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From: Alberto G. M. <alb...@cn...> - 2024-06-12 08:33:49
|
Dear all, The Xmipp team has released the new version of Xmipp. Please welcome to *Xmipp 3.24.06 - Oceanus. * For this version we have updated 179 files, more than 16000 lines added and 7643 lines removed. The main new features of Xmipp are described here <https://i2pc.github.io/docs/Releases/Releases-xmipp-program/index.html#oceanus>, those of the plugin scipion-em-xmipp arehere <https://i2pc.github.io/docs/Releases/Releases-scipion-em-xmipp/index.html#oceanus>and those of the plugin scipion-em-xmippTomo are here. Feel free toinstall it <https://i2pc.github.io/docs/Installation/Requirements/index.html>, test it, report any problems if they arise and above all enjoy it!You can update *scipion-em-xmipp* and *scipion-em-xmippTomo* with the plugin manager of Scipion or running/.///scipion3 installp -p scipion-em-xmipp and //.///scipion3 installp -p scipion-em-xmippTomo/ We would like to take this opportunity to remind you that we have a documentation web page <https://i2pc.github.io/docs/index.html>, with information about the installation process, requirements, release details, tips for developers, and also the list of publications of this great software named Xmipp /Xmipp team/ -- Alberto García Mena National Center for Biotechnology - CSIC Facility software support & Xmipp team @ Biocomputing Unit / I2PC |
|
From: Grigory S. <sha...@gm...> - 2024-01-05 23:28:29
|
Dear Claudio, stk is the SPIDER format (along with spi, vol etc.). If you want to use Chimera, you could rename stk to vol, then it will recognize it. Otherwise, Scipion has several built-in viewers that can display volumes. 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, Jan 5, 2024 at 11:15 PM Grosman, Claudio <gr...@il...> wrote: > Dear Scipion team members, > > I am trying to filter a map using the xmipp3 - filter volumes protocol. > Among the output files I see an stk file, but *I do not see an mrc file > that could be opened with, say ChimeraX*. > > Is the protocol meant o work like this? Is only an stk file generated as a > result? > > Muchas gracias, por adelantado! > > > > Claudio > > > -- > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Grosman, C. <gr...@il...> - 2024-01-05 23:14:51
|
Dear Scipion team members, I am trying to filter a map using the xmipp3 - filter volumes protocol. Among the output files I see an stk file, but _*I do not see an mrc file that could be opened with, say ChimeraX*_. Is the protocol meant o work like this? Is only an stk file generated as a result? Muchas gracias, por adelantado! Claudio -- |
|
From: Pablo C. M. <pc...@cn...> - 2023-12-07 12:43:14
|
You are probably missing xmipp binaries.
scipion3 installb xmippSrc
Should do the installation. In case there is any error send it here and
some xmipp developer will help you.
El 07/12/2023 a las 11:34, Lugmayr, Wolfgang escribió:
> Hi Grigory,
>
> yes, this has no problems:
> $ scipion inspect xmipp3
> Scipion v3.3.0 - Eugenius
> Plugin: xmipp3
> >>> constants: loaded
> >>> convert: loaded
> >>> protocols: loaded
> >>> wizards: loaded
> >>> viewers: loaded
> >>> tests: loaded
>
> but how do i get now rid of the message???
> >>> WARNING: Image library not found!
> > Please install Xmipp to get full functionality.
>
> cheers,
> wolfgang
>
> ------------------------------------------------------------------------
> *From: *"Grigory Sharov" <sha...@gm...>
> *To: *"Mailing list for Scipion users"
> <sci...@li...>
> *Sent: *Thursday, 7 December, 2023 11:18:55
> *Subject: *[EXT] Re: [scipion-users] scipion 3.3 - xmipp 3.23.11.0 -
> No module named 'xmipp.constants'; 'xmipp' is not a package
>
> Hi Wolfgang,
> you should use "scipion3 inspect xmipp3" instead
>
> 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
> e-mail: gs...@mr...
>
>
> On Thu, Dec 7, 2023 at 9:58 AM Lugmayr, Wolfgang <w.l...@uk...> wrote:
>
> hi,
>
> i made an new fresh installation of scipion 3.3 (incl. new
> miniconda) with only stable tomo plugins and got the following error:
> >>> WARNING: Image library not found!
> > Please install Xmipp to get full functionality.
> (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion
> plugin manager window)
>
> the plugin manager thinks its installed:
> scipion-em-xmipp 23.11.0.0 [X]
> scipion-em-xmipp2 [ ]
> scipion-em-xmipptomo 3.23.11.0 [X]
>
> and with inspect i get:
> $ scipion3 inspect xmipp
> Scipion v3.3.0 - Eugenius
>
> >>> WARNING: 'import xmipp' is deprecated for the xmipp binding.
> Plugin: xmipp
> >>> constants: error -> Traceback (most recent call last):
> File
> "/gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/inspect_plugins.py",
> line 74, in getSubmodule
> m = importlib.import_module('%s.%s' % (name, subname))
> File
> "/gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/miniconda/envs/scipion3/lib/python3.8/importlib/__init__.py",
> line 127, in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
> File "<frozen importlib._bootstrap>", line 991, in _find_and_load
> File "<frozen importlib._bootstrap>", line 970, in
> _find_and_load_unlocked
> ModuleNotFoundError: No module named 'xmipp.constants'; 'xmipp' is
> not a package
> :
>
> do i need a development version of the core packages?
> $ scipion3 update
> Scipion v3.3.0 - Eugenius
> The package scipion-pyworkflow is up to date. Your version is 3.3.1
> The package scipion-em is up to date. Your version is 3.4.0
> The package scipion-app is up to date. Your version is 3.3.0
> Scipion is up to date.
>
> cheers,
> wolfgang
>
> p.s.
> the last lines of the xmipp install:
> :
> Compiling xmippViz----------------------------------------
> Done. Visit compileLOG.txt for details
>
> * Xmipp has been successfully compiled *
> > > > Don't forget to install! < < <
>
>
> CC variable found in the environment with this value:
> /gpfs/cssb/software/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-11.3.0-2jqkvfzltuxvi4y5v6j35ie2qosqhjdk/bin/gcc.
> CXX variable found in the environment with this value:
> /gpfs/cssb/software/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-11.3.0-2jqkvfzltuxvi4y5v6j35ie2qosqhjdk/bin/g++.
