Re: [scipion-users] Masking issue -- 10x difference

[Grigory S. <sha...@gm...>]

Hi,

You can check the output log for the protocol to see the executed relion
command. I think you have lowpass filtering enabled so the threshold you
choose must be selected on a filtered volume.

On Thu, Dec 10, 2020, 08:47 Dmitry Semchonok <Sem...@gm...> wrote:

> Dear colleagues,
>
>
>
> It may be the bug of issue happening after the particle polishing with the
> relion masking 3D protocol.
>
>
>
> It seems that it has a 10x times issue.
>
> So, adjusting the volume threshold in chimera (for 3D mask protocol and
> then postprocessing) till no extra noise is appeared we get the value for
> ex. 0.00658. But if you then put this value to the relion 3D mask protocol
> you get completely dark images. At the same time if you set the threshold
> value 0.000658 you get the fine mask.
>
>
>
> I am not sure what causes that but I noticed that behaviour happening
> sometimes after the execution of the Bayesian polishing.
>
>
>
> Sincerely,
>
> Dmitry
>
>
> P.s. it will be great to have unbiased protocol for masking
>  Or is there any exist already?
>
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