scipion-users — Mailing list for Scipion users

[scipion-users] Scipion installation and using Relion's MOTIONCOR2

[ROMAN A. <romanaguirre@g.ucla.edu>]

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

Re: [scipion-users] Issues with Xmipp installation - help

[Karim R. <kar...@um...>]

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

Re: [scipion-users] Issues with Xmipp installation - help

[Alberto G. M. <alb...@cn...>]

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

[scipion-users] Issues with Xmipp installation - help

[Karim R. <kar...@um...>]

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]

Re: [scipion-users] Problems with my software

[Pablo C. <pc...@cn...>]

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*

Re: [scipion-users] Problems with my software

[Grigory S. <sha...@gm...>]

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
>

[scipion-users] Problems with my software

[robin <rob...@u-...>]

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

Re: [scipion-users] Import particles from cryoSPARC

[Grigory S. <sha...@gm...>]

Hi,

I think you could use the import particles protocol and provide a cs file
directly, without need for any motion correction or ctf estimation in
scipion.

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 Mon, Mar 27, 2023 at 2:16 PM Ioannis Skalidis <joh...@gm...>
wrote:

> Dear all,
>
> I started an analysis in Scipion of a dataset I have originally analyzed
> in cryoSPARC. I redid the motion correction and ctf estimation in
> Scipion and ideally, I would like to import the already clean particle
> set I have from the cryoSPARC workspace. Could you advise me on how to
> proceed?
>
> Should I use the "import particles" tool? Is it possible to directly
> import the extracted single-particle images, or do I just import the
> particle locations and then re-extract from the newly, in-scipion motion
> corrected images?
>
> Thank you for your input!
>
> Ioannis.
>
> --
>
>
>
> Skalidis Ioannis, MSc
> Biochemistry & Cryo-EM Scientist
> PhD Candidate
> Kastritis Laboratory for Biomolecular Research
> Cryo-Electron Microscopy & Computational Structural Biology
>
> ________________________________________________
> Martin-Luther-Universität Halle-Wittenberg
> Biozentrum, Room A.2.21
> IWE ZIK HALOmem NWG III
> "Kryo-Elektronenmikroskopie an Membranproteinkomplexen"
> Weinbergweg 22, 06120 Halle
> tel: +49 345 5524986
> web (Lab): https://blogs.urz.uni-halle.de/kastritislab/
> web (HALOmem): https://www.halomem.de/en/
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

[scipion-users] Import particles from cryoSPARC

[Ioannis S. <joh...@gm...>]

Dear all,

I started an analysis in Scipion of a dataset I have originally analyzed 
in cryoSPARC. I redid the motion correction and ctf estimation in 
Scipion and ideally, I would like to import the already clean particle 
set I have from the cryoSPARC workspace. Could you advise me on how to 
proceed?

Should I use the "import particles" tool? Is it possible to directly 
import the extracted single-particle images, or do I just import the 
particle locations and then re-extract from the newly, in-scipion motion 
corrected images?

Thank you for your input!

Ioannis.

-- 



Skalidis Ioannis, MSc
Biochemistry & Cryo-EM Scientist
PhD Candidate
Kastritis Laboratory for Biomolecular Research
Cryo-Electron Microscopy & Computational Structural Biology

________________________________________________
Martin-Luther-Universität Halle-Wittenberg
Biozentrum, Room A.2.21
IWE ZIK HALOmem NWG III
"Kryo-Elektronenmikroskopie an Membranproteinkomplexen"
Weinbergweg 22, 06120 Halle
tel: +49 345 5524986
web (Lab): https://blogs.urz.uni-halle.de/kastritislab/
web (HALOmem): https://www.halomem.de/en/

[scipion-users] Xmipp-3.23.03 - Kratos released

[Alberto G. M. <alb...@cn...>]

Dear all,

The Xmipp team has released the new version of Xmipp. Please welcome to 
*Xmipp 3.23.03-Kratos. *

For this version we have updated 390 files; the main new features are 
these 
<https://github.com/I2PC/xmipp/blob/devel/CHANGELOG.md>*,***including 
new protocols and improved protocols as resolution-FSO, FlexAlign and 
Subtract projection. Feel free toinstall 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* with the plugin manager or 
with/.///scipion3 installp -p scipion-em-xmipp/