>
> Installing -----------------------------------------------
> Xmipp installed on
> /gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/software/em/xmippSrc-v3.23.11.0/build
>
> Linking to Scipion ---------------------------------------
> Xmipp linked to Scipion on
> /gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/software/em/xmipp
> ************************************************************
> * *
> * Xmipp Nereus has been successfully installed, enjoy it! *
> * *
> ************************************************************
>
>
>
> --
> Universitätsklinikum Hamburg-Eppendorf (UKE)
> @ Centre for Structral Systems Biology (CSSB)
> @ Deutsches Elektronen-Synchrotron (DESY)
> Notkestrasse 85 Gebäude 15
> 22607 Hamburg, Germany
> Tel.: +49 40 8998-87652
> Email: wol...@cs...
> http://www.cssb-hamburg.de/
>
>
> _______________________________________________
> 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
--
Pablo Conesa
*Scipion <http://scipipon.i2pc.es> cryo-em workflow engine developer at
Madrid, among many others.*
Join us in Discord <https://discord.gg/TzS5VTKQbY> |
|
From: Grigory S. <sha...@gm...> - 2023-12-07 10:41:21
|
inspect command only checks the plugin (python code), not the compiled
binaries. You'll need to check compileLOG.txt for any errors.
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 Thu, Dec 7, 2023 at 10:35 AM Lugmayr, Wolfgang <w.l...@uk...> wrote:
> Hi Grigory,
>
> yes, this has no problems:
> $ scipion inspect xmipp3
> Scipion v3.3.0 - Eugenius
> Plugin: xmipp3
> >>> constants: loaded
> >>> convert: loaded
> >>> protocols: loaded
> >>> wizards: loaded
> >>> viewers: loaded
> >>> tests: loaded
>
> but how do i get now rid of the message???
> >>> WARNING: Image library not found!
> > Please install Xmipp to get full functionality.
>
> cheers,
> wolfgang
>
> ------------------------------
> *From: *"Grigory Sharov" <sha...@gm...>
> *To: *"Mailing list for Scipion users" <
> sci...@li...>
> *Sent: *Thursday, 7 December, 2023 11:18:55
> *Subject: *[EXT] Re: [scipion-users] scipion 3.3 - xmipp 3.23.11.0 - No
> module named 'xmipp.constants'; 'xmipp' is not a package
>
> Hi Wolfgang,
> you should use "scipion3 inspect xmipp3" instead
>
> 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
> e-mail: gs...@mr...
>
>
> On Thu, Dec 7, 2023 at 9:58 AM Lugmayr, Wolfgang <w.l...@uk...> wrote:
>
>> hi,
>>
>> i made an new fresh installation of scipion 3.3 (incl. new miniconda)
>> with only stable tomo plugins and got the following error:
>> >>> WARNING: Image library not found!
>> > Please install Xmipp to get full functionality.
>> (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin
>> manager window)
>>
>> the plugin manager thinks its installed:
>> scipion-em-xmipp 23.11.0.0 [X]
>> scipion-em-xmipp2 [ ]
>> scipion-em-xmipptomo 3.23.11.0 [X]
>>
>> and with inspect i get:
>> $ scipion3 inspect xmipp
>> Scipion v3.3.0 - Eugenius
>>
>> >>> WARNING: 'import xmipp' is deprecated for the xmipp binding.
>> Plugin: xmipp
>> >>> constants: error -> Traceback (most recent call last):
>> File
>> "/gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/inspect_plugins.py",
>> line 74, in getSubmodule
>> m = importlib.import_module('%s.%s' % (name, subname))
>> File
>> "/gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/miniconda/envs/scipion3/lib/python3.8/importlib/__init__.py",
>> line 127, in import_module
>> return _bootstrap._gcd_import(name[level:], package, level)
>> File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
>> File "<frozen importlib._bootstrap>", line 991, in _find_and_load
>> File "<frozen importlib._bootstrap>", line 970, in
>> _find_and_load_unlocked
>> ModuleNotFoundError: No module named 'xmipp.constants'; 'xmipp' is not a
>> package
>> :
>>
>> do i need a development version of the core packages?
>> $ scipion3 update
>> Scipion v3.3.0 - Eugenius
>> The package scipion-pyworkflow is up to date. Your version is 3.3.1
>> The package scipion-em is up to date. Your version is 3.4.0
>> The package scipion-app is up to date. Your version is 3.3.0
>> Scipion is up to date.
>>
>> cheers,
>> wolfgang
>>
>> p.s.
>> the last lines of the xmipp install:
>> :
>> Compiling xmippViz----------------------------------------
>> Done. Visit compileLOG.txt for details
>>
>>
>> * Xmipp has been successfully compiled *
>> > > > Don't forget to install! < < <
>>
>>
>> CC variable found in the environment with this value:
>> /gpfs/cssb/software/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-11.3.0-2jqkvfzltuxvi4y5v6j35ie2qosqhjdk/bin/gcc.
>> CXX variable found in the environment with this value:
>> /gpfs/cssb/software/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-11.3.0-2jqkvfzltuxvi4y5v6j35ie2qosqhjdk/bin/g++.
>>
>> Installing -----------------------------------------------
>> Xmipp installed on
>> /gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/software/em/xmippSrc-v3.23.11.0/build
>>
>> Linking to Scipion ---------------------------------------
>> Xmipp linked to Scipion on
>> /gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/software/em/xmipp
>>
>>
>> ************************************************************
>> * *
>> * Xmipp Nereus has been successfully installed, enjoy it! *
>> * *
>> ************************************************************
>>
>>
>>
>> --
>> Universitätsklinikum Hamburg-Eppendorf (UKE)
>> @ Centre for Structral Systems Biology (CSSB)
>> @ Deutsches Elektronen-Synchrotron (DESY)
>> Notkestrasse 85 Gebäude 15
>> 22607 Hamburg, Germany
>> Tel.: +49 40 8998-87652
>> Email: wol...@cs...
>> http://www.cssb-hamburg.de/
>>
>>
>> _______________________________________________
>> 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
>
|
|
From: Lugmayr, W. <w.l...@uk...> - 2023-12-07 10:34:50
|
Hi Grigory,
yes, this has no problems:
$ scipion inspect xmipp3
Scipion v3.3.0 - Eugenius
Plugin: xmipp3
>>> constants: loaded
>>> convert: loaded
>>> protocols: loaded
>>> wizards: loaded
>>> viewers: loaded
>>> tests: loaded
but how do i get now rid of the message???
>>> WARNING: Image library not found!
