Well, actually you probably haven't subtracted the "dark R" value from your final R. This and other values are available in a "dark folder" on your hard drive, which is impossible to see/read, but which contains a lot of important information which will make your structure have a much higher impact factor. You can probably make a maximum-likelihood approximation of the appropriate values, and apply them to your structure so that your R values correspond the majority in the PDB.
HTH, JPK On Fri, Apr 1, 2011 at 8:30 AM, Edward A. Berry <ber...@upstate.edu> wrote: > Do you have a list of dark-matter-aware PDB refinement programs? > Adding dark matter and refining in TNT or Xplor gives me exactly > the same R as without. Furthermore the final refined files have > lost the dark matter as far as I can see. This leads me to believe > these programs are completely ignoring the dark matter. > > Ed > > Ethan Merritt wrote: >> >> Hi to all on ccp4bb: >> >> What better day to announce the availability of a breakthrough technique >> in macromolecular crystallography? >> >> Given recent discussion and in particular James Holton's suggestion that >> the problem of disordered sidechains is a problem akin to the difficulty >> of describing dark matter and dark energy... >> >> I am happy to announce a new crystallographic tool that can improve your >> model by accounting for an often-neglected physical property. A detailed >> explanation, references, and a preliminary implementation of the program >> can be downloaded from >> >> http://skuld.bmsc.washington.edu/DarkMatter >> >> -- >> Ethan A Merritt >> Karmic Diffraction Project >> Fine crystallography since April 1, 2011 >> "What goes around, comes around - usually as a symmetry equivalent" >> > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *******************************************
