Hi, thanks to everyone who replied!

Yes, indeed, "relion_image_handler --com" on mask works well.

Conversion from Chimera values suggested by Daniel also works, giving 
the same XYZ.

Thanks again!

Leo

Prof. Leonid Sazanov
IST Austria
Am Campus 1
A-3400 Klosterneuburg
Austria

Phone: +43 2243 9000 3026
E-mail: [log in to unmask]

On 28/01/19 21:00, Takanori Nakane wrote:
> Hi,
>
> XYZ is in pixels, not Angstrom, and the origin is the center of the box.
>
> I don't know how Chimera's "measure center" works.
>
> The most reliable way is to use "relion_image_handler --com" on the
> mask. You can also open the map in relion_display, select the
> right slice and "show the original image" and click on the image.
> The coordinate is printed in the terminal.
>
> Best regards,
>
> Takanori Nakane
>
> On 2019/01/28 18:32, Leonid Sazanov wrote:
>> Hi,
>>
>> I wanted to use new re-centering option on XYZ in particle extraction 
>> in Relion3-beta-20181204 build, but it is not clear how exactly to 
>> get those XYZ values for focused refinement. I tried in Chimera 
>> "measure center" of map containing area of interest, which seems to 
>> give sensible numbers: 198, 202, 147 for 432 pixel box.
>> I then used directly these values as XYZ for re-centering, but that 
>> does not seem to work. The error is "particle55 lies completely 
>> outside micrograph" which should not be the case as the same particle 
>> set works fine if re-extracted with re-centering to 0,0,0.
>>
>> Any info highly appreciated!
>> Thanks!
>>
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