> Please install Xmipp to get full functionality.
cheers,
wolfgang
From: "Grigory Sharov" <sha...@gm...>
To: "Mailing list for Scipion users" <sci...@li...>
Sent: Thursday, 7 December, 2023 11:18:55
Subject: [EXT] Re: [scipion-users] scipion 3.3 - xmipp 3.23.11.0 - No module named 'xmipp.constants'; 'xmipp' is not a package
Hi Wolfgang,
you should use "scipion3 inspect xmipp3" instead
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
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Thu, Dec 7, 2023 at 9:58 AM Lugmayr, Wolfgang < [ mailto:w.l...@uk... | w.l...@uk... ] > wrote:
hi,
i made an new fresh installation of scipion 3.3 (incl. new miniconda) with only stable tomo plugins and got the following error:
>>> WARNING: Image library not found!
> Please install Xmipp to get full functionality.
(Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window)
the plugin manager thinks its installed:
scipion-em-xmipp 23.11.0.0 [X]
scipion-em-xmipp2 [ ]
scipion-em-xmipptomo 3.23.11.0 [X]
and with inspect i get:
$ scipion3 inspect xmipp
Scipion v3.3.0 - Eugenius
>>> WARNING: 'import xmipp' is deprecated for the xmipp binding.
Plugin: xmipp
>>> constants: error -> Traceback (most recent call last):
File "/gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/inspect_plugins.py", line 74, in getSubmodule
m = importlib.import_module('%s.%s' % (name, subname))
File "/gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/miniconda/envs/scipion3/lib/python3.8/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 970, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'xmipp.constants'; 'xmipp' is not a package
:
do i need a development version of the core packages?
$ scipion3 update
Scipion v3.3.0 - Eugenius
The package scipion-pyworkflow is up to date. Your version is 3.3.1
The package scipion-em is up to date. Your version is 3.4.0
The package scipion-app is up to date. Your version is 3.3.0
Scipion is up to date.
cheers,
wolfgang
p.s.
the last lines of the xmipp install:
:
Compiling xmippViz----------------------------------------
Done. Visit compileLOG.txt for details
* Xmipp has been successfully compiled *
> > > Don't forget to install! < < <
CC variable found in the environment with this value: /gpfs/cssb/software/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-11.3.0-2jqkvfzltuxvi4y5v6j35ie2qosqhjdk/bin/gcc.
CXX variable found in the environment with this value: /gpfs/cssb/software/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-11.3.0-2jqkvfzltuxvi4y5v6j35ie2qosqhjdk/bin/g++.
Installing -----------------------------------------------
Xmipp installed on /gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/software/em/xmippSrc-v3.23.11.0/build
Linking to Scipion ---------------------------------------
Xmipp linked to Scipion on /gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/software/em/xmipp
************************************************************
* *
* Xmipp Nereus has been successfully installed, enjoy it! *
* *
************************************************************
--
Universitätsklinikum Hamburg-Eppendorf (UKE)
@ Centre for Structral Systems Biology (CSSB)
@ Deutsches Elektronen-Synchrotron (DESY)
Notkestrasse 85 Gebäude 15
22607 Hamburg, Germany
Tel.: +49 40 8998-87652
Email: [ mailto:wol...@cs... | wol...@cs... ]
[ http://www.cssb-hamburg.de/ | http://www.cssb-hamburg.de/ ]
_______________________________________________
scipion-users mailing list
[ mailto:sci...@li... | sci...@li... ]
[ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ]
_______________________________________________
scipion-users mailing list
sci...@li...
https://lists.sourceforge.net/lists/listinfo/scipion-users
|
|
From: Grigory S. <sha...@gm...> - 2023-12-07 10:19:15
|
Hi Wolfgang,
you should use "scipion3 inspect xmipp3" instead
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 Thu, Dec 7, 2023 at 9:58 AM Lugmayr, Wolfgang <w.l...@uk...> wrote:
> hi,
>
> i made an new fresh installation of scipion 3.3 (incl. new miniconda) with
> only stable tomo plugins and got the following error:
> >>> WARNING: Image library not found!
> > Please install Xmipp to get full functionality.
> (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin
> manager window)
>
> the plugin manager thinks its installed:
> scipion-em-xmipp 23.11.0.0 [X]
> scipion-em-xmipp2 [ ]
> scipion-em-xmipptomo 3.23.11.0 [X]
>
> and with inspect i get:
> $ scipion3 inspect xmipp
> Scipion v3.3.0 - Eugenius
>
> >>> WARNING: 'import xmipp' is deprecated for the xmipp binding.
> Plugin: xmipp
> >>> constants: error -> Traceback (most recent call last):
> File
> "/gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/inspect_plugins.py",
> line 74, in getSubmodule
> m = importlib.import_module('%s.%s' % (name, subname))
> File
> "/gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/miniconda/envs/scipion3/lib/python3.8/importlib/__init__.py",
> line 127, in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
> File "<frozen importlib._bootstrap>", line 991, in _find_and_load
> File "<frozen importlib._bootstrap>", line 970, in
> _find_and_load_unlocked
> ModuleNotFoundError: No module named 'xmipp.constants'; 'xmipp' is not a
> package
> :
>
> do i need a development version of the core packages?
> $ scipion3 update
> Scipion v3.3.0 - Eugenius
> The package scipion-pyworkflow is up to date. Your version is 3.3.1
> The package scipion-em is up to date. Your version is 3.4.0
> The package scipion-app is up to date. Your version is 3.3.0
> Scipion is up to date.
>
> cheers,
> wolfgang
>
> p.s.
> the last lines of the xmipp install:
> :
> Compiling xmippViz----------------------------------------
> Done. Visit compileLOG.txt for details
>
>
> * Xmipp has been successfully compiled *
> > > > Don't forget to install! < < <
>
>
> CC variable found in the environment with this value:
> /gpfs/cssb/software/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-11.3.0-2jqkvfzltuxvi4y5v6j35ie2qosqhjdk/bin/gcc.
> CXX variable found in the environment with this value:
> /gpfs/cssb/software/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-11.3.0-2jqkvfzltuxvi4y5v6j35ie2qosqhjdk/bin/g++.
>
> Installing -----------------------------------------------
> Xmipp installed on
> /gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/software/em/xmippSrc-v3.23.11.0/build
>
> Linking to Scipion ---------------------------------------
> Xmipp linked to Scipion on
> /gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/software/em/xmipp
>
>
> ************************************************************
> * *
> * Xmipp Nereus has been successfully installed, enjoy it! *
> * *
> ************************************************************
>
>
>
> --
> Universitätsklinikum Hamburg-Eppendorf (UKE)
> @ Centre for Structral Systems Biology (CSSB)
> @ Deutsches Elektronen-Synchrotron (DESY)
> Notkestrasse 85 Gebäude 15
> 22607 Hamburg, Germany
> Tel.: +49 40 8998-87652
> Email: wol...@cs...
