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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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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
*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 _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s
-- Dorothee Liebschner, PhD (she/her) Research Scientist Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Web: https://phenix-online.org
participants (2)
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Dorothee Liebschner
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Renuka Kadirvelraj