Are you sure the Fobs and Fc are on the same approximate scale?
Eleanor
Sarah Yohannan wrote:
Hi,
I have a bit of a mystery that I cannot figure out. I took a pdb file
and back-calculated the structure factors in CNS and then merged my
calculated F's (and fake sigmas) with observed F's into one file. So,
the hkl file has both Fcalc and Fobs with fake and real sigmas, and
the test set. Next, I made a 2fofc map, with Fcalc's and sigma and it
looked fine. Then, I removed some coordinates from the PDB file, ran
generate, and made a new 2fofc map with the same parameters and input
hkl with this new pdb. I looked at this map, and the density from the
coordinates I removed is gone! Why would the density disappear? I
haven't found an obvious error, but there must be one. Any ideas?
Sincerely,
Sarah Yohannan
Post-doctoral Fellow
Department of Cellular & Molecular Physiology
Yale School of Medicine
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