You can also perform 3D classification without alignment, k=1 and 1 iteration. Since there is no alignment the reference for this job is ignored so use anything. It’s basically the same as relion_reconstruct.
Randy
> On Dec 8, 2020, at 11:46 PM, Dieter Blaas <[log in to unmask]> wrote:
>
> Hi Takanori,
>
> I do not know whether the few pixels matter but I preferred doing it correctly :-)
>
> the negative values did the job :-)
>
> I did it in two steps.
>
> Everything fine, thank you very much,
>
> bw Dieter
>
> ------------------------------------------------------------------------
> Dieter Blaas,
> Max Perutz Laboratories
> Medical University of Vienna,
> Inst. Med. Biochem., Vienna Biocenter (VBC),
> Dr. Bohr Gasse 9/3,
> A-1030 Vienna, Austria,
> Tel: 0043 1 4277 61630,
> Mobile: 0043 699 1942 1659
> e-mail: [log in to unmask]
> ------------------------------------------------------------------------
>
>> On 09.12.2020 08:13, Takanori Nakane wrote:
>> Hi,
>>
>> Probably the difference of a few pixels does not matter, do it?
>>
>> > I also tried by using the parameters --shift_x --shift_y --shift_z either with the values above or with subtracted values but I did not get anywhere.
>>
>> Did you try the NEGATIVE of the values?
>> To bring (40.6018 , 21.9723 , 144.542) into the origin, you have to
>> translate by the opposite of this amount.
>>
>> Did you perform --new_box after --shift_x/y/z as a separate step?
>> I don't remember if it works in this case, but in general, it is safer
>> to apply different operations in separate runs of relion_image_handler,
>> because the order of operations is not dictated by the order of arguments
>> and often leads to unexpected results.
>>
>> Finally, you can generate the reference by running relion_reconstruct
>> on the subtracted particle STAR file. Since you don't need high resolution,
>> you can use the first few thousand particles alone (or even fewer with
>> higher symmetry).
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>>> On 2020/12/09 7:00, Dieter Blaas wrote:
>>> Hi,
>>>
>>> I run particle subtraction in relion-3.1.1: What is the best way to obtain a (reference) map with the corresponding smaller box (e.g. 150 px)?
>>>
>>> In "Particle subtraction" I used a mask (450 px) to keep the region of interest and received this message: "+ The subtracted particles will be re-centred on projections of 3D-coordinate: (*40.6018 , 21.9723 , 144.542*)". I then tried obtaining a 150 px reference map from the original map by running "relion_image_handler --i original_450.mrc --o recentred_original_450.mrc --shift_com" and obtained "center of mass: *x= 38.1937 y= 23.074 z= 145.534. *So, the centres of mask and map diverge slightly upon making the final 150px box with "relion_image_handler --i recentred_original_450_box.mrc --i final_recentred_150_box.mrc --new_box 150.
>>>
>>> I also tried by using the parameters --shift_x --shift_y --shift_z either with the values above or with subtracted values but I did not get anywhere.
>>>
>>> Thank you for indicating the correct procedure!
>>>
>>> best, Dieter
>>>
>>> ------------------------------------------------------------------------
>>> Dieter Blaas
>>> Max Perutz Laboratories
>>> Medical University of Vienna,
>>> Inst. Med. Biochem., Vienna Biocenter (VBC),
>>> Dr. Bohr Gasse 9/3,
>>> A-1030 Vienna, Austria,
>>> Tel: 0043 1 4277 61630,
>>> Mobile: 0043 699 1942 1659
>>> e-mail:[log in to unmask]
>>> ------------------------------------------------------------------------
>>>
>>>
>>> ------------------------------------------------------------------------------------------------------------------------------------------------------
>>>
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>>>
>>
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