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

Marin van Heel marin.vanheel at googlemail.com
Thu Sep 14 08:07:08 PDT 2017

Dear All,

We have implemented an FSC as function of (preferential) orientation in 
IMAGIC-4D, which, apart  from the conventional isotropic FSC, produces 
two additional FSC curves per direction: one for the structure factors 
within a 0-60° cone of the direction under scrutiny (FSC(<60°)), and one 
for the 60-90° cone (FSC(>60°)). This has the advantage that the correct 
statistical thresholds (1/2bit) are the same for both curves. 



On 11/09/2017 20:35, Dmitry Lyumkis wrote:
> 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.
> Regards,
> Dmitry
> Anisotropy program: https://github.com/nysbc/Anisotropy
> Tilting: https://www.ncbi.nlm.nih.gov/pubmed/28671674
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     Prof Dr Ir Marin van Heel

     Laboratório Nacional de Nanotecnologia - LNNano
     CNPEM/LNNano, Campinas, Brazil

     tel:    +55-19-3518-2316
     mobile  +55-19-981809332
                  (041-19-981809332 TIM)
     Skype:  Marin.van.Heel
     email:  marin.vanheel(A_T)gmail.com
     and:    mvh.office(A_T)gmail.com

     Emeritus Professor of Cryo-EM Data Processing
     Leiden University
     Mobile NL: +31(0)652736618

     Emeritus Professor of Structural Biology
     Imperial College London
     Faculty of Natural Sciences
     email: m.vanheel(A_T)imperial.ac.uk


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