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

Sjors Scheres scheres at mrc-lmb.cam.ac.uk
Tue May 30 07:12:53 PDT 2017


Yes, of course!
:-)
Sjors



On 05/30/2017 02:55 PM, Marin van Heel 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
>>>
>>

-- 
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
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