Xmipp-Team


-- 
Alberto García Mena
National Center for Biotechnology - CSIC
Facility software support & Xmipp team @ Biocomputing Unit / I2PC

[scipion-users] error with relion autopicking LoG

[Stefano C. <ste...@un...>]

Hi! I'm trying the relion tutorial with Scipion3. When running 
relion-autopiching LoG I've got the following error:

   Protocol failed: Command ' relion_autopick  --pickname autopick 
--odir "./" --LoG --shrink 0 --lowpass 20.000  --i 
input_micrographs.star --LoG_diam_min 150.000 --LoG_diam_max 180.000 
--LoG_adjust_threshold 0.000 --LoG_upper_threshold 5.000' returned 
non-zero exit status 127.

I tried with different batch sizes in "streaming" and with single and 
multiple MPI processes, but always have the same error..
How can I fix it?
thank you

Stefano

Re: [scipion-users] problem with xmipp deepLearning plugin

[Pablo C. <pc...@cn...>]

Hi David, xmippLib is provided by xmipp when is is instaalled


"Physicaly" it should be linked at SCIPION_HOME/software/binding/

scipion3 run 'ls -l $SCIPION_HOME/software/binding/'

will list its content.

I'm getting this:

pablo@youyou ~/desarrollo $ scipion run 'ls -l 
$SCIPION_HOME/software/bindings/'
Scipion v3.0.13 - Eugenius
total 32
drwxr-xr-x 2 pablo pablo 4096 oct 14 12:04 __pycache__
lrwxrwxrwx 1 pablo pablo   69 dic 29 12:32 sh_alignment -> 
../../../../desarrollo/xmippBundle/build/bindings/python/sh_alignment
lrwxrwxrwx 1 pablo pablo   69 dic 29 12:32 _swig_frm.so -> 
../../../../desarrollo/xmippBundle/build/bindings/python/_swig_frm.so
lrwxrwxrwx 1 pablo pablo   70 dic 29 12:32 xmipp_base.py -> 
../../../../desarrollo/xmippBundle/build/bindings/python/xmipp_base.py
lrwxrwxrwx 1 pablo pablo   76 dic 29 12:32 xmipp_conda_envs.py -> 
../../../../desarrollo/xmippBundle/build/bindings/python/xmipp_conda_envs.py
lrwxrwxrwx 1 pablo pablo   68 dic 29 12:32 xmippLib.so -> 
../../../../desarrollo/xmippBundle/build/bindings/python/xmippLib.so
lrwxrwxrwx 1 pablo pablo   65 dic 29 12:32 xmipp.py -> 
../../../../desarrollo/xmippBundle/build/bindings/python/xmipp.py
lrwxrwxrwx 1 pablo pablo   68 dic 29 12:32 xmippViz.py -> 
../../../../desarrollo/xmippBundle/build/bindings/python/xmippViz.py


xmippLib.so turns into a python package as import xmippLib


If all looks correct try this

scipion3 python

 > import xmippLib


If this does not fail, then I'd say the deeplearning environment is not 
set properly.


Let us know ho it goes.

Cheers!


