Hi Wim,
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. This, however, doesn't agree with the behavior
of getProtonResFromCarbRes() function, which returns both "a" and "b"
protons for each carbon. This is not exactly what I need. I want to be
able to fix the connection between Cga and Hga, etc. and then just get
Hga from Cga resonance. Should I simply stop using a and b in my
assignments and switch to the stereospecific nomenclature?
Cheers
Igor
Wim Vranken wrote:
>Hi Igor,
>
>Tim will send something based on the Analysis code, but attached two
>low-level functions that do what you ask for (if I understood correctly).
>They're not very error-resistant though... .
>
>
>
>>1. Using an arbitrary assigned resonance as an input, return all
>>resonances assigned to protonated carbons for the residue that the
>>selected resonance belongs to.
>>
>>
>
>In attached file, this is the function getResidueProtCarbResFromRes().
>Note that, to speed things up significantly, you could keep a dictionary
>of the resonance->atom links instead of finding them again each time
>(though the current code is more illustrative I suppose).
>
>
>
>>2. Using carbon resonance as an input, return resonance for the
>>connected protons.
>>
>>
>
>In attached file, this is getProtonResFromCarbRes(). Note that in case of
>an ambiguous assignment, it will return all the possible proton resonances
>(so if you've got an ambiguous CGa for VAL, you'll get the HG1* and HG2*
>resonances back).
>
>The getResonancesForAtoms() function might go into ccp.general.Util, if
>nothing of the kind is there yet...
>
>Hope that helps,
>
>Wim
>
>
--
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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