Start a new ARIA project with ANSIG data:
- For reading the chemical shifts, specify an ANSIG crosspeaks export file in
the
ppm file
field of each spectrum.
- For reading the NOEs, specify an ANSIG crosspeaks export file or
general NOE file in the
NOE file
field of each spectrum.
- If your ANSIG crosspeaks export file contains more than one spectrum,
you have to split it up in different crosspeaks export files which
contain the NOE spectra. You can use the module SplitAnsigCpeFile.py
from the /aria/python directory.
1. Edit the directory names:
For 2D spectra:
Your ANSIG general NOE file contains lines like this:
2 1 Pro HA 4.532 1 Pro HB1 2.520 4515noesy -1.0 3.7553E-01 8.0960E-01
Each line contains the following fields:
dimensionality, sequence number 1, residue 1, assignment 1, ppm 1,
sequence number 2, residue 2, assignment 2, ppm 2,
peaknumber, spectrum name, mixing time, absolute intensity, relative intensity
Your ANSIG crosspeaks export file contains lines like this:
7.175730E-01 2.128294E+01 1.000000E+00noesy 0 6 3 6 0 6748 044 44 Val Val HG2# HB
Each line contains the following fields:
ppm 1, ppm 2, intensity, spectrum name, symmetry connection, F1
connnections (prev, next), F2 connnections (prev, next),
corresponding connections (prev, next),
aa 1, aa 2,
residue number 1, residue number 2,
atomname 1, atomname 2,
For 3D spectra:
Your ANSIG general NOE file contains lines like this:
3 1 Pro HA 4.532 1 Pro CA 62.79 1 Pro HB1 2.520 4515Cnoesy3 -1.0 3.7553E-01 8.0960E-01
Each line contains the following fields:
dimensionality, sequence number 1, residue 1, assignment 1, ppm 1,
sequence number 2, residue 2, assignment 2, ppm 2,
sequence number 3, residue 3, assignment 3, ppm 3,
peaknumber, spectrum name,
mixing time, absolute intensity, relative intensity
Your ANSIG crosspeaks export file contains lines like this:
7.175730E-01 2.128294E+01 2.005964E+00 1.000000E+00hcchtoc 0 6 3 6 3 0 0 6748 044 44 44 Val Val Val HG2#CG2 HB
Each line contains the following fields:
ppm 1, ppm 2, ppm 3, intensity, spectrum name, symmetry connection, F1
connnections (prev, next), F2 connnections (prev, next), F3 connnections (prev, next),
corresponding connections (prev, next),
aa 1, aa 2, aa3,
residue number 1, residue number 2, residue number 3,
atomname 1, atomname 2, atomname 3
For 4D spectra:
Your ANSIG general NOE file contains lines like this:
4 1 Pro HA 4.532 1 Pro CA 62.79 1 Pro HB1 1 Pro CB 52.13 2.520 4515Cnoesy4 -1.0 3.7553E-01 8.0960E-01
Each line contains the following fields:
dimensionality, sequence number 1, residue 1, assignment 1, ppm 1,
sequence number 2, residue 2, assignment2, ppm 2,
sequence number 3, residue 3, assignment3, ppm 3,
sequence number 4, residue 4, assignment4, ppm 4,
peaknumber, spectrum name, mixing time, absolute intensity, relative intensity
Your ANSIG crosspeaks export file contains lines like this:
7.175730E-01 2.128294E+01 2.005964E+00 3.534624E+01 1.000000E+00hcchtoc 0
6 3 6 3 0 0 0 0 6748 044 44 44 44 Val Val Val Val
HG2#CG2 HB CB
Each line contains the following fields:
ppm 1, ppm 2, ppm 3, ppm 4, intensity, spectrum name, symmetry connection, F1
connnections (prev, next), F2 connnections (prev, next), F3 connnections (prev, next), F4 connnections (prev, next),
corresponding connections (prev, next),
aa 1, aa 2, aa3, aa4,
residue number 1, residue number 2, residue number 3, residue number 4,
atomname 1, atomname 2, atomname 3, atomname 4
Sequence file:
There are three possibilities:
use an ANSIG .seq file
use a CNS sequence file which should only contain amino acids in 3-letter code
(with spaces or linebreaks as dividers) like that: ASP GLU GLY TRP
use a PDB file
- Please take a look at your general NOE files/crosspeak export files
first before filling out the following form.
You have to specify in which column (counted from left to right and from 1 to 4)
the heteronuclei and protons can be found.
- In the 2D case both heteronuclei have to be set to
not available
.
In the 3D case the heteronucleus 2 has to be set to not available
.
- The PPMD values are the deltas for the chemical shifts which build the frequency windows for
the assignment of the NOE peaks.
They have to be specified for every used frequency of all the spectra.
- The segid must have 4 characters or must be blank.
- You have to specify absolute paths for all files and directories.
- Don't use pathnames with more than 80 characters (otherwise CNS will complain).
- Unused fields should be blank.
- Always be careful and take a look at the generated .tbl files in the corresponding spectrum directory.