Hi, I have a question on difference density maps. We are soaking in a substrate into my enzyme and am trying to see if it is in there by looking at difference density maps. We looked at an fobs-(fobs-fcalc) map and see density and 5 sigma at each catalytic active site in roughly the same place, its not great, but it seems like there is something there. so then, I thought I would confirm this by an fobs-fobs map. But I just used the phenix fobs-fobs difference electron density map and I dont see anything there. So I am curious as to an explanation of the difference. Any ideas? Raj
Hi Raj,
We looked at an fobs-(fobs-fcalc) map and see density and 5 sigma at each catalytic active site in roughly the same place, its not great, but it seems like there is something there.
I might be missing something, but the fobs-(fobs-fcalc) map to me seems like a simple fcalc map, where it's not too surprising that you see something... Which PDB model did you use as a phase_source in phenix.fobs_minus_fobs_map? If you like, you can send me the two data files and a PDB file and tell where you are expecting to see the differences. I will then play with this... Pavel.
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Pavel Afonine -
rpai＠berkeley.edu