Two more nuances about map comparison and scaling:

- one you will find here:

https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2012_07.pdf#page=16

- and another one is.. 'sigma' (rmsd) scaled maps appear to be of the two kinds where in one case rmsd is calculate using the whole unit cell volume and in the other case using only macro-molecular region. The latter is clearly better making it solvent content independent. Which one of the two modern programs use isn't well documented.

Pavel

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

 

 

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