Thanks, Tim.
I now understand the rational behind a and b ambiguity. If the
proton/carbon link through the experiment type works well, this is a
very useful option for the assignments.
One thing would be nice to have in addition to the strip plot - tile
display for HSQC spectrum. Then I can get a strip plot for the whole
residue plus the positions of 13C-HSQC peaks for each carbon/proton
pair. As I remember, you mentioned that the tools for a tile plot are
implemented, but not in use currently.
Cheers
Igor
Tim Stevens wrote:
>>The functions you sent me work perfectly, but I still don't fully
>>understand the use of a and b in atom names. I assumed that they are
>>alternatives to setereospecific assignments and should be used when you
>>don't have the information for stereospecific assignments, to connect
>>proton and carbon atoms.
>>
>>
>
>The "a" and "b" labels are just to give a different identifier compared to
>the stereospecific ones. They are not for the user to connect carbons to
>protons, this connection comes automatically from knowledge of experiment
>types.
>
>There is a dedicated link in the data model that can be used to describe
>covalently bound resonances (whether assigned or not). However, this is
>not yet used in Analysis. It will go in, but isn't something I want to
>rush.
>
>
>
>
>>This, however, doesn't agree with the behavior of
>>getProtonResFromCarbRes() function, which returns both "a" and "b"
>>protons for each carbon.
>>
>>
>
>A Val Cga assignment means a connection to both Cg1 and Cg2 - because it
>could be either. This is why both sets of protons are picked up. To use
>the connectivity information that results from peak assignment I suggest
>trying the function:
>
> ccpnmr.analysis.AssignmentBasic getOnebondResonance()
>
>Or you could set and use Resonance.covalentlyBound in your scripts.
>
>Hope this helps,
>
>T.
>
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>
>
--
Dr. Igor Barsukov
Biological NMR Centre,
University of Leicester
PO Box 138,
University Road,
Henry Wellcome Building,
Leicester LE1 9HN
UK
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