Hi Renu, you may try using a Polder omit map for the region rather than a
simulated annealing map. You may also check if the red density is due to a
symmetry related molecule that is not modeled well. Hope it helps.
JP
On Tuesday, July 23, 2024 at 04:50:00 PM CDT, Renuka Kadirvelraj
<[email protected]> wrote:
#yiv8512769868 P {margin-top:0;margin-bottom:0;}Hi CCP4bb, We would greatly
appreciate your advice regarding an odd problem that has cropped up with one of
our crystal structures. We have a protein structure in space group P6(3)22 at
2.1 A resolution and in the final refinement stages with Rwork of 0.20 and
Rfree of 0.22. When we ran simulated annealing to rebuild an outlier Lysine
residue in a loop (using Phenix), the Sim Omit map showed the positive density
expected from the omission of the loop (colored green in attached pics).
However, flanking the positive density, there is a complimentary negative
density (in red). We are puzzled as to the cause of the appearance of the
negative density. Can you help us? Many thanks,Renu
---------------------------------------------Renu Kadirvelraj, Ph.D.Research
Scientist
A428, Biochemistry and Molecular Biology120, East Green StreetUniversity of
GeorgiaAthens, GA 30602Tel: (706) 583 0303
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