On 31/1/23 18:14, Hoover, David (NIH/CIT) [E] via scipion-users wrote:
> Hi,
>
> We're trying to use the deepLearning toolkit package as part of xmipp, 
> and have run into problems.
>
> The latest gives this error message:
>
> 00001:   === XMIPP_WARNING ===
> 00002:   Do not apply large scale factor using B-splines choose 
> fourier option.
> 00003:   === XMIPP_WARNING ===
> 00004:   Do not apply large scale factor using B-splines choose 
> fourier option.
> 00005:   Using TensorFlow backend.
> 00006:   Traceback (most recent call last):
> 00007:     File 
> "/usr/local/apps/scipion/3.0.12/scipion/software/em/xmipp/bin/xmipp_deepRes_resolution", 
> line 35, in <module>
> 00008:       import xmippLib
> 00009:   ModuleNotFoundError: No module named 'xmippLib'
> 00010:   Traceback (most recent call last):
> 00011:     File 
> "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", 
> line 202, in run
> 00012:       self._run()
> 00013:     File 
> "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", 
> line 253, in _run
> 00014:       resultFiles = self._runFunc()
> 00015:     File 
> "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", 
> line 249, in _runFunc
> 00016:       return self._func(*self._args)
> 00017:     File 
> "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/xmipp3/protocols/protocol_resolution_deepres.py", 
> line 236, in resolutionStep
> 00018:       self.runJob("xmipp_deepRes_resolution", params, 
> numberOfMpi=1,
> 00019:     File 
> "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", 
> line 1480, in runJob
> 00020:       self._stepsExecutor.runJob(self._log, program, arguments, 
> **kwargs)
> 00021:     File 
> "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", 
> line 65, in runJob
> 00022:       process.runJob(log, programName, params,
> 00023:     File 
> "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", 
> line 55, in runJob
> 00024:       return runCommand(command, env, cwd)
> 00025:     File 
> "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", 
> line 70, in runCommand
> 00026:       check_call(command, shell=True, stdout=sys.stdout, 
> stderr=sys.stderr,
> 00027:     File 
> "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/subprocess.py", 
> line 364, in check_call
> 00028:       raise CalledProcessError(retcode, cmd)
> 00029:   subprocess.CalledProcessError: Command ' 
> xmipp_deepRes_resolution  -dl 
> /usr/local/apps/scipion/3.0.12/scipion/software/em/xmipp/models/deepRes/model_w13.h5 
> -i  Runs/000817_XmippProtDeepRes/extra/originalVolume.vol -m 
> Runs/000817_XmippProtDeepRes/tmp/binaryMask.vol -s  1.660000 -o 
> Runs/000817_XmippProtDeepRes/extra/deepRes_resolution.vol' returned 
> non-zero exit status 1.
> 00030:   Protocol failed: Command ' xmipp_deepRes_resolution  -dl 
> /usr/local/apps/scipion/3.0.12/scipion/software/em/xmipp/models/deepRes/model_w13.h5 
> -i  Runs/000817_XmippProtDeepRes/extra/originalVolume.vol -m 
> Runs/000817_XmippProtDeepRes/tmp/binaryMask.vol -s  1.660000 -o 
> Runs/000817_XmippProtDeepRes/extra/deepRes_resolution.vol' returned 
> non-zero exit status 1.
>
> Is there an xmippLib package that needs to be installed?  I can find 
> an xmippLib.so file, but python will not accept this as a package.
>
> Any insight would be helpful.
>
> David
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*

[scipion-users] problem with xmipp deepLearning plugin

[Hoover, D. (NIH/C. [E] <hoo...@hp...>]

Hi,

We're trying to use the deepLearning toolkit package as part of xmipp, and have run into problems.

The latest gives this error message:

00001:   === XMIPP_WARNING ===
00002:   Do not apply large scale factor using B-splines choose fourier option.
00003:   === XMIPP_WARNING ===
00004:   Do not apply large scale factor using B-splines choose fourier option.
00005:   Using TensorFlow backend.
00006:   Traceback (most recent call last):
00007:     File "/usr/local/apps/scipion/3.0.12/scipion/software/em/xmipp/bin/xmipp_deepRes_resolution", line 35, in <module>
00008:       import xmippLib
00009:   ModuleNotFoundError: No module named 'xmippLib'
00010:   Traceback (most recent call last):
00011:     File "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 202, in run
00012:       self._run()
00013:     File "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 253, in _run
00014:       resultFiles = self._runFunc()
00015:     File "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 249, in _runFunc
00016:       return self._func(*self._args)
00017:     File "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/xmipp3/protocols/protocol_resolution_deepres.py", line 236, in resolutionStep
00018:       self.runJob("xmipp_deepRes_resolution", params, numberOfMpi=1,
00019:     File "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1480, in runJob
00020:       self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
00021:     File "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob
00022:       process.runJob(log, programName, params,
00023:     File "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 55, in runJob
00024:       return runCommand(command, env, cwd)
00025:     File "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 70, in runCommand
00026:       check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
00027:     File "/usr/local/apps/scipion/3.0.12/mamba/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call
00028:       raise CalledProcessError(retcode, cmd)
00029:   subprocess.CalledProcessError: Command ' xmipp_deepRes_resolution  -dl /usr/local/apps/scipion/3.0.12/scipion/software/em/xmipp/models/deepRes/model_w13.h5 -i  Runs/000817_XmippProtDeepRes/extra/originalVolume.vol -m  Runs/000817_XmippProtDeepRes/tmp/binaryMask.vol -s  1.660000 -o  Runs/000817_XmippProtDeepRes/extra/deepRes_resolution.vol' returned non-zero exit status 1.
00030:   Protocol failed: Command ' xmipp_deepRes_resolution  -dl /usr/local/apps/scipion/3.0.12/scipion/software/em/xmipp/models/deepRes/model_w13.h5 -i  Runs/000817_XmippProtDeepRes/extra/originalVolume.vol -m  Runs/000817_XmippProtDeepRes/tmp/binaryMask.vol -s  1.660000 -o  Runs/000817_XmippProtDeepRes/extra/deepRes_resolution.vol' returned non-zero exit status 1.

