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.
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
69.HN:71.HN
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)
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.
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 In such cases the ppm file is no longer valid for folded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