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Dear Ethan, the "optical resolution" is equivalent to the width of the origin peak in a Patterson synthesis. Since a Patterson is nothing but a convolution of the electron density map with itself, the width of the Patterson origin peak should be equivalent to the minimum distance two peaks in the electron density map can be apart to be resolvable. Thus, the optical resolution should give a more or less unbiased view on the "true" resolution of the data. Btw, the "optical resolution" has been implemented in the program SFCHECK by Alexei Vagin. It can be easily calculated from any amplitude or intensity file. Cheers, Manfred. ******************************************************************** * * * Dr. Manfred S. Weiss * * * * Team Leader * * * * EMBL Hamburg Outstation Fon: +49-40-89902-170 * * c/o DESY, Notkestr. 85 Fax: +49-40-89902-149 * * D-22603 Hamburg Email: [EMAIL PROTECTED] * * GERMANY Web: www.embl-hamburg.de/~msweiss/ * * * ******************************************************************** On Fri, 28 Apr 2006, Ethan Merritt wrote: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > On Friday 28 April 2006 08:20 am, [EMAIL PROTECTED] wrote: > > > > There are two somewhat separate questions here: (1) what data to use in > > refinement and (2) how to define a "nominal resolution" that will give the > > outside world a good idea of how far out the data extended, which needs > > some vague sort of uniform standard. I'd suggest the answers are (1) any > > datum you believe you really did measure should be thrown into the pot and > > I agree. > > > (2) the reported nominal resolution should be where I/sigI falls below 2, > > This sounds like voodoo statistics to me. Can you suggest any mathematical > basis for choosing an I/sig(I) limit of 2 rather than some other number? > > It also implies that the resolution/accuracy of the map and structural model > is entirely captured by I/sig(I) of the data, which is not true. > Consider how much cleaner maps become if you are able to do NCS averaging. > > Peter Zwart already mentioned Cruickshank's empirical DPI indices > (reported by refmac, so you all can use them, right?) > These incorporate more information, and are a more direct indicator of > expected model quality. DPI does not, however, answer the question > of whether it would have been useful to process the data to higher > resolution. > > Question: > > I've recently seen some papers report "optical resolution". > Where does that number come from? > > > > -- > Ethan A Merritt > Biomolecular Structure Center > University of Washington, Seattle WA >