Is there an xmippLib package that needs to be installed?  I can find an xmippLib.so file, but python will not accept this as a package.

Any insight would be helpful.

David
-- 
David Hoover, Ph.D.
Computational Biologist
High Performance Computing Services,
Center for Information Technology,
National Institutes of Health
12 South Dr., Rm 2N207
Bethesda, MD 20892, USA
TEL: (+1) 301-435-2986
Email: hoo...@hp...

Re: [scipion-users] Install on computer cluster

[Pablo C. <pc...@cn...>]

Sorry if we missed this.

Yes,  you and anyone else is welcome to join our discord workspace we 
you'll get more direct contact with users and developers.

Regarding pySeg...you need very specific version of gcc and g++ (from 5 
to 7 are the only valid ones). Not sure if you need something else.

Latest version of the plugin is doing this check and informing you is 
not compatible versions are found.


On 29/1/23 18:48, Grigory Sharov wrote:
> Dear Chuchu,
>
> If you haven't got any replies by now, I'd suggest joining our discord 
> channel (https://discord.gg/MXWSKvy2). You might be able to reach 
> pyseg plugin developers there.
>
> I have installed pyseg only once (manually, it has failed via scipion) 
> and it was not on a cluster. I might share some brief compilation 
> instructions on Monday.
>
> 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, Jan 27, 2023 at 3:03 PM Chuchu Wang <cc...@st...> wrote:
>
>     Dear Scipion Team,
>
>     Happy New Year!
>     I tried to install Scipion and the PySeg plug-in on our computer
>     cluster, but because of many conflicts, it failed to work.
>     I wonder if you know any Stanford Sherlock users who successfully
>     installed your app (esp. PySeg plug-in) and ran it smoothly, I
>     would like to ask for his/her favor to share the installation steps.
>
>     Best,
>     Chuchu
>
>     --
>
>     Chuchu Wang, Ph.D.
>
>     Postdoc | Axel T. Brunger Lab
>
>     Molecular & Cellular Physiology | Stanford Medicine
>     Howard Hughs Medical Institute at Stanford
>
>     Clark Center Rm. E300C,
>
>     318 Campus Drive, CA. 94305
>
>
>     _______________________________________________
>     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*

Re: [scipion-users] Install on computer cluster

[Grigory S. <sha...@gm...>]

Dear Chuchu,

If you haven't got any replies by now, I'd suggest joining our discord
channel (https://discord.gg/MXWSKvy2). You might be able to reach
pyseg plugin developers there.

I have installed pyseg only once (manually, it has failed via scipion) and
it was not on a cluster. I might share some brief compilation instructions
on Monday.

