Missing connections
The user of smartnotebook will most likely suspect a missing connection
when no logical extension to the current chain exists when one is expected.
See the figure below.
Missing connections are going to happen, it is important for the
user to be familiar with this section.
- First, ask yourself how confident you are with the current chain. Were
there reasonable alternatives that you did not explore while you built the
chain? You should really check these out first and make sure they don't
lead to the correct solution.
- Consider the possibility that one of the chemical shifts can be
reasonably assigned outside the default chemical shift range. Try moving
the standard deviation slider of the best fit
window
to a bit higher level and re-do the connection search. You are hoping for
a match that allows you to add several more connections to the chain.
Then your assignment of that particular chemical shift becomes believable.
- Is it possible that the connection chains back to itself? Smartnotebook
is just not capable of handling this
worst case scenario for overlap.
-
If the above has failed, you now have to seriously consider that there
is a mistake in peakpicking.
Smartnotebook provides no tools for finding missing peakpicks, however
nmrview provides some. You could work with the nmrview windows currently
provided (or create new ones) and
manually flip through planes of spectral data looking for the missing
connectivity. If you find the correct pattern, turn on the peak labels
and see which peak or peaks didn't get picked. These peaks need to be
added to your input peakpick files!
If the peaks have been picked make sure the values are close to being
correct. It is possible that what visually looks like a correct pattern
is just outside the pattern error tolerance. Correcting the peak that is
slightly off will fix the problem. If the peak picking is close then
perhaps the software has erred. I will look at such an example if you
send me a screen snapshot of the labelled spectra and the relevant
parts of the peakpick files. At this point you have no choice but
to manually create the missing connection.
-
If you cannot find the pattern even with manual methods, consider the
case that the peaks are overlapped to be indetectable.
Consider your experiment set and whether there are any conditions
which explain why the peaks are not detectable.
If you are updating peaklists, you must either restart snb or go to
the Configure/Update window .
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Questions to:
bionmrwebmaster@biochem.ualberta.ca