Re: [scipion-users] obstacles during relion 3d autoref map deposition to https://deposit-pdbe.wwpdb.org

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

Hi Dmitry,

Scipion does not create output mrc files, Relion does. Afaik, the pixel
size has been written by Relion in the output mrc files since many years.
So, unless you modified the output mrc in some way I don't see how it is
possible for this problem o happen.

I've just created a test deposition and uploaded Relion in Scipion output
mrc map from 3D refinement without any issues. The website asks you to
provide pixel size and contour level anyway.

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 Fri, Apr 24, 2020 at 11:00 AM Dmitry A. Semchonok <sem...@gm...>
wrote:

> Dear colleagues,
>
>
>
> There is an issue while depositing maps to the
>
> https://deposit-pdbe.wwpdb.org/deposition/
>
>
>
> After you load the maps – the website doesn’t except them.
>
> The error message is that they are it the wrong format. But they are not.
>
>
>
> So
>
> The maps were obtained in the relion 3D auto-refinement.
>
> And it seems that the info about pixel size / box-size is missing.
> Therefore the website -
>
> https://deposit-pdbe.wwpdb.org/deposition/ can not read it.
>
>
>
> I will try
>
>
>
> relion_image_handler --i INPUTMAP.mrc --o OUTPUTMAP.mrc --angpix XXX
> --new_box
>
>
>
> If this is the reason and the cure mentioned above helps I will report
> after.
>
>
>
> Is it possible to fix that issue for the future from the SCIPION directly
> (to get the maps with readable parameters for
> https://deposit-pdbe.wwpdb.org) ?
>
>
>
> Thank you!
>
>
>
> Sincerely,
>
> Dmitry
>
>
>
>
>
>
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
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