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

[Dmitry S. <Sem...@gm...>]

Dear Carlos Oscar and Grigory,

Thank you for your answers.

The following image illustrates the problem.

1. Thank you Carlos Oscar — on the image below I compared the Xmipp masking and is works as it should based on the correct threshold.
2. Thank you Grigory — no the binning value seems to be ok.


Sincerely,
Dmitry













> On 10. Dec 2020, at 11:32, Grigory Sharov <sha...@gm...> wrote:
> 
> 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... <mailto: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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