[3dem] [ccpem] Correlation coefficient em structures

Marin van Heel marin.vanheel at googlemail.com
Wed Oct 11 07:05:33 PDT 2017

Hallo Eike,

Steve is right... complicated topic!

You may want to look at some of the original papers on this issue:

1) George Harauz and Marin van Heel, Exact filters for general geometry 
three dimensional reconstruction, Optik 73 (1986) 146-156.
2) Marin van Heel and George Harauz, Resolution criteria for three 
dimensional reconstructions, Optik 73 (1986) 119-122
3) Marin van Heel, Similarity measures between images, Ultramicroscopy 
21 (1987) 95-100.
4) Marin van Heel, Michael Schatz, and Elena Orlova, Correlation 
functions revisited, Ultramicroscopy 46 (1992) 304-316.
5) Marin van Heel: Unveiling ribosomal structures: the final phases. 
Current Opinions in Structural Biology 10 (2000) 259-264.

My 5 cents...


PS There are more pennies in my purse, and I can provide you with the 
pdfs if needed.

On 11/10/2017 10:28, Ludtke, Steven J wrote:
> Hi Eike,
> correlation coefficient is not normally a very useful metric for 
> comparing two different maps, unless they happen to be generated in 
> nearly identical ways. It can be useful for looking at self-symmetry 
> and a few other things, but it is extremely sensitive to alignment, 
> and perhaps even more importantly, to how the maps have been filtered. 
>  Normally if you wish to compare two maps you would do it using an 
> FSC, which is resolution dependent and not sensitive to filtration 
> differences. While this will give you a curve instead of a single 
> number, it is much more useful in assessing how two maps differ. While 
> there are many different tools you can use to generate one, this is 
> EMAN2's method:
> e2proc3d.py map1.mrc fsccurve.txt --calcfsc map2.mrc # any input file 
> format is fine
> To see the results:
> e2display.py --plot fsccurve.txt
> An alternative which can compute local FSC, and also produce a locally 
> filtered average map based on the local resolution:
> e2fsc.py map1.mrc map2.mrc --output fscmap.hdf --outfilt localfiltmap.mrc
> If the maps are not properly aligned, you can do something like before 
> computing the FSC:
> e2proc3d.py map1.mrc map1_aligned.mrc --align rotate_translate_3d_tree 
> --alignref map2.mrc
>> On Oct 11, 2017, at 7:08 AM, Schulz, Eike-Christian 
>> xxxxxxxxxxxxxxxxxxxxxxx wrote:
>> ****CAUTION:*** This email is not from a BCM Source. Only click links 
>> or open attachments you know are safe.*
>> ------------------------------------------------------------------------
>> Dear all,
>> Is there a way to calculate structural similarity of electron density 
>> maps in electron microscopy? I am looking for a solution that would 
>> report e.g. a correlation coefficient …
>> With best regards,
>> Eike
> --------------------------------------------------------------------------------------
> Steven Ludtke, Ph.D.
> Charles C. Bell, Jr. Professor of Biochemistry and Mol. Biol.


     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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