[3dem] [ccpem] Combining datasets with ctf parameters from ctffind & gctf

[Marin van Heel]

Hi Sjors and Jin,

This type of anisotropy has a name: Astigmatism!
It may sound pedantic but anisotropy in EM normally refers to a 
magnification anisotropy, not to astigmatism.

Cheers,

Marin


On 29/05/2017 18:51, Sjors Scheres wrote:
> Hi Jin,
> In the case of anisotropy your Thon rings are elliptical instead of
> circular because the defocus in one direction (defocusU) is not the same
> as the defocus in the perpendicular direction (defocusV). DefocusAngle
> describes the direction of this anisotropy. It is defined as the angle
> between defocusU and the X-axis (if I remember correctly...). Both
> ctffind4 and gctf estimate anisotropy for every micrograph, but if your
> microscope was well aligned, then you may have hardly any anisotropy in
> the data. This will result in very similar defocusU and defocusV values
> for each micrograph. In that case, defocusAngle doesn't mean anything, and
> can vary wildly between the different programs. I suspect this is what is
> happening, but you can just check by plotting defocusU values against
> defocusV values for the entire dataset. I suspect you can mix your
> particles as you want without large effects on the reconstruction.
> HTH,
> Sjors
>
>
>> Hi All,
>>
>> This may be very trivial thing. I am going to combine particles from two
>> dataset. And each dataset was processed with ctffind4 and gctf. I found
>> each program gives similar defocus values but different defocus angles per
>> image. What does defocus angle do in CTF and would it be okay to combine
>> the data from different softwares?
>>
>> Thanks in advance,
>>
>> Jin
>>
>
-- 
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     Prof Dr Ir Marin van Heel

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     Laboratório Nacional de Nanotecnologia - LNNano
     CNPEM/ABTLuS, Campinas, Brazil
     Brazilian mobile phone  +55-19-981809332
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