[3dem] Program for evaluating anisotropy in cryo-EM

Dmitry Lyumkis dlyumkis at salk.edu
Mon Sep 11 11:35:35 PDT 2017

Dear colleagues,

I would like to point your attention to a program that we've been developing to quantitatively evaluate anisotropy in cryo-EM maps. This program generates a “3D FSC” array, effectively a set of 1D FSC curves computed over all angular directions, which can be displayed and visualized as a 3D map (e.g. in Chimera). This 3D FSC array quantitatively describes directional resolution across Euler space, thus revealing the extent of anisotropy in EM density maps, and further highlighting where and how preferred specimen orientation is effecting your reconstruction. This program has been developed in conjunction with our efforts to study the benefits of tilting in single particle experiments<https://www.ncbi.nlm.nih.gov/pubmed/28671674>, and we have found that this tool is generally useful to quantitatively evaluate any cryo-EM reconstruction. Thus, we are now using it routinely (and reporting the results in manuscripts). The only inputs to the program are the two half-maps arising from your refinement.

The standalone program can be found here<https://github.com/nysbc/Anisotropy> and can be used with any reconstruction, provided that the half-maps are present. The only requirement is to have Anaconda3 (a distribution of Python3) installed on your system.

Hope you find it useful, and feel free to contact me privately with any questions or comments.



Anisotropy program: https://github.com/nysbc/Anisotropy
Tilting: https://www.ncbi.nlm.nih.gov/pubmed/28671674
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