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openstructure

Summary

Source: https://openstructure.org/

License: LGPL-2.0

Path: /opt/em/openstructure (v1.4), /software/openstructure (v>=2.3)

Documentation: https://openstructure.org/

openstructure aims to provide an open-source, modular, flexible, molecular modelling and visualization environment. It is targeted at interested method developers in the field of structural bioinformatics.

Using openstructure version 2.3 or newer

openstructure 2.3.1 is embedded into a singularity container. The applications can be used either through simple wrapper scripts, or singularity itself

module load maxwell openstructure/2.3.1
which dng 
     /software/openstructure/2.3.1/bin/dng

The applications supported by the singularity image are

  • ost - OpenStructure binary
  • dng - openstructure GUI
  • ost-ipython - OST-powered iPython shell
  • ost-lddt - The Local Distance Difference Test
  • ost-molck - Molecular checker
  • ost-chemdicttool - Creating or update a compound library

The wrapper for dng looks like this:

singularity run --nv --app dng --bind /run/user,/software,/asap3,/beegfs,/gpfs /software/openstructure/2.3.1/ost-gui.sif "$@"

# Notes:
# --nv        adds nvidia support, doesn't harm if no GPU is available
# --app dng   run dng. applications can be listed with singularity run-help /software/openstructure/2.3.1/ost-gui.sif
# --bind /run/user,/software,/asap3,/beegfs,/gpfs   filesystems available for the application. /home is always there. 
#
# The singularity recipe used to build the image: /software/openstructure/2.3.1/singularity/S1

Using openstructure v1.4

The GUI for openstructure is called dng. For sake of simplicity you can also launch dng by invoking openstructure. To initialize the environment use the module command:

[elx]% xwhich openstructure

 Provides by module(s)
   ... module load maxwell openstructure/1.4; which openstructure: /opt/em/openstructure/1.4/bin/openstructure

 Documentation: https://confluence.desy.de/display/IS/openstructure
 URL:           https://openstructure.org/
 Manual:        https://openstructure.org/docs/
 License:       LGPL-3.0

[elx]$ realpath /opt/em/openstructure/1.4/bin/openstructure
/software/opt/em/openstructure/1.4/bin/dng