> http://www.cssb-hamburg.de/
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
|
|
From: Lugmayr, W. <w.l...@uk...> - 2023-12-07 09:58:05
|
hi,
i made an new fresh installation of scipion 3.3 (incl. new miniconda) with only stable tomo plugins and got the following error:
>>> WARNING: Image library not found!
> Please install Xmipp to get full functionality.
(Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window)
the plugin manager thinks its installed:
scipion-em-xmipp 23.11.0.0 [X]
scipion-em-xmipp2 [ ]
scipion-em-xmipptomo 3.23.11.0 [X]
and with inspect i get:
$ scipion3 inspect xmipp
Scipion v3.3.0 - Eugenius
>>> WARNING: 'import xmipp' is deprecated for the xmipp binding.
Plugin: xmipp
>>> constants: error -> Traceback (most recent call last):
File "/gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/miniconda/envs/scipion3/lib/python3.8/site-packages/scipion/install/inspect_plugins.py", line 74, in getSubmodule
m = importlib.import_module('%s.%s' % (name, subname))
File "/gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/miniconda/envs/scipion3/lib/python3.8/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 970, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'xmipp.constants'; 'xmipp' is not a package
:
do i need a development version of the core packages?
$ scipion3 update
Scipion v3.3.0 - Eugenius
The package scipion-pyworkflow is up to date. Your version is 3.3.1
The package scipion-em is up to date. Your version is 3.4.0
The package scipion-app is up to date. Your version is 3.3.0
Scipion is up to date.
cheers,
wolfgang
p.s.
the last lines of the xmipp install:
:
Compiling xmippViz----------------------------------------
Done. Visit compileLOG.txt for details
* Xmipp has been successfully compiled *
> > > Don't forget to install! < < <
CC variable found in the environment with this value: /gpfs/cssb/software/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-11.3.0-2jqkvfzltuxvi4y5v6j35ie2qosqhjdk/bin/gcc.
CXX variable found in the environment with this value: /gpfs/cssb/software/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-11.3.0-2jqkvfzltuxvi4y5v6j35ie2qosqhjdk/bin/g++.
Installing -----------------------------------------------
Xmipp installed on /gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/software/em/xmippSrc-v3.23.11.0/build
Linking to Scipion ---------------------------------------
Xmipp linked to Scipion on /gpfs/cssb/software/centos7/x86_64/scipion/3.x-tomo/software/em/xmipp
************************************************************
* *
* Xmipp Nereus has been successfully installed, enjoy it! *
* *
************************************************************
--
Universitätsklinikum Hamburg-Eppendorf (UKE)
@ Centre for Structral Systems Biology (CSSB)
@ Deutsches Elektronen-Synchrotron (DESY)
Notkestrasse 85 Gebäude 15
22607 Hamburg, Germany
Tel.: +49 40 8998-87652
Email: wol...@cs...
http://www.cssb-hamburg.de/
|
|
From: Alberto G. M. <alb...@cn...> - 2023-11-28 09:52:55
|
Dear all, The Xmipp team has released the new version of Xmipp. Please welcome to *Xmipp 3.23.11- Nereus. * For this version we have updated 122 files, more than 3300 lines added and 2936 lines removed. The main new features of Xmipp are described here <https://i2pc.github.io/docs/Releases/Releases-xmipp-program/index.html#nereus>, those of the plugin scipion-em-xmipp are here <https://i2pc.github.io/docs/Releases/Releases-scipion-em-xmippTomo/index.html#nereus> and those of the plugin scipion-em-xmippTomo are here <https://github.com/I2PC/scipion-em-xmipptomo/blob/devel/CHANGES.md>. Feel free to install it <https://github.com/I2PC/xmipp#standalone-installation>, test it, report any problems <https://github.com/I2PC/xmipp/issues> if they arise and above all enjoy it!You can update *scipion-em-xmipp* and *scipion-em-xmippTomo* with the plugin manager of Scipion or running/.///scipion3 installp -p scipion-em-xmipp and //.///scipion3 installp -p scipion-em-xmippTomo/ We would like to take this opportunity to inform you that we have a new documentation web page <https://i2pc.github.io/docs/index.html>, with information about the installation process, requirements, release details, tips for developers, and also the list of publications of this great software named Xmipp /Xmipp team/ -- Alberto García Mena National Center for Biotechnology - CSIC Facility software support & Xmipp team @ Biocomputing Unit / I2PC |
|
From: Alberto G. M. <alb...@cn...> - 2023-11-23 08:42:07
|
Hello Arparna, Please review your cmake version and visit this guide aboutCmake-Centos <https://i2pc.github.io/docs/Installation/InstallationNotes/index.html#centos> and about installing Xmipp in Centos <https://i2pc.github.io/docs/Installation/InstallationNotes/index.html#installing-on-centos-7>: Let us know any update and join the Discord channel for more direct conversation. Thanks On 23/11/23 9:09, Pablo Conesa Mingo wrote: > > I'm sorry about this, Aparna. > > Proably someone from xmipp team can help you with this. > > Let me suggest you to Join our discord workspace for a more direct > conversation: https://discord.gg/TzS5VTKQbY > > El 23/11/2023 a las 7:28, Aparna Kumari (via scipion Mailing List) > escribió: >> >> Hi All, >> >> I am trying to install Scipion and Xmipp in our cluster environment >> but facing issue from few weeks. Although Scipion is getting >> installed successfully but Xmipp is failing with error failed to >> install googletest dependence but in compile log error says compiler >> greater than equal to c++14 is required . I need help as this >> software is very important for us. >> >> 1: I am doing it in conda environment. >> 2. Scipion getting installed but Xmipp failing >> 3. OS: centos 7.9.2 >> 4. conda version:23.5.2 >> 5. compile logs have been attached with this email >> 6. Scipion version I am trying to install: >> 7.gcc:10.4.0 >> 8. Cuda:11.0.3 >> 9. oepnmpi:4.1.0 >> 10. xmipp config file and error screenshot below: >> >> >> Regards, >> Aparna >> ------------------------------------------------ >> Aparna Kumari >> Sr. Scientist >> Information Technology Group, >> CSIR-Centre for Cellular and Molecular Biology >> Habsiguda,Uppal Road,Hyderabad-500007 >> Telangana, India >> >> Phone(Office):040-27192771 >> >> > -- > Pablo Conesa > *Scipion <http://scipipon.i2pc.es> cryo-em workflow engine developer > at Madrid, among many others.* > Join us in Discord <https://discord.gg/TzS5VTKQbY> > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Alberto García Mena National Center for Biotechnology - CSIC Facility software support & Xmipp team @ Biocomputing Unit / I2PC |
