Dear Andy, Many years ago, we tended to store F rather than I because it was easier to fit it onto the fixed format punched cards. Reflections that we couldn'd see by eye on the films were called 'less thans' and left out, so there were no negative intensities.
The question of refinement against I or F and related issues were investigated by a commission of the IUCr; however in their report [Acta Cryst. A45 (1989) 63-75] they did not come to a decisive conclusion. Despite this, these days almost all small molecule structures are refined against I using a weighting scheme based on the experimental sigma(I). This enables all the data to be used and facilitates the refinement of twinned structures. Indeed if you submitted a small molecule structure for publication based on a refinement against F with the negative intensities left out it would probably be rejected by the all-powerful CHECKCIF because of inadequate data completeness. On the other hand, a TRUNCATE approach would be less suitable for small molecules because heavy atoms on special positions etc. could invalidate the assumed structure factor distribution. For macromolecules the weighting schemes are less dominated by the intensity esds and the final R values are much higher (20% rather than 3%) so problems in converting sigma(I) to sigma(F) (such as the effect of pseudotranslational NCS on the assumed distribution) have less influence. So the decision of whether to refine against I or F is less important, and may depend more on the technical details of the refinement program you are using. Best wishes, 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: > Professor Sheldrick, > > My apologies for the wording of my statement about popular refinement > programs, I regret I was not clear that I had only looked at some of the > manuals for available programs that happen to also be popular :) > Thank you for your reply to my question. I'm glad that your response > confirmed some of my understanding of the proper treatment of the data. > Indeed part of the reason for my questions was because I was concerned that my > original intensities were overwritten with post-Truncate, scaled values. > With regards to refining against amplitudes or intensities, I looked > at section 2.4 in the SHELXL manual, but I'm still not sure when to choose > refinement against amplitudes or refinement against intensities if you have > the option of both. Let me ask the question a different way. Are there > particular programs, phasing/methods or stages of refinement that benefit from > refining against intensities vs. amplitudes for programs that offer both > options? > > Thanks again, > -Andy Torelli > > 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 > > > ============================================= > > > > > > > > -- > > ============================================= > Andrew T. Torelli Ph.D. > Postdoctoral Associate > Laboratory of Steven E. Ealick > Department of Chemistry and Chemical Biology > Cornell University > ============================================= > >
