Re: [scipion-users] export particles and metadata

[C.J. <bi...@gm...>]

Thanks! After update xmipp, it works now.

Pablo Conesa <pc...@cn...> 于2022年6月9日周四 06:50写道：

> 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 The package scipion-pyworkflow is out of date.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 The package scipion-em is out of date.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 The package scipion-app is out of date.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 The package scipion-pyworkflow is out of date.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 The package scipion-em is out of date.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 The package scipion-app is out of date.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 <+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
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>>
>>
>> _______________________________________________
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>>
>> --
>> - Alberto GM -
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>
>
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> --
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
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