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Hallo Eike,<br>
<br>
Steve is right... complicated topic!<br>
<br>
You may want to look at some of the original papers on this issue:<br>
<br>
1) George Harauz and Marin van Heel, Exact filters for general
geometry three dimensional reconstruction, Optik 73 (1986)
146-156.<br>
2) Marin van Heel and George Harauz, Resolution criteria for three
dimensional reconstructions, Optik 73 (1986) 119-122<br>
3) Marin van Heel, Similarity measures between images,
Ultramicroscopy 21 (1987) 95-100.<br>
4) Marin van Heel, Michael Schatz, and Elena Orlova, Correlation
functions revisited, Ultramicroscopy 46 (1992) 304-316.<br>
5) Marin van Heel: Unveiling ribosomal structures: the final
phases. Current Opinions in Structural Biology 10 (2000) 259-264.<br>
<br>
My 5 cents... <br>
<br>
Marin.<br>
<br>
PS There are more pennies in my purse, and I can provide you with
the pdfs if needed. <br>
<br>
On 11/10/2017 10:28, Ludtke, Steven J wrote:<br>
</div>
<blockquote type="cite"
cite="mid:05C5A455-877C-415F-879D-6707B117845D@bcm.edu">
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Hi Eike,
<div class="">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:</div>
<div class=""><br class="">
</div>
<div class="">e2proc3d.py map1.mrc fsccurve.txt --calcfsc
map2.mrc <span class="Apple-tab-span" style="white-space:pre">
</span># any input file format is fine</div>
<div class=""><br class="">
</div>
<div class="">To see the results:</div>
<div class="">e2display.py --plot fsccurve.txt</div>
<div class=""><br class="">
</div>
<div class="">An alternative which can compute local FSC, and also
produce a locally filtered average map based on the local
resolution:</div>
<div class="">e2fsc.py map1.mrc map2.mrc --output fscmap.hdf
--outfilt localfiltmap.mrc</div>
<div class=""><br class="">
</div>
<div class="">If the maps are not properly aligned, you can do
something like before computing the FSC:</div>
<div class="">e2proc3d.py map1.mrc map1_aligned.mrc
--align rotate_translate_3d_tree --alignref map2.mrc </div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On Oct 11, 2017, at 7:08 AM, Schulz,
Eike-Christian xxxxxxxxxxxxxxxxxxxxxxx wrote:</div>
<br class="Apple-interchange-newline">
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<p class="MsoNormal"><span style="font-size:11.0pt"
class="">Dear all, <o:p class="">
</o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"
class=""><o:p class=""> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"
class="">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 …<o:p
class=""></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"
class=""><o:p class=""> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"
class="">With best regards,<o:p class=""></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"
class=""><o:p class=""> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"
class="">Eike<o:p class=""></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"
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<p class="MsoNormal"><span style="font-size:11.0pt"
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<font class="" face="Courier"><span style="font-size:
14px;" class="">--------------------------------------------------------------------------------------<br
class="">
Steven Ludtke, Ph.D.<br class="">
Charles C. Bell, Jr. Professor of Biochemistry and
Mol. Biol. </span></font><br class="">
</div>
</div>
</div>
<br class="">
</div>
</blockquote>
<p><br>
</p>
<pre class="moz-signature" cols="72">--
==============================================================
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
marin.vanheel(A_T)lnnano.cnpem.br
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
--------------------------------------------------
I receive many emails per day and, although I try,
there is no guarantee that I will actually read each incoming email. </pre>
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