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 27, 2023 at 3:03 PM Chuchu Wang <cc...@st...> wrote:

> Dear Scipion Team,
>
> Happy New Year!
> I tried to install Scipion and the PySeg plug-in on our computer cluster,
> but because of many conflicts, it failed to work.
> I wonder if you know any Stanford Sherlock users who successfully
> installed your app (esp. PySeg plug-in) and ran it smoothly, I would like
> to ask for his/her favor to share the installation steps.
>
> Best,
> Chuchu
>
> --
>
> Chuchu Wang, Ph.D.
>
> Postdoc | Axel T. Brunger Lab
>
> Molecular & Cellular Physiology | Stanford Medicine
> Howard Hughs Medical Institute at Stanford
>
> Clark Center Rm. E300C,
>
> 318 Campus Drive, CA. 94305
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

Re: [scipion-users] Segmentation error while running Scipion

[Pablo C. <pc...@cn...>]

Hi Jessie:

the ">>> WARNING: Image library not found!" means xmipp was not 
installed properly.

"scipion3 installb xmippSrc" should do it.

The next error, "sh: line 1: 36766 Segmentation fault      (core dumped) 
python -m scipion "


Well, we are going to need more information. Does it happens when 
launching Scipion? or while using the GUI.

On 27/1/23 15:04, Malit Jessie James Limlingan wrote:
> Good day. I recently installed Scipion, and was following this guide 
> Denoising, Membrane Segmentation and Annotation and Directional 
> Picking 
> <https://scipion-em.github.io/docs/release-3.0.0/docs/user/denoising_mbSegmentation_pysegDirPicking/tomosegmemTV-pySeg-workflow.html#tomosegmemtv-pyseg-workflow>. 
> I can follow the steps until tomogram denoting, however after 
> installing scipion-em-tomosegmemtv 
> <https://github.com/scipion-em/scipion-em-tomosegmemtv> and 
> scipion-em-pyseg <https://github.com/scipion-em/scipion-em-pyseg>, 
> whenever I run Scipion I come across with this error;
>
> Scipion v3.0.12 - Eugenius
>
>  >>> WARNING: Image library not found!
>   > Please install Xmipp to get full functionality.
> (Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin 
> manager window)
>
>
> /data/Jessie/miniconda3/envs/scipion3/lib/python3.8/site-packages/_distutils_hack/__init__.py:33: 
> UserWarning: Setuptools is replacing distutils.
> warnings.warn("Setuptools is replacing distutils.")
> sh: line 1: 36766 Segmentation fault      (core dumped) python -m scipion
>
> Can you help us resolve the error? Thank you very much!
>
> Regards,
> Jessie
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*

[scipion-users] Segmentation error while running Scipion

[Malit J. J. L. <jm...@mo...>]

Good day. I recently installed Scipion, and was following this guide Denoising, Membrane Segmentation and Annotation and Directional Picking<https://scipion-em.github.io/docs/release-3.0.0/docs/user/denoising_mbSegmentation_pysegDirPicking/tomosegmemTV-pySeg-workflow.html#tomosegmemtv-pyseg-workflow>. I can follow the steps until tomogram denoting, however after installing scipion-em-tomosegmemtv<https://github.com/scipion-em/scipion-em-tomosegmemtv> and scipion-em-pyseg<https://github.com/scipion-em/scipion-em-pyseg>, whenever I run Scipion I come across with this error;

Scipion v3.0.12 - Eugenius

 >>> WARNING: Image library not found!
  > Please install Xmipp to get full functionality.
(Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window)


/data/Jessie/miniconda3/envs/scipion3/lib/python3.8/site-packages/_distutils_hack/__init__.py:33: UserWarning: Setuptools is replacing distutils.
  warnings.warn("Setuptools is replacing distutils.")
sh: line 1: 36766 Segmentation fault      (core dumped) python -m scipion

Can you help us resolve the error? Thank you very much!

Regards,
Jessie

Re: [scipion-users] Rotate_Particles function is no longer available?

[Roberto M. <ro...@cn...>]

Hi,

     I do not think what you are looking for is available. Something
related to that problem is

1)  In the plugin atomstruct there is a protocol called convert_sym
that is able to change projection rotation directions between
different icosahedral symmetries (sorry only works for icosahedral
symmetries)
     Eventually we will add more possibilities here.
2) I guess the plugin localrec can be used to achieve your goal using
a hack. Although if you do not have previous experience with this
software I do not recommend this option and be aware that I have not
test the following procedure.
    You will need to execute the protocol "localrec-define
subparticles" with the option "align subparticles" set to true. This
protocol will rotate the projection directions so that a used defined
vector becomes parallel to the z-axis. It is important that the
magnitud of the user-defined-vector would be as small as possible (for
example 0.000001) otherwise the center of the particles will be moved.
Then the protocol localrec-extract-particles needs to be executed
using as subparticle-size-box the size of the original images.

