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Dear All,<br>
<br>
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<span class="inf">°</span>
cone of the direction under scrutiny (FSC(<span class="inf"><60°</span>)),
and one for the 60-90<span class="inf">°</span> cone (FSC(><span
class="inf">60°</span>)). This has the advantage that the
correct statistical thresholds (1/2bit) are the same for both
curves.
(<a class="moz-txt-link-freetext" href="http://journals.iucr.org/m/issues/2017/05/00/kf5002/index.html">http://journals.iucr.org/m/issues/2017/05/00/kf5002/index.html</a>)<br>
<br>
Cheers,<br>
<br>
Marin<br>
<br>
<br>
On 11/09/2017 20:35, Dmitry Lyumkis wrote:<br>
</div>
<blockquote type="cite"
cite="mid:867F3A07-4EA9-44D5-9064-625452CAF2D7@salk.edu">
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<span style="font-family: HelveticaNeue;" class="">Dear
colleagues,</span>
<div style="font-family: HelveticaNeue;" class=""><br class="">
</div>
<div style="font-family: HelveticaNeue;" class="">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 <a
href="https://www.ncbi.nlm.nih.gov/pubmed/28671674" class=""
moz-do-not-send="true">tilting in single particle experiments</a>, 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.</div>
<div style="font-family: HelveticaNeue;" class=""><br class="">
</div>
<div style="font-family: HelveticaNeue;" class="">The standalone
program <a href="https://github.com/nysbc/Anisotropy" class=""
moz-do-not-send="true">can be found here</a> 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. </div>
<div style="font-family: HelveticaNeue;" class=""><br class="">
</div>
<div style="font-family: HelveticaNeue;" class="">Hope you find it
useful, and feel free to contact me privately with any questions
or comments. </div>
<div style="font-family: HelveticaNeue;" class=""><br class="">
</div>
<div style="font-family: HelveticaNeue;" class="">Regards,</div>
<div style="font-family: HelveticaNeue;" class=""><br class="">
</div>
<div style="font-family: HelveticaNeue;" class="">Dmitry</div>
<div style="font-family: HelveticaNeue;" class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><font class="" face="HelveticaNeue">Anisotropy
program: </font><span style="font-family: HelveticaNeue;"
class=""><a href="https://github.com/nysbc/Anisotropy"
class="" moz-do-not-send="true">https://github.com/nysbc/Anisotropy</a></span></div>
<div class=""><font class="" face="HelveticaNeue">Tilting: <a
href="https://www.ncbi.nlm.nih.gov/pubmed/28671674" class=""
moz-do-not-send="true">https://www.ncbi.nlm.nih.gov/pubmed/28671674</a></font></div>
<br>
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</pre>
</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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