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Hi Simon, it is the line-width on a 'per peak' basis, and I do have the error but assumed no-one would be interested so didn't include it! I'll talk to the others about how to report it back for the next release. The error is calculated from successive MCMC samples - it's effectively the standard deviation of many 'fits'. Noise in spectra != noise in line-width, but both are estimated - but then lost as again I didn't think anyone would be interested! I haven't tried using FuDA, but if there are some important things that FuDA can do and the peak separator can't then I'll look into getting that integrated into the open source analysis code. Dan On 25 Nov 2010, at 11:46, S.P. Skinner wrote: > Hi Dan > > The R2 dia is the linewidth as far as I can see, but does the output contain a per peak linewidth, with accompanying error and if so how is the error calculated? Is the noise estimated or is a standard deviation of all peaks used? > > Regards > > Simon > > On 11/25/2010 12:08 PM, Daniel O'Donovan wrote: >> Hi Simon! >> >> If the "R2 dia" is the line-width of the peak-shape (when fitted with a Gaussian or Lorentzian) then yes. If not, then do let me know what that is and I can get on to adding it in. >> >> Best, Dan >> >> On 25 Nov 2010, at 10:55, S.P. Skinner wrote: >> >>> Hi Dan >>> >>> Does it also provide an output from which the R2 dia can be determined? >>> >>> Simon >>> >>> On 11/25/2010 11:26 AM, Daniel O'Donovan wrote: >>>> Hi Simon, >>>> >>>> I don't know if you know this - but the 'Peak Separator' program in Analysis already does what the FuDA program intends to (and you don't even need to leave CCPN!). >>>> >>>> I'm also working on a more powerful version of the Peak Separator that I hope to release in the coming weeks / days. >>>> >>>> Dan >>>> >>>> On 25 Nov 2010, at 09:50, S.P. Skinner wrote: >>>> >>>>> Dear Rasmus >>>>> >>>>> We have one peptide wherein the proline adopts three conformations, thereby giving three resonances of differing intensities. We wish to use the FUDA program to perform linewidth analysis and therefore require a sparky formatted peak list. We wanted to assign each proline resonance corresponding to each conformation in order that three separate peak lists could be exported for this analysis. But using three different chains did not prove effective. >>>>> >>>>> Regards >>>>> >>>>> Simon >>>>> >>>>> On 11/24/2010 03:19 PM, Rasmus Fogh wrote: >>>>>> Dear Simon, >>>>>> >>>>>> Not sure I understand this. You have three different peptides in your sample? Do you also have three different chains in your MolSystem (you should)? Are you assigning the different peaks to different chains? Do all the peptides have a Pro-4? Why are you trying to assign a new resonance to something that is already assigned elsewhere, instead of assigning the peak to the same pre-existing resonance? >>>>>> >>>>>> Some more details might help, >>>>>> >>>>>> Rasmus >>>>>> >>>>>> --------------------------------------------------------------------------- >>>>>> Dr. Rasmus H. Fogh Email: [log in to unmask] >>>>>> Dept. of Biochemistry, University of Cambridge, >>>>>> 80 Tennis Court Road, Cambridge CB2 1GA, UK. FAX (01223)766002 >>>>>> >>>>>> On Tue, 23 Nov 2010, S.P. Skinner wrote: >>>>>> >>>>>>> Hi All >>>>>>> >>>>>>> I am using a 1H-13C HSQC spectrum of three separate molecules all in one. I am attempting to assign more than one peak to a C-H resonance. When I attempt to assign a resonance in a sister list of a spectrum, that has already been assigned previously in another list, the message: Redundant resonance: There are more resonances (3) than atoms set for 4Pro HD3/HD2. The reason for multiple assignment is that the three different peptides have different intensities and therefore require their own assignment. >>>>>>> >>>>>>> Any suggestions on how to circumvent this problem? >>>>>>> >>>>>>> Kind Regards >>>>>>> >>>>>>> Simon Skinner >>>>>>> >>>>>>> -- >>>>>>> Simon P Skinner >>>>>>> Protein Chemistry Group >>>>>>> Leiden Institute of Chemistry, Universiteit Leiden >>>>>>> Phone: +31 71 527 6089 / Fax: +31 71 527 4349 >>>>>>> E-mail : [log in to unmask] >>>>>>> >>>>> -- >>>>> Simon P Skinner >>>>> Protein Chemistry Group >>>>> Leiden Institute of Chemistry, Universiteit Leiden >>>>> Phone: +31 71 527 6089 / Fax: +31 71 527 4349 >>>>> E-mail : [log in to unmask] >>>> Daniel O'Donovan >>>> [log in to unmask] >>> -- >>> Simon P Skinner >>> Protein Chemistry Group >>> Leiden Institute of Chemistry, Universiteit Leiden >>> Phone: +31 71 527 6089 / Fax: +31 71 527 4349 >>> E-mail : [log in to unmask] >> Daniel O'Donovan >> [log in to unmask] > > -- > Simon P Skinner > Protein Chemistry Group > Leiden Institute of Chemistry, Universiteit Leiden > Phone: +31 71 527 6089 / Fax: +31 71 527 4349 > E-mail : [log in to unmask] Daniel O'Donovan [log in to unmask]