Hi
I am having difficulties using FormatConverter to read in a cyana assignment
table (xeasy-final.prot) after a cyana calculation into Analysis.
I have non-stereo specifically assignments in my project and I export them
in cyana2.1 format to use in Cyana.
eg. In my shiftlist I have assignments
Hda* 0.734
Hdb* 0.835
Cda 22.928
Cdb 24.882
I export these and in my exported cyana shift list these are mapped to QD1
and QD2 (a to 1, b to 2)
QD1 0.734
QD2 0.835
CD1 22.928
CD2 24.882
After the cyana calculation "Atomes with consistent swapping in 20 or more
strcutures" get swopped such that
QD1 0.835
QD2 0.734
CD1 24.882
CD2 22.928
However, now when I attempt to read in my assignment table from the final
cycle of the cyana calculation (xeasy-final.prot) and the assigned peak list
(13c-xeasy-cycle7.peaks) into Analysis using FormatConverter (using
Import-Combined files-chemical shift and peaks) I run into the problem that
the mapping of these swopped assignments get muddled. It now gives the
values as
Hda* 0.835
Hdb* 0.734
Cda 24.882
Cdb 22.928
If I try to merge the imported shift list and the original shift list it
combines Hda* at 0.734 with Hda* at 0.835 and gives large standard
deviations. Essentially the two shift lists are incompatible. This problem
is the same for all stereospecific atoms.
My question is how does Format Converter map 1 &2 in cyana table to A & B
in Analysis? How does it know which one is which? I would have expected it
would have matched them based on chemical shift (to give smallest SD) but
this doesnt seem to be the case?
Cheers
Ben
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