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

[Jose Maria Carazo]

Dear Jin,

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.

Wbw..JM

On Tue, May 30, 2017 at 3:55 PM, Marin van Heel <
marin.vanheel at googlemail.com> wrote:

>
> 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
>>>
>>>
>> --
> ==============================================================
>
>     Prof Dr Ir Marin van Heel
>
>     Research Professor at:
>
>     Laboratório Nacional de Nanotecnologia - LNNano
>     CNPEM/ABTLuS, Campinas, Brazil
>     Brazilian mobile phone  +55-19-981809332
>                            (041-19-981809332 TIM)
>
> ----------------------------------------------
>
>
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-- 
Prof. Jose-Maria Carazo
Biocomputing Unit, Head, CNB-CSIC
Spanish National Center for Biotechnology
Darwin 3, Universidad Autonoma de Madrid
28049 Madrid, Spain


Cell: +34639197980
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