|
From: Pablo C. M. <pc...@cn...> - 2023-11-23 08:25:31
|
I'm sorry about this, Aparna. Proably someone from xmipp team can help you with this. Let me suggest you to Join our discord workspace for a more direct conversation: https://discord.gg/TzS5VTKQbY El 23/11/2023 a las 7:28, Aparna Kumari (via scipion Mailing List) escribió: > > Hi All, > > I am trying to install Scipion and Xmipp in our cluster environment > but facing issue from few weeks. Although Scipion is getting installed > successfully but Xmipp is failing with error failed to install > googletest dependence but in compile log error says compiler greater > than equal to c++14 is required . I need help as this software is very > important for us. > > 1: I am doing it in conda environment. > 2. Scipion getting installed but Xmipp failing > 3. OS: centos 7.9.2 > 4. conda version:23.5.2 > 5. compile logs have been attached with this email > 6. Scipion version I am trying to install: > 7.gcc:10.4.0 > 8. Cuda:11.0.3 > 9. oepnmpi:4.1.0 > 10. xmipp config file and error screenshot below: > > > Regards, > Aparna > ------------------------------------------------ > Aparna Kumari > Sr. Scientist > Information Technology Group, > CSIR-Centre for Cellular and Molecular Biology > Habsiguda,Uppal Road,Hyderabad-500007 > Telangana, India > > Phone(Office):040-27192771 > > -- Pablo Conesa *Scipion <http://scipipon.i2pc.es> cryo-em workflow engine developer at Madrid, among many others.* Join us in Discord <https://discord.gg/TzS5VTKQbY> |
|
From: Pablo C. M. <p.c...@gm...> - 2023-10-30 16:09:03
|
Dear Scipion users, or not. We are starting a regular set of SHORT (1hour) meetings (1 per month) to keep in touch with Scipion users or not, and at the same time share our progress with you. The main objectives for this regular meetings are: 1. *Know from us*: Update you with the latest changes released or what is about to come. 1.(not a typo, as important as the above) *Know from you*: Listen to you about anything you want to tell us, improvements, what you like, what you don't like, how to addess your em processing problems... There will be "Scipion developers", "Xmipp developers", "Plugins developers" and expert Scipion users: A whole team at your disposal to help you or listen to your ideas. In general the Agenda would be: 1.- Scipion update (15-20) mins aprox: 2.- Your time. Please, feel free to prepare some slides, share your desktop, just raise your hand and unmute yourself.... this is 100% informal, bring your case or suggestions. It will be strictly 1 hour. So if something remains untuched will be thouche on the next month meeting. You can also send me in advance an agenda item so it is already considered and will take precedence over other questions. We think this would be a nice scenario to contact users with other users and developers. We will not longer use sci...@li.... We have moved to https://discord.gg/TzS5VTKQbY (everyone is welcome to join now that is unlimited) This time it will be this Thursday, 2nd Nov at 16:00 (CET) It will be at https://conectaha.csic.es/b/pab-kc8-xpd-cwl No need to register, just connect! Hope to find you there, Pablo. |
|
From: Alberto G. M. <alb...@cn...> - 2023-07-14 09:34:40
|
Dear all, The Xmipp team has released the new version of Xmipp. Please welcome to *Xmipp 3.23.07- Morpheus. * For this version we have updated 192 files, more than 16000 lines added and 4000 lines removed. The main new features of Xmipp are described here <https://github.com/I2PC/xmipp/blob/devel/CHANGELOG.md>, those of the plugin scipion-em-xmipp are here <https://github.com/I2PC/scipion-em-xmipp/blob/devel/CHANGES.md> and those of the plugin scipion-em-xmippTomoare here <https://github.com/I2PC/scipion-em-xmipptomo/blob/devel/CHANGES.md>. Feel free to install it <https://github.com/I2PC/xmipp#standalone-installation>, test it, report any problems <https://github.com/I2PC/xmipp/issues> if they arise and above all enjoy it!You can update *scipion-em-xmipp* and *scipion-em-xmippTomo* with the plugin manager of Scipion or running/.///scipion3 installp -p scipion-em-xmipp /or///.///scipion3 installp -p scipion-em-xmippTomo/ /Xmipp team/// -- Alberto García Mena National Center for Biotechnology - CSIC Facility software support & Xmipp team @ Biocomputing Unit / I2PC |
|
From: Grigory S. <sha...@gm...> - 2023-06-29 13:04:58
|
Please do not drop the CC to the mailing list. Xmipp installation has failed because you are missing dependencies. Dependencies installation also failed because in the first log file you have: environment: line 5: __conda_exe: command not found > environment: line 6: __conda_exe: command not found Is your conda initialized in ~/.bashrc or ~/.bash_profile ? I think your issue is described here: https://stackoverflow.com/a/69654559 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 Thu, Jun 29, 2023 at 1:06 PM Low, John J. <jl...@mc...> wrote: > Grigory, > > > > I have attached the logs from my first two attempts to install Xmipp. > > > > Install.log.2 is the log from my third attempt. > > > > The second to last line in install.log.2 is: > > > > /home/jlow/.conda/envs/scipion3/bin/python -m pip install > scipion-em-xmipp==23.3.0.3 > > > > Which looks similar to the command in step 6. I did not capture the exact > command that I used to install Xmipp. > > > > Should I try to reinstall Scipion and then Xmipp with all the dependencies > in my environment. Did my three sequential installs corrupt my scipion3 > environment? > > > > John > > *From: *Grigory Sharov <sha...@gm...> > *Date: *Thursday, June 29, 2023 at 3:29 AM > *To: *Low, John J. <jl...@mc...>, Mailing list for Scipion users < > sci...@li...> > *Subject: *Re: [scipion-users] My Scipion installation fails the > pwem.tests.data.test_data test. > > Hello Jon, > > > > 1) to update scipion core packages you can run "scipion update" - this > should get you to 3.1.0 > > 2) xmipp binaries are not installed or not linked/detected by scipion. Did > you follow step 6 in the guide? If yes, could you attach the full > install.log? > > > 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 Wed, Jun 28, 2023 at 3:52 PM Low, John J. <jl...@mc...