Eleanor, Any ideas if the 0.01 in truncate is just being used as "arbitrary small number to prevent overflow", or if it's serving another purpose? I wasn't sure from reading truncate.f.
Thanks, Pete Eleanor Dodson wrote: > Truncate doesnt "truncate" intensities or modify them in any way except > to apply a guesstimate of the absolute likely scale based on the no of > residues in the asymmetric unit. Truncation is only applied to the > amplitudes for negative or very weak intensities. Obv. you cant take the > square root of a negative number so this procedure keeps a (small) > bvalue for the amplitude, which is better than discarding it. weak > amplitudes/intensities provide useful information for refinement > programs as well as strong ones > > If you have input I(+) and I(-) then Imean is the weighted average of > these two, but you also retain I(+) and I(-) if you want to use these > for later calculations > > Eleanor > > > George M. Sheldrick wrote: >> Well, I suppose that it doesn't qualify as a "popular refinement program" >> but section 2.4 of the SHELX manual discusses the question of refinement >> against amplitudes or intensities. If you are refining against >> intesities, >> there is no need to "truncate" the data, indeed it would be definitely >> counter-productive to use TRUNCATE to convert I and sig(I) to F and >> sig(F) >> and then to convert these back to I and sig(I). For SHELXL it is also >> not necessary to scale the data so that they are on an absolute scale. >> I personally believe in refining against the data you actually measured >> without compromising them in any way, but I appreciate that I am in a >> small minority. >> >> George >> >> Prof. George M. Sheldrick FRS >> Dept. Structural Chemistry, >> University of Goettingen, >> Tammannstr. 4, >> D37077 Goettingen, Germany >> Tel. +49-551-39-3021 or -3068 >> Fax. +49-551-39-22582 >> >> >> On Fri, 7 Nov 2008, Andy Torelli wrote: >> >> >>> To the CCP4 community, >>> >>> I have a question about ImportScaled. When I select both the "Keep >>> the input intensities in the output file" and the "Run Truncate..." >>> options, >>> the output MTZ file contains IMEAN and SIGIMEAN values that are >>> different from >>> the input intensity file. Specifically, the values are multiplied by >>> 1/100th >>> of the SCALE term reported in the log file that is calculated from >>> the Wilson >>> Plot during the Truncate procedure. However, when the "Run Truncate..." >>> option is not selected, the output MTZ file contains unaltered IMEAN and >>> SIGIMEAN values that match the input file. >>> >>> After reading the recent CCP4 threads regarding Truncate as well as >>> the program documentation, I still have a few questions: >>> >>> 1. My understanding is that this scaling of the intensities is done >>> to bring >>> them to an (approximate) absolute scale and therefore can only be >>> performed >>> when Truncate is run simultaneously (because the Wilson Plot is >>> necessary to >>> calculate the appropriate scale factor). However, why is the scaling >>> equal to >>> 1/100 of the SCALE term from the Wilson Plot (i.e. why not exactly >>> the SCALE >>> term)? >>> >>> 2. For programs that use intensities as a target for refinement, is it >>> necessary to have the intensities scaled in this way or is it also >>> valid to >>> use the unaltered (scaled only) intensities? >>> >>> 3. On a related note, when is it best to refine against intensities vs. >>> amplitudes? I have not been able to find recent literature that >>> pertains to >>> macromolecular crystallography and the documentation I've looked at for >>> popular refinement programs that offer both targets do not provide >>> guidelines >>> as far as I can tell. If anyone could recommend some literature, I >>> would >>> really appreciate it. >>> >>> Thank you very much for your time, >>> Best Regards, >>> -Andy Torelli >>> >>> -- >>> >>> ============================================= >>> Andrew T. Torelli Ph.D. >>> Postdoctoral Associate >>> Department of Chemistry and Chemical Biology >>> Cornell University >>> ============================================= >>> >>> >>> >> >> >>