  hope this helps

On Mon, Jan 23, 2023 at 3:53 PM Leonardo Talachia Rosa via
scipion-users <sci...@li...> wrote:
>
> Dear Scipion team,
> I hope you are well.
>
> I´m working with a Phage in which I need to change the symmetry axis of the particles and the 3D volume in order to do a symmetry_relaxation refinement. I saw similar approaches suggested in the links below.
>
> https://github.com/OPIC-Oxford/localrec/wiki/Tips-and-tricks#TnT-2 - Reorienting all particles
> https://www.nature.com/articles/s41467-021-24455-4 -
>
> Methods section - Decoupling D 3d symmetry for asymmetric (C 1) reconstruction
>
>
> However, the relion_rotate_particles.py is not recognized in the scipion command line, and I do not see a way to do a similar job using the scipion GUI. I installed the latest version of LocalRec plugin, but still the command is not recognised.
> Am I missing something obvious or this function has been disabled in the latest updates for some reason?
> Any other suggestions on how to do this rotation would also be welcome.
>
> Thank you for your time,
> Kind wishes,
> Leonardo
>
> --
> *************************
> Leonardo TALACHIA ROSA, PhD
> PostDoctoral Researcher
> Microbiology and Structural Biology
> Instituto de Química, Universidade de São Paulo - IQ-USP
> Av. Prof. Lineu Prestes, 748 - Butantã, São Paulo - SP
> **************************
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users

Re: [scipion-users] Rotate_Particles function is no longer available?

[Grigory S. <sha...@gm...>]

Hi Leonardo,

I think you are looking at very outdated documentation.

PS. The script you are looking for is here:
https://github.com/OPIC-Oxford/localrec/blob/devel/scripts/relion_rotate_particles.py
but it no longer exists in the plugin

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 Mon, Jan 23, 2023 at 2:54 PM Leonardo Talachia Rosa via scipion-users <
sci...@li...> wrote:

> Dear Scipion team,
> I hope you are well.
>
> I´m working with a Phage in which I need to change the symmetry axis of
> the particles and the 3D volume in order to do a symmetry_relaxation
> refinement. I saw similar approaches suggested in the links below.
>
> https://github.com/OPIC-Oxford/localrec/wiki/Tips-and-tricks#TnT-2 -
> Reorienting all particles
> https://www.nature.com/articles/s41467-021-24455-4 -
> Methods section - Decoupling *D* 3d symmetry for asymmetric (*C* 1)
> reconstruction
>
> However, the relion_rotate_particles.py is not recognized in the scipion
> command line, and I do not see a way to do a similar job using the scipion
> GUI. I installed the latest version of LocalRec plugin, but still the
> command is not recognised.
> Am I missing something obvious or this function has been disabled in the
> latest updates for some reason?
> Any other suggestions on how to do this rotation would also be welcome.
>
> Thank you for your time,
> Kind wishes,
> Leonardo
>
> --
> *************************
> Leonardo TALACHIA ROSA, PhD
> PostDoctoral Researcher
> Microbiology and Structural Biology
> Instituto de Química, Universidade de São Paulo - IQ-USP
> Av. Prof. Lineu Prestes, 748 - Butantã, São Paulo - SP
> **************************
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

[scipion-users] Rotate_Particles function is no longer available?

[Leonardo T. R. <leo...@us...>]

Dear Scipion team,
I hope you are well.

I´m working with a Phage in which I need to change the symmetry axis of the
particles and the 3D volume in order to do a symmetry_relaxation
refinement. I saw similar approaches suggested in the links below.

https://github.com/OPIC-Oxford/localrec/wiki/Tips-and-tricks#TnT-2 -
Reorienting all particles
https://www.nature.com/articles/s41467-021-24455-4 -
Methods section - Decoupling *D* 3d symmetry for asymmetric (*C* 1)
reconstruction

However, the relion_rotate_particles.py is not recognized in the scipion
command line, and I do not see a way to do a similar job using the scipion
GUI. I installed the latest version of LocalRec plugin, but still the
command is not recognised.
Am I missing something obvious or this function has been disabled in the
latest updates for some reason?
Any other suggestions on how to do this rotation would also be welcome.

