Hi,
> On the "Searches" tab of CTF job-type in Relion3, there are some
> parameters to set. These parameters and their default values in the
> Relion30 tutorial are:
> ? FFT box size (pix): 512
> ? Minimum resolution (A): 30
> ? Maximum resolution (A): 7.1
> ? Minimum defocus cvalue (A): 5000
> ? Maximum defocus cvalue (A): 50000
> ? Defocus step size (A): 500
> ? Amount of astigmatism (A): 100
>
> I wonder what the "FFT box size" mean? Is it related to the particle
> diameter?
No. This is the size of the power spectrum. Please read the CTFFIND paper.
> How to set the other paramter? Is it OK to use the default?
I often change the minimum and maximum defocus range to what I expect.
For example, if this is a VPP dataset collected closer to focus,
I would specify 2000 to 15000, for example.
For other parameters, the default works fine in almost all cases.
(The default of "Maximum resolution" should be 5 not 7.1)
> For the Manual particle picking job type, in the "Display", I don't
> understand the setting of the following parameters:
> ? Sigma contrast: 3
> ? White value: 0
> ? Black value: 0
> About the , the tutorial states that "black will be 3 standard deviation
> below the mean and white will be 3 standard deviations above the mean". I
> wonder why the "white value" and the "black value" are both set to 0. If
> the "mean" value of the grey-scale is 0, they why the the "white value"
> and the "black value" are set to 3 and -3 respectively?
You are right. When white and black values are omitted, they are
automatically set
according to the sigma contrast.
Best regards,
Takanori Nakane
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