[phenixbb] Question about RMSD vs e/A^3
sacha at igbmc.fr
Wed Mar 30 07:30:02 PDT 2022
You can find some useful comments here :
"Metrics for comparison of crystallographic maps". Acta Cryst., D70, 2593-2606 (2014)
With best regards,
From: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> On Behalf Of Vatsal Purohit
Sent: Wednesday, March 30, 2022 4:01 PM
To: phenixbb at phenix-online.org
Subject: [phenixbb] Question about RMSD vs e/A^3
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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