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Re: [scipion-users] export particles and metadata
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From: Pablo C. <pc...@cn...> - 2022-06-09 13:50:10
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You need to update the core: These messages you are getting: The package scipion-pyworkflow is out of date. Your version is 3.0.18, the latest is 3.0.20. The package scipion-em is out of date. Your version is 3.0.13, the latest is 3.0.17. The package scipion-app is out of date. Your version is 3.0.9, the latest is 3.0.10. Means there is new code that is recomended to update. It can be done with: "scipion3 update" On 9/6/22 0:20, C.J. wrote: > Hi, > > I followed the guide > (https://github.com/I2PC/xmipp#standalone-installation) and install > xmipp and link to scipion in |scipion.conf. > | > But there is some issue when launch scipion. > $ scipion > Scipion v3.0.9 - Eugenius > The package scipion-pyworkflow is out of date. Your version is 3.0.18, > the latest is 3.0.20. > The package scipion-em is out of date. Your version is 3.0.13, the > latest is 3.0.17. > The package scipion-app is out of date. Your version is 3.0.9, the > latest is 3.0.10. > > error when importing from xmipp3.protocols: cannot import name > 'setMRCSamplingRate' from 'pwem.convert.headers' > (/data2/sw/scipion3/scipion-em/pwem/convert/headers.py) > File > "/data2/sw/xmipp/xmipp-bundle/src/scipion-em-xmipp/xmipp3/protocols/protocol_rotate_volume.py", > line 30, in <module> > Check the plugin manager (Configuration->Plugins in Scipion manager > window) > or use 'scipion installp --help --checkUpdates' in the command line > to check for upgrades, > it could be a versions compatibility issue. > > There is still no xmipp in scipion GUI. Do I still miss anything? > > Thanks! > Jianhao > > > Alberto Garcia Mena <alb...@cn...> 于2022年6月6日周一 > 01:20写道： > > Hi again, > > To install xmipp devel please follow this guide: > https://github.com/I2PC/xmipp#standalone-installation > > On 4/6/22 1:08, C.J. wrote: >> Hi, I try to install xmipp but there is a question in the output >> log (see attached picture). How can I response to the question? I >> can't click it or type in the log. It's only a text display in >> the output log. >> >> Thanks! >> Jianhao >> >> <jam...@gm...> 于2022年5月27日周五 15:23写道： >> >> I think you need xmipp. emlib can point to that. >> >> Best wishes >> James >> >>> On 27 May 2022, at 23:53, C.J. <bi...@gm...> wrote: >>> >>> >>> Hi, >>> >>> I have some issue (see the attached picture) while exporting >>> particles. Did I miss something when installing SCIPION? >>> >>> Thanks! >>> Jianhao >>> >>> Serban Ilca <SI...@ny...> 于2022年5月27日周五 12:14写道： >>> >>> Hi Jianhao, >>> >>> As Grigory pointed out, you can indeed run 'relion - >>> export particles' on the output of 'localrec - extract >>> subparticles' to accomplish what you want. >>> >>> Cheers, >>> Serban >>> ------------------------------------------------------------------------ >>> *From:* C.J. <bi...@gm...> >>> *Sent:* 27 May 2022 13:18 >>> *To:* Mailing list for Scipion users >>> <sci...@li...> >>> *Subject:* Re: [scipion-users] export particles and >>> metadata >>> Hi, these particles are re-extracted by localrec. Soooo, >>> i don't think relion can do that. >>> >>> Jianhao >>> >>> Grigory Sharov <sha...@gm...> >>> 于2022年5月27日周五 02:26写道： >>> >>> Hi, >>> >>> I don't know about localrec plugin but relion plugin >>> has an export particle protocol that does exactly that. >>> >>> 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 <tel:+44%201223%20267228> >>> e-mail: gs...@mr... >>> >>> >>> On Fri, May 27, 2022 at 12:32 AM C.J. >>> <bi...@gm...> wrote: >>> >>> Hi, >>> >>> I run localrec in SCIPION v3.0.9 to extract >>> subparticles. But how can I export both >>> particles and metadata into relion3 star file >>> and particles? >>> >>> Thank you! >>> Jianhao >>> _______________________________________________ >>> 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 >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> Untitled.png_______________________________________________ >>> 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 >> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users > -- > - Alberto GM - > _______________________________________________ > 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 -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
