ctffind4 problems analyzing micrographs recorded with phase plate

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k.barragan
ctffind4 problems analyzing micrographs recorded with phase plate

Hi,

I have a question concerning ctffind-4.1.10.

I'm using ctffind4 to analyze micrographs recorded with a phase plate.

But I get funny results:

1. I get negative phase shift although I limit the phase shift from 0 to 2.0

2. I get also phase shifts which are far beyond the borders I defined in the input file (phase shift 2.7 rad: input file limited to 2.0)

Is this a known behaviour for ctffind4 or am I doing something wrong?

 

Thanks,

Kristina

alexis
Hi Kristina,

Hi Kristina,

While what you are describing is a bit unusual and may suggest something suboptimal about either the input image, the input parameters, or/and possibly the program, it is not completely unexpected. This is because the search for parameter values proceeds, broadly speaking, in two steps: (1) an exhaustive (grid) search withth the min, max and step parameters you specified. This first step cannot find results outside of the range you specify. But step (2) is a local minimization based on gradient descent starting from the end point of step 1. This gradient descent may well lead outside of the boundaries you specified.

I hope this helps. If you would like, I'd be happy to look at a typical image from your dataset which shows this behavior. If so, please upload & share an image and copy/paste all your inputs to ctffind4. 

Cheers,
Alexis

k.barragan
Hi Alexis,

Hi Alexis,

I have uploaded two micrographs and a picture with the settings I have used for ctffind4.

It would be great if you could have a look.

Thanks,

Kristina

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