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

Pavel Afonine pafonine at lbl.gov
Wed Mar 30 08:27:44 PDT 2022

Two more nuances about map comparison and scaling:

- one you will find here:


- 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.


On 3/30/22 07:30, Alexandre OURJOUMTSEV wrote:
> Dear Vatsal,
> You can find some useful comments here :
> "Metrics for comparison of crystallographic maps". /Acta Cryst., 
> /D*70*/,///2593-2606 (2014)
> With best regards,
> Sacha Urzhumtsev
> *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
> 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
> vatsal.purohit at emory.edu <mailto:vatsal.purohit at emory.edu>| 346-719-9409
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