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> 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. ------------------------------------------------------------------------------- Dr Tim Stevens Email: [log in to unmask] Department of Biochemistry [log in to unmask] University of Cambridge Phone: +44 1223 766022 (office) 80 Tennis Court Road +44 7816 338275 (mobile) Old Addenbrooke's Site +44 1223 364613 (home) Cambridge CB2 1GA WWWeb: http://www.bio.cam.ac.uk/~tjs23 United Kingdom http://www.pantonia.co.uk ------------------------------------------------------------------------------- ------ +NH3CH(CH(CH3)OH)C(O)NHCH(CH(CH3)CH2CH3)C(O)NHCH(CH2CH2SCH3)CO2- ------- -------------------------------------------------------------------------------