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

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

Hi,

lowpass 15A requires a different threshold than low pass -1.

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gs...@mr...


On Thu, Dec 10, 2020 at 2:19 PM Dmitry Semchonok <Sem...@gm...>
wrote:

> Dear Grigory,
>
> Yes indeed it worked.
> Thank you!
>
> I still would like to understand why the recommended settings that are
> described in the Help for te protocol run: ProtRelionCreateMask do not work?
> As you see in this Help the 15-20 angstrom lowpass filter may work as
> well.
>
> Please see my test image below.
>
> Sincerely,
> Dmitry
>
>
>
>
>
> On 10. Dec 2020, at 14:39, Grigory Sharov <sha...@gm...>
> wrote:
>
> Hi,
>
> I've checked this and as I said before your comparison is wrong. Set in
> relion lowpass to -1, extend and soft edge to 0 and then the same threshold
> as in xmipp will give you (almost) the same volume.
>
> Best regards,
> Grigory
>
>
> --------------------------------------------------------------------------------
> Grigory Sharov, Ph.D.
>
> MRC Laboratory of Molecular Biology,
> Francis Crick Avenue,
> Cambridge Biomedical Campus,
> Cambridge CB2 0QH, UK.
> tel. +44 (0) 1223 267228 <+44%201223%20267228>
> e-mail: gs...@mr...
>
>
> On Thu, Dec 10, 2020 at 10:53 AM Dmitry Semchonok <Sem...@gm...>
> wrote:
>
>> I guess it happens not often, but I noticed that happening more ofter
>> after the bayesian polishing.
>>
>> The log shows the same values as I set in.
>>
>> Please let me know in case you want see the problem on our server
>> directly (if it can help somehow).
>>
>>
>> Sincerely,
>> Dmitry
>>
>>
>>
>>
>> On 10. Dec 2020, at 11:51, Grigory Sharov <sha...@gm...>
>> wrote:
>>
>> I'll check this, thanks
>>
>> On Thu, Dec 10, 2020, 10:48 Dmitry Semchonok <Sem...@gm...> wrote:
>>
>>> 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...>
>>> 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?
>>>>
>>>> _______________________________________________
>>>> scipion-users mailing list
>>>> sci...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>>
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>
>>>
>>> <Screenshot 2020-12-10 at 11.40.39.png><Screenshot 2020-12-10 at
>> 11.40.39.png>
>>
>>
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