Thanks Vim!
I had only tried to run FC automatically and it wasn't doing anything
particularly useful. I had to abort once because I chose a bad option, but
then your suggestion seems to have worked pretty well - I only have 9
unassigned resonances now, some of which I suspect are amide sidechain
protons that may have had different assignments in different spectra of
the Sparky project.
If I could offer two suggestions for future improvement:
1. The match resonances popup didn't have a good option for doing
everything all at once; where there were one or more residues with no
"mismatched" shifts there was a gap and I had to run linkResonances 8 or 9
times to get everything. Later runs went faster though as it learned about
each amino acid type, and this was quicker and less error prone that
fixing 200+ assignments manually.
2. After fixing the atom types (Hba/Hbb -> HB2/HB3 in your example), I got
a number of popups about having only one prochiral and asking if the
second should be assigned to the same shift or left unassigned. Is it
possible to add an option to leave everything missing as unassigned? While
I'm sure most of them probably are degenerate, I like to leave unobserved
shifts unassigned
Cheers,
Andrew
--
Dr. Andrew Fowler | University of Iowa
Associate Director | B291 Carver Biomedical Research
Building
Medical NMR Facility | Iowa City, IA 52242
319-384-2937 (office) | 319-335-7273 (fax)
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On 3/10/11 2:13 AM, "Wim Vranken" <[log in to unmask]> wrote:
>Hi Andrew,
>
>I fear you prepared too carefully: the FC does not recognize HBa/HBb
>type naming because it's not in use anywhere except 'inside' CCPN as
>it were.
>
>At this point your assignments should be in CCPN but are not linked to
>the atoms - you can try to rerun linkResonances (from Process->Run
>linkresonances, say No to the question asking you to run it
>automatically, after a couple of other questions you should get popups
>asking you what the HBb/HBa names mean in terms of atom assignment -
>link them to the HB2/HB3 option in the atom names dropdown, same for
>all other ones).
>
>Hope that helps,
>
>Wim
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