Hi Renu,
What do you mean when you say you calculated a Sim Omit map? Did you calculate a Composite Omit map with Simulated Annealing Option? Or did you run simulated annealing and then calculated an OMIT map?
Best wishes,
Dorothee

On Wed, Jul 31, 2024 at 3:59 PM Renuka Kadirvelraj <renu@uga.edu> wrote:
Presence of negative density in Sim Omit map
 
Hi Phenixbb,
 
We would 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, the Sim Omit map showed the positive density expected from the omission of the loop (contour level 3 sigma, 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 Biology
120, East Green Street
University of Georgia
Athens, GA 30602
Tel: (706) 583 0303
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--
Dorothee Liebschner, PhD (she/her)
Research Scientist
Molecular Biophysics and Integrated Bioimaging Division
Lawrence Berkeley National Laboratory
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