Re: [scipion-users] Installing chimera plugin

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Or you are pointing to chimera 1.13.

What gives you "scipion3 config -p chimera"

On 4/11/21 20:05, Grigory Sharov wrote:
> 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 <tel:+44%201223%20267228>
> e-mail: gs...@mr... <mailto:gs...@mr...>
>
>
> On Thu, Nov 4, 2021 at 3:57 PM Lynn Radamaker 
> <lyn...@un... <mailto: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
>     <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
>     <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
>     _______________________________________________
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>
>
>
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-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*

Re: [scipion-users] Installing chimera plugin

Image processing framework to integrate EM software packages.

Re: [scipion-users] Installing chimera plugin