Re: [scipion-users] export particles and metadata

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

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The package scipion-pyworkflow is out of date.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The package scipion-em is out of date.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The package scipion-app is out of date.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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