> wrote: > > Grigory, > > > > As far as I can tell, I have installed xmipp and I still get the same > error. > > > > I have attached my most recent install log (Install.log.2), the output > from the command “scipion tests pwem.tests.data.test_data &> > pwem.tests.data.test_data.log” and the output from the “command scipion > installp --help --checkUpdates &>checkupdates.log.” > > > > I have some packages which need to be updated based on the following from > the console output from the scipion command. > > > > The package scipion-pyworkflow is out of date. Your version is 3.0.32, the > latest is 3.1.0. > > The package scipion-em is out of date. Your version is 3.0.27, the latest > is 3.1.0. > > The package scipion-app is out of date. Your version is 3.0.12, the latest > is 3.1.0. > > > > How do I update these packages? > > > > John Low > > > > *From: *Grigory Sharov <sha...@gm...> > *Date: *Wednesday, June 28, 2023 at 5:04 AM > *To: *Mailing list for Scipion users <sci...@li...> > *Cc: *Low, John J. <jl...@mc...> > *Subject: *Re: [scipion-users] My Scipion installation fails the > pwem.tests.data.test_data test. > > Dear Jon, > > > > I would not expect it to pass all tests since you have not installed xmipp. > > > 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 Wed, Jun 28, 2023 at 11:01 AM Low, John J. via scipion-users < > sci...@li...> wrote: > > To Whom It May Concern: > > > > I followed the instructions at > https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html > to install scipion. > > > > My build passes the basic tests > pyworkflowtests.tests.test_object.TestObject and > pyworkflowtests.tests.test_mappers but fails the pwem.tests.data.test_data > test. > > > > I have attached the output from the failed test. > > > > Could someone please help me debug this failed test? > > > > Thanks! > > > > John J. Low > Argonne National Laboratory > > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
|
From: Grigory S. <sha...@gm...> - 2023-06-29 08:29:09
|
Hello Jon, 1) to update scipion core packages you can run "scipion update" - this should get you to 3.1.0 2) xmipp binaries are not installed or not linked/detected by scipion. Did you follow step 6 in the guide? If yes, could you attach the full install.log? 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 Wed, Jun 28, 2023 at 3:52 PM Low, John J. <jl...@mc...> wrote: > Grigory, > > > > As far as I can tell, I have installed xmipp and I still get the same > error. > > > > I have attached my most recent install log (Install.log.2), the output > from the command “scipion tests pwem.tests.data.test_data &> > pwem.tests.data.test_data.log” and the output from the “command scipion > installp --help --checkUpdates &>checkupdates.log.” > > > > I have some packages which need to be updated based on the following from > the console output from the scipion command. > > > > The package scipion-pyworkflow is out of date. Your version is 3.0.32, the > latest is 3.1.0. > > The package scipion-em is out of date. Your version is 3.0.27, the latest > is 3.1.0. > > The package scipion-app is out of date. Your version is 3.0.12, the latest > is 3.1.0. > > > > How do I update these packages? > > > > John Low > > > > *From: *Grigory Sharov <sha...@gm...> > *Date: *Wednesday, June 28, 2023 at 5:04 AM > *To: *Mailing list for Scipion users <sci...@li...> > *Cc: *Low, John J. <jl...@mc...> > *Subject: *Re: [scipion-users] My Scipion installation fails the > pwem.tests.data.test_data test. > > Dear Jon, > > > > I would not expect it to pass all tests since you have not installed xmipp. > > > 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 Wed, Jun 28, 2023 at 11:01 AM Low, John J. via scipion-users < > sci...@li...> wrote: > > To Whom It May Concern: > > > > I followed the instructions at > https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html > to install scipion. > > > > My build passes the basic tests > pyworkflowtests.tests.test_object.TestObject and > pyworkflowtests.tests.test_mappers but fails the pwem.tests.data.test_data > test. > > > > I have attached the output from the failed test. > > > > Could someone please help me debug this failed test? > > > > Thanks! > > > > John J. Low > Argonne National Laboratory > > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > |
|
From: Grigory S. <sha...@gm...> - 2023-06-28 10:04:41
|
Dear Jon, I would not expect it to pass all tests since you have not installed xmipp. 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 Wed, Jun 28, 2023 at 11:01 AM Low, John J. via scipion-users < sci...@li...> wrote: > To Whom It May Concern: > > > > I followed the instructions at > https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html > to install scipion. > > > > My build passes the basic tests > pyworkflowtests.tests.test_object.TestObject and > pyworkflowtests.tests.test_mappers but fails the pwem.tests.data.test_data > test. > > > > I have attached the output from the failed test. > > > > Could someone please help me debug this failed test? > > > > Thanks! > > > > John J. Low > Argonne National Laboratory > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Low, J. J. <jl...@mc...> - 2023-06-26 20:35:23
|
To Whom It May Concern: I followed the instructions at https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html to install scipion. My build passes the basic tests pyworkflowtests.tests.test_object.TestObject and pyworkflowtests.tests.test_mappers but fails the pwem.tests.data.test_data test. I have attached the output from the failed test. Could someone please help me debug this failed test? Thanks! John J. Low Argonne National Laboratory |
|
From: Grigory S. <sha...@gm...> - 2023-06-21 09:36:11
|
Hello Roman, most likely you are running out of RAM (process killed by Linux OOM). Motioncorr process needs at least frame width ∗ height ∗ (frames + 2 + threads per mpi) ∗ 4 bytes of RAM. Try to increase the number of threads if possible. PS. Your dose per frame is wrong (cannot be 45), but that is not related to the error. 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 Wed, Jun 21, 2023 at 8:23 AM Pablo Conesa <pc...@cn...