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Dear Jin,
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<div class="">conversely, you can use CTER facility in SPHIRE package (<a href="http://sphire.mpg.de/wiki/doku.php" class="">http://sphire.mpg.de/wiki/doku.php</a>).</div>
<div class=""><br class="">
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<div class="">It estimates error bounds of CTF parameters and it contains simple set of graphical tools that</div>
<div class="">allow one to reject/set to zero parameters that were found to be unreliable. Therefore, instead of using</div>
<div class="">essentially random astigmatism angles that do no good it will set the astigmatism amplitudes</div>
<div class="">to zero based on significance thresholds set by the user.</div>
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</div>
<div class="">Regards,<br class="">
<div class="">
<div style="color: rgb(0, 0, 0); font-family: Arial; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;">
— <br class="">
Pawel A. Penczek, Ph.D.<br class="">
Professor<br class="">
Structural Biology Imaging Center, Director<br class="">
The University of Texas<br class="">
phone: 713-500-5416<br class="">
fax: 713-500-0652<br class="">
<a href="https://med.uth.edu/bmb/faculty/pawel-a-penczek/" class="">https://med.uth.edu/bmb/faculty/pawel-a-penczek/</a></div>
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<blockquote type="cite" class="">
<div class="">On May 30, 2017, at 9:46 AM, Jose Maria Carazo <<a href="mailto:carazo@cnb.csic.es" class="">carazo@cnb.csic.es</a>> wrote:</div>
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<div dir="ltr" class="">Dear Jin,
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<div class="">You may want to check on a CTF Challenge we did a couple of years ago (Marabini et al. JSB 2015) for a more in depth analysis but, essentially, to assign a value to the astigmatism angle when your astigmatism is very small is not a very stable
process. </div>
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<div class="">Wbw..JM</div>
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<div class="gmail_extra"><br class="">
<div class="gmail_quote">On Tue, May 30, 2017 at 3:55 PM, Marin van Heel <span dir="ltr" class="">
<<a href="mailto:marin.vanheel@googlemail.com" target="_blank" class="">marin.vanheel@googlemail.com</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br class="">
Hi Sjors and Jin,<br class="">
<br class="">
This type of anisotropy has a name: Astigmatism!<br class="">
It may sound pedantic but anisotropy in EM normally refers to a magnification anisotropy, not to astigmatism.<br class="">
<br class="">
Cheers,<br class="">
<br class="">
Marin<br class="">
<br class="">
<br class="">
On 29/05/2017 18:51, Sjors Scheres wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Jin,<br class="">
In the case of anisotropy your Thon rings are elliptical instead of<br class="">
circular because the defocus in one direction (defocusU) is not the same<br class="">
as the defocus in the perpendicular direction (defocusV). DefocusAngle<br class="">
describes the direction of this anisotropy. It is defined as the angle<br class="">
between defocusU and the X-axis (if I remember correctly...). Both<br class="">
ctffind4 and gctf estimate anisotropy for every micrograph, but if your<br class="">
microscope was well aligned, then you may have hardly any anisotropy in<br class="">
the data. This will result in very similar defocusU and defocusV values<br class="">
for each micrograph. In that case, defocusAngle doesn't mean anything, and<br class="">
can vary wildly between the different programs. I suspect this is what is<br class="">
happening, but you can just check by plotting defocusU values against<br class="">
defocusV values for the entire dataset. I suspect you can mix your<br class="">
particles as you want without large effects on the reconstruction.<br class="">
HTH,<br class="">
Sjors<br class="">
<br class="">
<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi All,<br class="">
<br class="">
This may be very trivial thing. I am going to combine particles from two<br class="">
dataset. And each dataset was processed with ctffind4 and gctf. I found<br class="">
each program gives similar defocus values but different defocus angles per<br class="">
image. What does defocus angle do in CTF and would it be okay to combine<br class="">
the data from different softwares?<br class="">
<br class="">
Thanks in advance,<br class="">
<br class="">
Jin<br class="">
<br class="">
</blockquote>
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</blockquote>
-- <br class="">
==============================<wbr class="">==============================<wbr class="">==<br class="">
<br class="">
Prof Dr Ir Marin van Heel<br class="">
<br class="">
Research Professor at:<br class="">
<br class="">
Laboratório Nacional de Nanotecnologia - LNNano<br class="">
CNPEM/ABTLuS, Campinas, Brazil<br class="">
Brazilian mobile phone <a href="tel:%2B55-19-981809332" value="+5519981809332" target="_blank" class="">
+55-19-981809332</a><br class="">
(041-19-981809332 TIM)<br class="">
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<div class="">Prof. Jose-Maria Carazo<br class="">
Biocomputing Unit, Head, CNB-CSIC<br class="">
Spanish National Center for Biotechnology</div>
<div class="">Darwin 3, Universidad Autonoma de Madrid</div>
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