hipassnyquist

[jychoi0616]

Dear team,

Could you let me know how to disable "hipassnyquist" option at all? I tried to put "0" or "false", then it gave errors of which it can't divide by 0. I don't like any blurring effect on the tomogram when deconvolve job is done. I tried to use a really little value such as 0.00000000000000001, but that didn't really show big difference from the default value of 0.02.

Thank you, Joy

[procyontao]

Hi Joy,

The hipassnyquist may change the contrast of tomogram but should not cause blurring effect. It is a high pass filter for very low resolution to account for the amplitude contrast.

I suggest you try to modify SNRfalloff or deconvolve strength to see whether the tomogram become less blurry.

[jychoi0616]

Hi,

Thank you for your reply. But are you sure?

Even in the tutorial (p.10), it says, "Another parameter hipassnyquist applies a high pass filter at very low frequency, changing this parameter might be helpful if the tomograms become too blurry."

Also, when I tested higher value (0.2) for hipassnyquist to see the effect, it was super blurry. (But putting extremely low value (0.000000000000000001) didn't give much change compared to 0.02, as I said earlier.)

As of SNRfalloff & deconvolve, I'm already using quite low value (0.5).

[procyontao]

Hi,

Sorry for the confusion.

The extremely low values is equivalent to disable hipassnyquist. Its value represents fraction to Nyquist frequency.

For example, your Nyquest resolution is 1 nm, and the hipassnyquest is 0.02. This means it only affect the low resolution range until 50nm, where as the information with resolution higher than 50nm will not change at all. Given it is already at very low resolution, changing hipassnyquest further close to zero will have minor effect.

I believe SNRfalloff can actually set to zero or maybe even negative.

[jychoi0616]

Hi Yuntao, Thank you! I'll try even lower value of SNRfalloff.