Dear Vatsal,

You can find some useful comments here :

"Metrics for comparison of crystallographic maps". Acta Cryst., D70, 2593-2606 (2014)

With best regards,

Sacha Urzhumtsev

From: [email protected] <[email protected]> On Behalf Of Vatsal Purohit
Sent: Wednesday, March 30, 2022 4:01 PM
To: [email protected]
Subject: [phenixbb] Question about RMSD vs e/A^3

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.

Regards,

Vatsal

Post-doctoral fellow, Davis Lab, Emory University

[email protected] | 346-719-9409