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Yes, when you use NOE bins the reference intensity is used to define the bins, with a value of 1.0 being at the reference value. The value defaults to the mean peak intensity, but can be set differently to whatever the user wants. This was put in after requests from people with carbohydrate spectra where they have proportionately few peaks, but know exactly how they want to calibrate things. This is why it is reference rather than average. With regard to your previous question, the target distance is just the best guess for the distance and would only really matter for some potential types to give an energy minimum. In general with this sort of thing the 1/r^6 method is recommended as it conveys more information than the NOE bins, which are a bit of a legacy (but do add flexibility). T. > I think I got how the average intensity is calculated. Am I right in > thinking that it is the ref intensity value from the "Generate Distance > Constraints" menu? If so, it might be easier to recognize if it read > avg. peak intensity for the NOE bin method. Ref intensity is a bit > confusing (IMHO) in this case. However, for the 1/r6 method, ref > intensity is very clear! Just a suggestion for future updates.... > > -J > > On Mar 9, 2007, at 9:31 AM, Johnny Eugene Croy wrote: > > > Okay, I got this far on the NOE question. I this case the help > > file in analysis contained the answers to most of my questions. > > However, in regards to the min NOE intensity, I still have a few > > questions. This value is defined as a relative intensity (min peak > > intensity/avg peak intensity), but I can't seem to find an easy way > > (in analysis) to calculate out the average peak intensity from my > > peak list. I guess I could export my peak list to excel and then > > calculate out the average peak volume, but it would be nice to have > > analysis do this for me, since all of the data is there anyway. It > > probably is lurking somewhere in analysis, but I can't seem to find > > it. > > > > -J > > > > On Mar 8, 2007, at 11:16 AM, Johnny Croy wrote: > > > >> Hi everyone, > >> > >> Just a quick question regarding the NOE bin settings. I don't quite > >> understand the definitions that are presented in the NOE Distance > >> Classes > >> menu. Min and Max distances are self-explanatory, but not quite > >> sure what > >> the target distance refers to? Also, the Min. NOE intensity is > >> also a bit > >> confusing. Is this supposed to be set to the raw intensity cutoff > >> for that > >> particular bin? The default values make me think that is not the > >> case. > >> > >> This is unreleated but I wanted to thank you all for the input on > >> the PDB > >> problems that I was having. I completely forgot that Format > >> Converter can > >> be used to convert "anything" to be CCP-friendly. It truly is a very > >> powerful component of this program! Thanks for your help! > >> > >> -J > > > > ------------------------------------------------------------ > > Johnny E. Croy, Ph.D. > > NIH Post-Doctoral Fellow > > University of Colorado, Boulder > > Wuttke Lab > > Campus Box 215 > > Cristol Chemistry > > Boulder, CO 80309-0215 > > > > Lab Phone: (303) 492-2369 > > Lab Fax: (303) 492-4576 > > > > ------------------------------------------------------------ > > > > > > ------------------------------------------------------------ > Johnny E. Croy, Ph.D. > NIH Post-Doctoral Fellow > University of Colorado, Boulder > Wuttke Lab > Campus Box 215 > Cristol Chemistry > Boulder, CO 80309-0215 > > Lab Phone: (303) 492-2369 > Lab Fax: (303) 492-4576 > > ------------------------------------------------------------ > > > ------------------------------------------------------------------------------- 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- ------- -------------------------------------------------------------------------------