Thank you for your time,
Kind wishes,
Leonardo

-- 
*************************
Leonardo TALACHIA ROSA, PhD
PostDoctoral Researcher
Microbiology and Structural Biology
Instituto de Química, Universidade de São Paulo - IQ-USP
Av. Prof. Lineu Prestes, 748 - Butantã, São Paulo - SP
**************************

Re: [scipion-users] Can't see import jobs

[Pablo C. <pc...@cn...>]

Actualy , if you are updated, just removing it sould work (without 
running scipion3 config).

On 23/1/23 14:44, Grigory Sharov wrote:
> Hello Nuno,
>
> I'd suggest removing (or moving it somewhere else for a backup) 
> config/protocols.conf as it seems to be corrupted. Then you can 
> generate one by running "scipion3 config".
>
> 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 Mon, Jan 23, 2023 at 1:40 PM Bustorff, Nuno 
> <n.b...@fz...> wrote:
>
>     Dear Pablo,
>
>     Indeed in view all they show up.
>
>     Do I need to install a plugin to show as well in Protocols SPA?
>
>     Best regards,
>
>     Nuno
>
>     *From:*Pablo Conesa <pc...@cn...>
>     *Sent:* Saturday, 21 January 2023 18:15
>     *To:* Mailing list for Scipion users
>     <sci...@li...>
>     *Subject:* Re: [scipion-users] Can't see import jobs
>
>     Hi, Nuno!.
>
>     Have you installed any plugin?
>
>     If you "open" the "View" dropdown on the top left (where is says
>     "Protocols SPA") and select "All": What does it show?
>
>     Cheers!
>
>     On 20/1/23 19:18, Bustorff, Nuno wrote:
>
>         Dear support team,
>
>         I cannot import anything in my project. Please see the photo
>         bellow.
>
>         Best regards,
>
>         Nuno
>
>         ___________________
>
>         Nuno Bustorff Silva
>
>         PhD Student
>
>         Forschungszentrum Jülich GmbH
>
>         Ernst-Ruska Centre for Microscopy and Spectroscopy with
>         Electrons / ER-C-3 Structural Biology
>
>         Institute for Biological Information Processing / IBI-6
>         Cellular Structural Biology
>
>         Wilhelm-Johnen-Straße, 52425 Jülich, Germany
>
>         Phone: +49 2461 61-85525
>
>         _https://go.fzj.de/erc3-ibi6 <https://go.fzj.de/erc3-ibi6>_
>
>         Email: n.b...@fz... <mailto:n.b...@fz...>
>
>
>
>
>         _______________________________________________
>
>         scipion-users mailing list
>
>         sci...@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
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*

Re: [scipion-users] Can't see import jobs

[Grigory S. <sha...@gm...>]

Hello Nuno,

I'd suggest removing (or moving it somewhere else for a backup)
config/protocols.conf as it seems to be corrupted. Then you can generate
one by running "scipion3 config".

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 Mon, Jan 23, 2023 at 1:40 PM Bustorff, Nuno <n.b...@fz...>
wrote:

> Dear Pablo,
>
>
>
> Indeed in view all they show up.
>
>
>
> Do I need to install a plugin to show as well in Protocols SPA?
>
>
>
>
>
> Best regards,
>
> Nuno
>
>
>
> *From:* Pablo Conesa <pc...@cn...>
> *Sent:* Saturday, 21 January 2023 18:15
> *To:* Mailing list for Scipion users <sci...@li...>
> *Subject:* Re: [scipion-users] Can't see import jobs
>
>
>
> Hi, Nuno!.
>
> Have you installed any plugin?
>
> If you "open" the "View" dropdown on the top left (where is says
> "Protocols SPA") and select "All": What does it show?
>
> Cheers!
>
> On 20/1/23 19:18, Bustorff, Nuno wrote:
>
> Dear support team,
>
>
>
> I cannot import anything in my project. Please see the photo bellow.
>
>
>
> Best regards,
>
> Nuno
>
>
>
>
>
>
>
> ___________________
>
> Nuno Bustorff Silva
>
> PhD Student
>
> Forschungszentrum Jülich GmbH
>
> Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons / ER-C-3
> Structural Biology
>
> Institute for Biological Information Processing / IBI-6 Cellular
> Structural Biology
>
> Wilhelm-Johnen-Straße, 52425 Jülich, Germany
>
> Phone: +49 2461 61-85525
>
> *https://go.fzj.de/erc3-ibi6 <https://go.fzj.de/erc3-ibi6>*
>
> Email: n.b...@fz...
>
>
>
>
>
>
> _______________________________________________
>
> scipion-users mailing list
>
> sci...@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
>

