[phenixbb] Question about RMSD vs e/A^3

Vatsal Purohit vpurohi at purdue.edu
Wed Mar 30 07:01:06 PDT 2022

Hi all,

I had a question about comparing structures based on RMSD comparisons vs e-/A^3. While the former seems to be more frequently used in structural studies with a standard value of 1.0 rmsd for 2Fo-Fc and 3.0 rmsd for Fo-Fc, there are differences in RMSD based on resolution. Hence, I wanted to ask if e-/A^3 could be a more appropriate comparison for looking at differences in electron density in a ligand-binding site between 2 structures of the same enzyme? So, here you would try and set e-/A^3 of all the maps (2Fo-Fc and Fo-Fc) to the same value.

The structures I’m referring to are between 2-2.5 angstroms in resolution.

I have also worked with the map sigma level comparison tool on PHENIX and wanted to know if that might be an alternate way to compare maps in 2 structures accordingly.


Post-doctoral fellow, Davis Lab, Emory University

vatsal.purohit at emory.edu <mailto:vatsal.purohit at emory.edu> | 346-719-9409

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