Re: [scipion-users] Installing chimera plugin

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

Dear Lynn,

it appears you do not
have /usr/local/bin/scipion/software/em/chimerax-1.2.5/bin/ChimeraX - main
binary file, which means chimerax installation did not work.

Have you tried removing /usr/local/bin/scipion/software/em/chimerax* and
installing again?

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, Nov 4, 2021 at 3:57 PM Lynn Radamaker <lyn...@un...>
wrote:

> Dear Scipion community,
>
> I have installed Scipion successfully and a number of plugins. However,
> the chimera plugin is giving problems. If I install it via the plugin
> manager, there are errors. I have tried uninstalling and reinstalling. If I
> install it with this command:
>
> $ scipion3 installp -p scipion-em-chimera
>
> Then it gives the following output:
> Scipion v3.0.9 - Eugenius
> Building scipion-em-chimera ...
> /home/ubuntu/.conda/envs/scipion3/bin/python -m pip install
> scipion-em-chimera==3.1.7
> Collecting scipion-em-chimera==3.1.7
>   Using cached scipion_em_chimera-3.1.7-py3-none-any.whl (95 kB)
> Requirement already satisfied: scipion-em in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> scipion-em-chimera==3.1.7) (3.0.13)
> Requirement already satisfied: tk-html-widgets in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> scipion-em-chimera==3.1.7) (0.4.0)
> Requirement already satisfied: scipion-pyworkflow>=3.0.15 in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> scipion-em->scipion-em-chimera==3.1.7) (3.0.17)
> Requirement already satisfied: biopython==1.76 in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> scipion-em->scipion-em-chimera==3.1.7) (1.76)
> Requirement already satisfied: tifffile in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> scipion-em->scipion-em-chimera==3.1.7) (2021.11.2)
> Requirement already satisfied: numpy in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> biopython==1.76->scipion-em->scipion-em-chimera==3.1.7) (1.18.4)
> Requirement already satisfied: configparser<=5.0.2 in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (5.0.2)
> Requirement already satisfied: tkcolorpicker<=2.1.3 in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (2.1.3)
> Requirement already satisfied: mpi4py<=3.0.3 in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (3.0.3)
> Requirement already satisfied: psutil<=5.8.0 in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (5.8.0)
> Requirement already satisfied: matplotlib==3.2.2 in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (3.2.2)
> Requirement already satisfied: bibtexparser<=1.2.0 in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (1.2.0)
> Requirement already satisfied: requests<=2.25.1 in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (2.25.1)
> Requirement already satisfied: pillow<=8.2.0 in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7) (8.2.0)
> Requirement already satisfied: kiwisolver>=1.0.1 in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7)
> (1.3.2)
> Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7)
> (3.0.4)
> Requirement already satisfied: cycler>=0.10 in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7)
> (0.11.0)
> Requirement already satisfied: python-dateutil>=2.1 in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7)
> (2.8.2)
> Requirement already satisfied: future>=0.16.0 in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7)
> (0.18.2)
> Requirement already satisfied: six>=1.5 in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> python-dateutil>=2.1->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7)
> (1.16.0)
> Requirement already satisfied: chardet<5,>=3.0.2 in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7)
> (4.0.0)
> Requirement already satisfied: urllib3<1.27,>=1.21.1 in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7)
> (1.26.7)
> Requirement already satisfied: idna<3,>=2.5 in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7)
> (2.10)
> Requirement already satisfied: certifi>=2017.4.17 in
> ./.conda/envs/scipion3/lib/python3.8/site-packages (from
> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-chimera==3.1.7)
> (2021.10.8)
> Installing collected packages: scipion-em-chimera
> Successfully installed scipion-em-chimera-3.1.7
> Done (0.54 seconds)
> Building chimerax-1.2.5 ...
>   Skipping command: wget -nv -c -O
> /usr/local/bin/scipion/software/em/void.tgz.part
> http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz
> mv -v /usr/local/bin/scipion/software/em/void.tgz.part
> /usr/local/bin/scipion/software/em/void.tgz
>   All targets exist.
> cd /usr/local/bin/scipion/software/em
> mkdir /usr/local/bin/scipion/software/em/chimerax-1.2.5
>   Skipping command: tar -xf void.tgz -C chimerax-1.2.5
>   All targets exist.
>   Skipping command: cd .. && python
> /home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/chimera/getchimera.py
> 1.2.5
>   All targets exist.
> cd /usr/local/bin/scipion/software/em/chimerax-1.2.5
> cd .. && tar -xf ChimeraX-1.2.5.tar.gz
> cd /usr/local/bin/scipion/software/em/chimerax-1.2.5
> mv ../chimerax-1.2.5-rc-2021.05.24/* .
>   Skipping command: Link 'chimerax-1.2.5 -> chimerax-1.2.5'
>   All targets exist.
> Done (6.28 seconds)
> Building scipionchimera-1.3 ...
>   Skipping command: wget -nv -c -O
> /usr/local/bin/scipion/software/em/void.tgz.part
> http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz
> mv -v /usr/local/bin/scipion/software/em/void.tgz.part
> /usr/local/bin/scipion/software/em/void.tgz
>   All targets exist.
> cd /usr/local/bin/scipion/software/em
> mkdir /usr/local/bin/scipion/software/em/scipionchimera-1.3
>   Skipping command: tar -xf void.tgz -C scipionchimera-1.3
>   All targets exist.
> cd /usr/local/bin/scipion/software/em/scipionchimera-1.3
>  --nogui --exit --cmd 'devel install
> /home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/chimera/Bundles/scipion'
> && touch installed-
> /bin/sh: 1: --nogui: not found
> Traceback (most recent call last):
>   File
> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py",
> line 470, in <module>
>     main()
>   File
> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/__main__.py",
> line 293, in main
>     installPluginMethods()
>   File
> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py",
> line 232, in installPluginMethods
>     plugin.installBin({'args': ['-j', numberProcessor]})
>   File
> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py",
> line 166, in installBin
>     environment.execute()
>   File
> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
> line 748, in execute
>     self._executeTargets(targetList)
>   File
> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
> line 690, in _executeTargets
>     tgt.execute()
>   File
> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
> line 221, in execute
>     command.execute()
>   File
> "/home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/scipion/install/funcs.py",
> line 161, in execute
>     assert glob(t), ("target '%s' not built (after "
> AssertionError: target
> '/usr/local/bin/scipion/software/em/scipionchimera-1.3/installed-' not
> built (after running ' --nogui --exit --cmd 'devel install
> /home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/chimera/Bundles/scipion'
> && touch installed-')
> Error at main: target
> '/usr/local/bin/scipion/software/em/scipionchimera-1.3/installed-' not
> built (after running ' --nogui --exit --cmd 'devel install
> /home/ubuntu/.conda/envs/scipion3/lib/python3.8/site-packages/chimera/Bundles/scipion'
> && touch installed-')
>
> The trouble seems to start with "/bin/sh: 1: --nogui: not found". I also
> cannot use chimerax in the GUI.
>
> I would greatly appreciate your help on this issue.
>
> Kind regards,
>
> Lynn Radamaker
>   _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

Re: [scipion-users] Installing chimera plugin

Image processing framework to integrate EM software packages.

Re: [scipion-users] Installing chimera plugin