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> Am a newbie, trying to work through a few spectra following a recent > (excellent) tutorial session. I'm beginning with an HNCO and HNcaCO, and > can't tell whether the carbonyls should be named "C" or "CO". There seems to > be at least two ways to assign an atom type in the non-root dimension of > these spectra, each giving different atom names: > > 1. r:assign:assign "Set Atom Type" brings up an atom browser, with only "C" > available as the atom type name for the carbonyl carbon. > > 2. m:Assignment:Link Peak Lists "Assign Target Non-root Resonances works > well (and is much faster) but assigns an atom type of "CO". Well it ought to be "C" and only ever so. That is the nomenclature. This has been fixed, en remote, with a patch. Just repeat the Link Peak Lists to put things straight. However this needs thinking about a bit more. What was happening is that the CO came from the atom site name in the reference experiments. Now ideally these could be IUPAC like the rest of CCPN, but "C" in reference experiments means any carbon... Any thoughts Rasmus? Do we need an atomSite.name for any old carbon given we definitely have an isotopeCode? I'm fairly ambivalent, as the 'CO' label is more for a shift range than anything else. Some more things to ponder: From a CA how do I know to go to a CO not a CB with a onebond transfer? What about arginine side chains that crop up in some backbone experiments? T. ------------------------------------------------------------------------------- Dr Tim Stevens Email: [log in to unmask] Department of Biochemistry [log in to unmask] University of Cambridge Phone: +44 1223 766018 (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- ------- -------------------------------------------------------------------------------