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<p>Hi Eike, <br>
</p>
<p>as already mentioned, it depends how the density maps were
created. If the two are from the same project or even within the
same data set, <a
href="https://spider.wadsworth.org/spider_doc/spider/docs/spider.html">SPIDER</a>
offers a convenient way to <a
href="https://spider.wadsworth.org/spider_doc/spider/docs/man/ccc.html">calculate
the cross correlation coefficients</a>. You can also apply a
mask to focus the ccc-calculation on specific areas.</p>
<p>Best</p>
<p><br>
Dario<br>
</p>
<br>
<div class="moz-cite-prefix">On 11.10.2017 16:05, Marin van Heel
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:a9c0da48-628d-b269-63c5-29a90bff2b40@googlemail.com">
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<div class="moz-cite-prefix"><br>
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"
class=""><o:p class=""> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"
class=""><o:p class=""> </o:p></span></p>
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<br class="">
<div class="">
<div dir="auto" style="word-wrap: break-word;
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-webkit-text-stroke-width: 0px;"> <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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