N          None                   None                    
Ap4Aase_new_3_mol1  11       GLU       150       N          None                   None                    
Ap4Aase_new_3_mol1  12       GLY       167       N          -0.7036626368123614    0.04681370194503697     
Ap4Aase_new_3_mol1  13       TYR       175       N          -0.747464566367261     0.03594640051809186     
Ap4Aase_new_3_mol1  14       ARG       200       N          -0.7524129557634996    0.04957018638401278

Figure 6.1: A Grace plot of the NOE value and error against the residue number. This is an example of the output of the user function grace.write.
\includegraphics[
width=0.9\textwidth,
bb=0 -1 826 521
]{graphics/screenshots/noe_analysis/grace}

The relax user manual (PDF), created 2016-10-28.