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