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I think its a question of scaling. Your script used the keyword NOSCALE in sfall, so the resulting output file has much larger Fcalc than Fobs, so I can well believe that 2Fo-Fc is negative. Your script, or ours from the GUI ? Anyway, personally I'd stick the files into refmac and let that produce weighted map coefficients. Does that explain it? m On Thu, 2006-09-28 at 11:35 +0300, Harry M. Greenblatt wrote: > > Dear All, > > > I addressed this issue to "management" but got no reply. > > > I wanted to make a map from a published structure, so I downloaded the > structure factors and the coordinates, and used the import facility to > go from mmcif to mtz. Then I ran sfall to generate fcalc and phicalc > from the coordinates. Then fft to make a 2fo-fc map. Looking at the > map in PyMOL and then in coot and contouring at 1.5sigma, it was > obvious that something had gone wrong. While looking in coot, and > pondering what could be wrong, I was idly scrolling the mouse wheel, > which changed the contour. When I got close to zero, the map suddenly > started looking better. Checking the fft output confirmed my > suspicions: the map, instead of going from -0.6 to +1.6, went from > -1.6 to +0.6. Contouring at -1.5sigma gave what one would expect from > a 2fo-fc map. So I guess the map that was calculated was Fc - 2Fo. > I checked the fft output again and confirmed that FP was F1, > whose multiplier, n, was +2.0 and that Fcalc was F2, whose multiplier, > m, was +1.0 and that I had asked for a nF1 - mF2 map. > > > Perhaps I did something wrong? Perhaps this is a bug in fft? > > > Thanks, > > > Harry > ------------------------------------------------------------------------- > > Harry M. Greenblatt > > Staff Scientist > > Dept of Structural Biology [EMAIL PROTECTED] > > Weizmann Institute of Science Phone: 972-8-934-3625 > > Rehovot, 76100 Facsimile: 972-8-934-4159 > > Israel > > > > >