> wrote: > Hi Roman, could you please post the full run.stderr? > On 21/6/23 1:34, ROMAN AGUIRRE wrote: > > Hello all, > I was recently at the data processing workshop at SLAC, and wanted to try > using Scipion on some of my data after seeing what its capable of. I > installed it on a WSL workstation, and starting Scipion and > installing plugins so far has not resulted in any errors. However, I ran > into problems right away when trying to use Relion's motioncor2. Although > it does say that the job is running, the output logs show the following > errors: > > on run.stdout, it shows > > 00207: relion_run_motioncorr --i PDC__00021_input.star --o output/ > --use_own --first_frame_sum 1 --last_frame_sum 40 --bin_factor 1.000000 > --bfactor 150 --angpix 1.36000 --patch_x 5 --patch_y 5 --group_frames 1 --j > 7 --gainref "/home/romana/Documents/gain_reference_7676x7420_190815s.mrc" > --gain_rot 0 --gain_flip 0 --grouping_for_ps 1 --dose_weighting > --dose_per_frame 45.000000 --preexposure 0.000000 > 00208: Using our own implementation based on MOTIONCOR2 algorithm > 00209: to correct beam-induced motion for the following micrographs: > 00210: * PDC__00021.tif > 00211: Correcting beam-induced motions using our own implementation ... > 00212: 000/??? sec ~~(,_,"> > [oo]Erasing.....movieFolder: > Runs/000118_ProtRelionMotioncor/tmp/movie_000016 > 00213: FINISHED: processMovieStep, step 17, time 2023-06-20 > 16:16:05.085374 > 00214: ERROR: Movie Runs/000002_ProtImportMovies/extra/PDC__00021.tif > couldn't be added to the output set. > 00215: [Errno 2] No such file or directory: > 'Runs/000118_ProtRelionMotioncor/extra/PDC__00021.star' > 00216: WARNING: Micrograph > Runs/000118_ProtRelionMotioncor/extra/PDC__00021_aligned_mic_DW.mrc was not > generated, can't add it to output set. > > and on run.stderr > > 00033: Killed > 00034: ERROR processing movie: PDC__00022.tif > > I was wondering what steps I could take to fix this. I have tried > uninstalling and re-installing the relion plugin, as well as checking that > all the proper dependencies are installed on my workstation. However, I > have been unable to pinpoint what is specifically causing the error. If > this is not the right place to ask for this type of help, please let me > know. Thank you for your time. > > Sincerely, > Roman Aguirre > > Roman Aguirre > PhD Student | Zhou Lab > UCLA | Chemistry and Biochemistry > romanaguirre@g.ucla.edu > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Pablo C. <pc...@cn...> - 2023-06-21 07:23:13
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Hi Roman, could you please post the full run.stderr? On 21/6/23 1:34, ROMAN AGUIRRE wrote: > Hello all, > I was recently at the data processing workshop at SLAC, and wanted to > try using Scipion on some of my data after seeing what its capable of. > I installed it on a WSL workstation, and starting Scipion and > installing plugins so far has not resulted in any errors. However, I > ran into problems right away when trying to use Relion's motioncor2. > Although it does say that the job is running, the output logs show the > following errors: > > on run.stdout, it shows > > 00207: relion_run_motioncorr --i PDC__00021_input.star --o output/ > --use_own --first_frame_sum 1 --last_frame_sum 40 --bin_factor > 1.000000 --bfactor 150 --angpix 1.36000 --patch_x 5 --patch_y 5 > --group_frames 1 --j 7 --gainref > "/home/romana/Documents/gain_reference_7676x7420_190815s.mrc" > --gain_rot 0 --gain_flip 0 --grouping_for_ps 1 --dose_weighting > --dose_per_frame 45.000000 --preexposure 0.000000 > 00208: Using our own implementation based on MOTIONCOR2 algorithm > 00209: to correct beam-induced motion for the following micrographs: > 00210: * PDC__00021.tif > 00211: Correcting beam-induced motions using our own implementation ... > 00212: 000/??? sec ~~(,_,"> > [oo]Erasing.....movieFolder: > Runs/000118_ProtRelionMotioncor/tmp/movie_000016 > 00213: FINISHED: processMovieStep, step 17, time 2023-06-20 > 16:16:05.085374 > 00214: ERROR: Movie > Runs/000002_ProtImportMovies/extra/PDC__00021.tif couldn't be added to > the output set. > 00215: [Errno 2] No such file or directory: > 'Runs/000118_ProtRelionMotioncor/extra/PDC__00021.star' > 00216: WARNING: Micrograph > Runs/000118_ProtRelionMotioncor/extra/PDC__00021_aligned_mic_DW.mrc > was not generated, can't add it to output set. > > and on run.stderr > > 00033: Killed > 00034: ERROR processing movie: PDC__00022.tif > > I was wondering what steps I could take to fix this. I have tried > uninstalling and re-installing the relion plugin, as well as checking > that all the proper dependencies are installed on my workstation. > However, I have been unable to pinpoint what is specifically causing > the error. If this is not the right place to ask for this type of > help, please let me know. Thank you for your time. > > Sincerely, > Roman Aguirre > > Roman Aguirre > PhD Student | Zhou Lab > UCLA | Chemistry and Biochemistry > romanaguirre@g.ucla.edu > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: ROMAN A. <romanaguirre@g.ucla.edu> - 2023-06-20 23:55:48
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Hello all,
I was recently at the data processing workshop at SLAC, and wanted to try
using Scipion on some of my data after seeing what its capable of. I
installed it on a WSL workstation, and starting Scipion and
installing plugins so far has not resulted in any errors. However, I ran
into problems right away when trying to use Relion's motioncor2. Although
it does say that the job is running, the output logs show the following
errors:
on run.stdout, it shows
00207: relion_run_motioncorr --i PDC__00021_input.star --o output/
--use_own --first_frame_sum 1 --last_frame_sum 40 --bin_factor 1.000000
--bfactor 150 --angpix 1.36000 --patch_x 5 --patch_y 5 --group_frames 1 --j
7 --gainref "/home/romana/Documents/gain_reference_7676x7420_190815s.mrc"
--gain_rot 0 --gain_flip 0 --grouping_for_ps 1 --dose_weighting
--dose_per_frame 45.000000 --preexposure 0.000000
00208: Using our own implementation based on MOTIONCOR2 algorithm
00209: to correct beam-induced motion for the following micrographs:
00210: * PDC__00021.tif
00211: Correcting beam-induced motions using our own implementation ...
00212: 000/??? sec ~~(,_,">
[oo]Erasing.....movieFolder:
Runs/000118_ProtRelionMotioncor/tmp/movie_000016
00213: FINISHED: processMovieStep, step 17, time 2023-06-20
16:16:05.085374
00214: ERROR: Movie Runs/000002_ProtImportMovies/extra/PDC__00021.tif
couldn't be added to the output set.
00215: [Errno 2] No such file or directory:
'Runs/000118_ProtRelionMotioncor/extra/PDC__00021.star'
00216: WARNING: Micrograph
Runs/000118_ProtRelionMotioncor/extra/PDC__00021_aligned_mic_DW.mrc was not
generated, can't add it to output set.
and on run.stderr
00033: Killed
00034: ERROR processing movie: PDC__00022.tif
I was wondering what steps I could take to fix this. I have tried
uninstalling and re-installing the relion plugin, as well as checking that
all the proper dependencies are installed on my workstation. However, I
have been unable to pinpoint what is specifically causing the error. If
this is not the right place to ask for this type of help, please let me
know. Thank you for your time.
