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Re: [scipion-users] obstacles during relion 3d autoref map deposition to https://deposit-pdbe.wwpdb.org
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From: Marta M. <mm...@cn...> - 2020-05-04 07:30:20
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Hi all, try to use the scipion protocol export_to_DB, it saves all the files you need to submit to EMDB in a directory in the right format for submitting. Wbw, MARTA Quoting Grigory Sharov <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 >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> -- Marta Martinez Gonzalez Biocomputing Unit (Lab B13) National Center for Biotechnology-CSIC Darwin, 3. Campus de la Universidad Autonoma de Madrid 28049 Madrid. Spain Tel:+34 915854510 Fax:+34 913720112 E-mail: mm...@cn... |
