Mike's Perl and NAWK scripts for converting NMRView to ARIA1.1

I have written the following scripts to help deal more easily with conversion to aria1.1 from nmrview.
A big caveat is my skills of programming and I would recommend seeing me before use, since some files
depend on others. In addition, the conversion of XPK files to correct methyl format is sequence dependent.
It needs to be altered for your sequence.

1)    runall

What does it do?

Convert an NMRView xpk file to aria1.1 format (uncalibrated).

In doing this it will also:

Keep manually assigned peaks in NMRVIEW with a weighting of 1.1
Deal with manual ambiguous assignments made in NMRview (see below for more info)
Converts methyl resonances to correct nomenclature (e.g. HG21 to HG2#, etc.) At present the script need to be altered for your protein sequence (lack of programming skills here)

Some other options:

It will ask for a tolerance in each dimension (+ and - the value given).
It will also ask for a ppm range to filter out water peaks if necessary. Manually assigned peaks are not removed.
It will also ask for integration or volumes. USE INTEGRATION AT PRESENT.

note on manual ambiguous assignments:

I have included an option to deal with ambiguous assignments that you have made in NMRVIEW. For this to work an ambiguous assignment can only occur in the 1H dimension (i.e. the "NOE" peak). Only two possibilities can be assigned (after all this is really what ARIA should do).
For this to work successfully the two possibilities must be separated by a "colon" in the xpk file
e.g. if  the noe peak goes to HN of 69 and 71

2) nmrviewppm.atomname.pl

What does it do?

Alters atom naming of the ppm (shift) file in nmrview. e.g. if you used only one name for methyls (HD11 becomes HD11. HD12, HD13).
Also it will add another atom if only a single shift value was given for degenerate methylene's (e.g. HB1/HB2). Note your nmrview seq file must be in the same directory. use this before converting to aria format (see 3)

3) nmrppm2ariashift.s

What does it do?

Will take the nmrview ppm shift file into aria format. It is recommended that you first use nmrviewppm.atomname.pl (see 2 above) before doing this.

4) conv13cppm.s

What does it do?

When you analyse a 13C NOESY, you normally folded the 13C dimension. In such cases the ppm file is no longer valid for folded resonances.
This script will "fold" the 13C ppm values to the correct values for aria analysis. Note you will need to alter the folded values for your own folding scheme.

download the scripts and some example data