Re: [scipion-users] Can't see import jobs

[Bustorff, N. <n.b...@fz...>]

Dear Pablo,

 

Indeed in view all they show up. 

 



Do I need to install a plugin to show as well in Protocols SPA?

 

 

Best regards,

Nuno

 

From: Pablo Conesa <pc...@cn...> 
Sent: Saturday, 21 January 2023 18:15
To: Mailing list for Scipion users <sci...@li...>
Subject: Re: [scipion-users] Can't see import jobs

 

Hi, Nuno!.

Have you installed any plugin?

If you "open" the "View" dropdown on the top left (where is says "Protocols SPA") and select "All": What does it show?

Cheers!

On 20/1/23 19:18, Bustorff, Nuno wrote:

Dear support team,

 

I cannot import anything in my project. Please see the photo bellow.



 

Best regards,

Nuno

 

 

 

___________________

Nuno Bustorff Silva

PhD Student

Forschungszentrum Jülich GmbH

Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons / ER-C-3 Structural Biology

Institute for Biological Information Processing / IBI-6 Cellular Structural Biology

Wilhelm-Johnen-Straße, 52425 Jülich, Germany

Phone: +49 2461 61-85525

 <https://go.fzj.de/erc3-ibi6> https://go.fzj.de/erc3-ibi6

Email:  <mailto:n.b...@fz...> n.b...@fz... 

 






_______________________________________________
scipion-users mailing list
sci...@li... <mailto:sci...@li...> 
https://lists.sourceforge.net/lists/listinfo/scipion-users

-- 
Pablo Conesa - Madrid Scipion <http://scipion.i2pc.es>  team

Re: [scipion-users] Can't see import jobs

[Pablo C. <pc...@cn...>]

Hi, Nuno!.

Have you installed any plugin?

If you "open" the "View" dropdown on the top left (where is says 
"Protocols SPA") and select "All": What does it show?

Cheers!

On 20/1/23 19:18, Bustorff, Nuno wrote:
>
> Dear support team,
>
> I cannot import anything in my project. Please see the photo bellow.
>
> Best regards,
>
> Nuno
>
> ___________________
>
> Nuno Bustorff Silva
>
> PhD Student
>
> Forschungszentrum Jülich GmbH
>
> Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons / 
> ER-C-3 Structural Biology
>
> Institute for Biological Information Processing / IBI-6 Cellular 
> Structural Biology
>
> Wilhelm-Johnen-Straße, 52425 Jülich, Germany
>
> Phone: +49 2461 61-85525
>
> _https://go.fzj.de/erc3-ibi6 <https://go.fzj.de/erc3-ibi6>_
>
> Email: n.b...@fz... <mailto:n.b...@fz...>
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*

[scipion-users] Can't see import jobs

[Bustorff, N. <n.b...@fz...>]

Dear support team,

 

I cannot import anything in my project. Please see the photo bellow.



 

Best regards,

Nuno

 

 

 

___________________

Nuno Bustorff Silva

PhD Student

Forschungszentrum Jülich GmbH

Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons / ER-C-3
Structural Biology

Institute for Biological Information Processing / IBI-6 Cellular Structural
Biology

Wilhelm-Johnen-Straße, 52425 Jülich, Germany

Phone: +49 2461 61-85525

 <https://go.fzj.de/erc3-ibi6> https://go.fzj.de/erc3-ibi6

Email:  <mailto:n.b...@fz...> n.b...@fz...