Sincerely,
Roman Aguirre
Roman Aguirre
PhD Student | Zhou Lab
UCLA | Chemistry and Biochemistry
romanaguirre@g.ucla.edu
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From: Karim R. <kar...@um...> - 2023-06-11 10:23:04
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Heya all, Thanks for your input. A clean reinstall in my own home directory worked wonders and took care of the issues. All the best, Karim ############################################## Karim Rafie; PhD, MRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå, Sweden [cid:image001.png@01D99C52.3CBCAE70] From: Alberto Garcia Mena <alb...@cn...> Sent: Thursday, June 8, 2023 1:19 PM To: sci...@li... Subject: Re: [scipion-users] Issues with Xmipp installation - help Hi Karim, The problem could be that you are installing Cython with conda and not with pip. Try to install Cython with pip install Cython and be sure your pip is updated python -m pip install pip --upgrade Note that the environment in which you do it, must be the same in which you install Xmipp. I hope it helps you, in any case let us know about your progress. Thanks On 8/6/23 11:13, Karim Rafie wrote: Hi all, I hope this email finds you well. I was hoping you could help me out with an issue regarding xmipp, especially scikit. Whenever I want to install xmipp (either through the plugin manager or command line) I run into the issue that scikit can't be installed (see attached the last couple of lines of the log/error output). It tells me that it needs Cython but even after installing Cython within conda, it still does not work. I'm a bit at my wits end so any help would be greatly appreciated. I'm running ubuntu 18.04.6. Cheers, Karim ############################################## Karim Rafie; PhD, MRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå, Sweden [cid:image001.png@01D99C52.3CBCAE70] _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users -- Alberto García Mena National Center for Biotechnology - CSIC Facility software support & Xmipp team @ Biocomputing Unit / I2PC |
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From: Alberto G. M. <alb...@cn...> - 2023-06-08 11:19:44
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Hi Karim, The problem could be that you are installing Cython with conda and not with pip. Try to install Cython with *pip install Cython* and be sure your pip is updated *python -m pip install pip --upgrade* Note that the environment in which you do it, must be the same in which you install Xmipp. I hope it helps you, in any case let us know about your progress. Thanks On 8/6/23 11:13, Karim Rafie wrote: > > Hi all, > > I hope this email finds you well. I was hoping you could help me out > with an issue regarding xmipp, especially scikit. > > Whenever I want to install xmipp (either through the plugin manager or > command line) I run into the issue that scikit can't be installed (see > attached the last couple of lines of the log/error output). > > It tells me that it needs Cython but even after installing Cython > within conda, it still does not work. > > I'm a bit at my wits end so any help would be greatly appreciated. > > I'm running ubuntu 18.04.6. > > Cheers, > > Karim > > ############################################## > > Karim Rafie; PhD, MRSC > > Postdoctoral Research Fellow > > Carlson Lab > > Department of Medical Biochemistry and Biophysics > > Umeå University > > Umeå, Sweden > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Alberto García Mena National Center for Biotechnology - CSIC Facility software support & Xmipp team @ Biocomputing Unit / I2PC |
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From: Karim R. <kar...@um...> - 2023-06-08 09:46:11
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Hi all, I hope this email finds you well. I was hoping you could help me out with an issue regarding xmipp, especially scikit. Whenever I want to install xmipp (either through the plugin manager or command line) I run into the issue that scikit can't be installed (see attached the last couple of lines of the log/error output). It tells me that it needs Cython but even after installing Cython within conda, it still does not work. I'm a bit at my wits end so any help would be greatly appreciated. I'm running ubuntu 18.04.6. Cheers, Karim ############################################## Karim Rafie; PhD, MRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå, Sweden [cid:image001.png@01D999FA.17035B70] |
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From: Pablo C. <pc...@cn...> - 2023-05-12 14:09:33
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Dear Robin, all. We are close to release tomography plugins... actually, they are silently released (intentionally) to test the release process and for us to get used to release our code. So, anyone willing to test tomography plugins, feel free to use them (kind of in BETA/production state) and report any issue. Grigory suggestion should also work. As for the streaming tab in import tilt series.... it has been removed. If you want to do streaming processing of tilt series you should follow the more tested path: Import movies (as if they where SPA) Motion correct them (as if they were SPA) Compose tilt series (THis one is new in tomo and is feed with "micrographs" and "mdoc path"). This one composes the tilt series on the fly stacking the images. Aretomo is on its way to be streamified, and more to come. NovaCTF and cryoCARE, might need some time to verify its status. You can always use Grigory's link to have them in devel mode. On 12/5/23 10:48, Grigory Sharov wrote: > Dear Robin, > > all tomography plugins are not listed in the Plugin manager because > they are still in beta testing. You can install them in development > mode from github (see here > <https://docs.google.com/document/d/119yxa9Wz4hksjIrAb26YA8rFJPzx-Rq0oy8VNQvp3kE/edit?usp=sharing>). > > > As for streaming, import tomo protocols do not have this tab. Instead > you should do the streaming via SPA (import and motion correction) and > then use the "tilt series composer" protocol. > > 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 12, 2023 at 9:22 AM robin <rob...@u-...> wrote: > > Hello, > > I am contacting you because I have some problems with my Scipion > software (v3.0.12 and Eugenius v3.0.31). > > The first one is that I don't have the complete list of plugins in > the plugin manager, for example I'm missing novaCTF or cryoCARE. > > The second one is that I don't have the streaming tab in the job > tomo-import tilt series movies or tomo-import tilt series. > > My Scipion software is installed on a Linux workstation (no > cluster). Are these problems due to an installation problem? > > Best regards, > > Robin ANGER > > Robin ANGER, PhD > Ingénieur de Recherche > Institut Européen de Chimie et de Biologie > 2 rue Robert Escarpit > 33607 Pessac, France > > > > > > > > > _______________________________________________ > 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* |
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From: Grigory S. <sha...@gm...> - 2023-05-12 08:48:39
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Dear Robin, all tomography plugins are not listed in the Plugin manager because they are still in beta testing. You can install them in development mode from github (see here <https://docs.google.com/document/d/119yxa9Wz4hksjIrAb26YA8rFJPzx-Rq0oy8VNQvp3kE/edit?usp=sharing>). As for streaming, import tomo protocols do not have this tab. Instead you should do the streaming via SPA (import and motion correction) and then use the "tilt series composer" protocol. 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 12, 2023 at 9:22 AM robin <rob...@u-...> wrote: > Hello, > > I am contacting you because I have some problems with my Scipion software > (v3.0.12 and Eugenius v3.0.31). > > The first one is that I don't have the complete list of plugins in the > plugin manager, for example I'm missing novaCTF or cryoCARE. > > The second one is that I don't have the streaming tab in the job tomo- > import tilt series movies or tomo-import tilt series. > > My Scipion software is installed on a Linux workstation (no cluster). Are > these problems due to an installation problem? > > Best regards, > > Robin ANGER > > Robin ANGER, PhD > Ingénieur de Recherche > Institut Européen de Chimie et de Biologie > 2 rue Robert Escarpit > 33607 Pessac, France > > > > > > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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