examples.md
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@@ -15,6 +15,7 @@ The following pages provide usage info and examples for select applications in t
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- [Local Reconstruction in SCIPION](examples/localrec_w_scipion)
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- [Locscale](examples/locscale)
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- [MiloPYP](examples/milopyp)
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+- [OpenNucleome](examples/opennucleome)
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- [PHENIX - phenix.rosetta_refine](examples/phenix.rosetta_refine)
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- [RoseTTAFold All-Atom](examples/rosettafold_all_atom)
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- [SCIPION - running tutorials without write privileges](examples/running_scipion_tutorials)
examples/opennucleome.md
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@@ -0,0 +1,87 @@
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+```
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+#!/usr/bin/env bash
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+
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+
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+
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+## SBGrid OpenNucleome Example
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+
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+## https://github.com/ZhangGroup-MITChemistry/OpenNucleome
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+
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+##
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+
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+## Run three tutorials from tutorials/init_configs dir 
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+
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+## Takes ~ 40 minutes on one NVIDIA GeForce GTX 1080 Ti
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+
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+##
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+
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+## James Vincent help@sbgrid.org
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+
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+## Jan 6, 2025
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+
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+
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+
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+export SBGRID_ALLOW=true    # sbgrid internal only
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+
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+
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+
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+echo "SBGrid OpenNucleome Example"
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+
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+
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+
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+## Start SBGrid environment
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+
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+export SBGRID_ALLOW=true   ## sbgrid dev only
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+
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+source /programs/sbgrid.shrc
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+
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+
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+
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+## Set OpenNucleome version - from command: $ sbgrid-info -l opennucleome
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+
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+export OPENNUCLEOME_X=1.3.0
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+
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+
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+
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+## Verify CUDA GPU for OpenNucleome
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+
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+python.opennucleome -m testInstallation
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+
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+
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+
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+## Get repo
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+
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+rm -rf ./OpenNucleome
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+
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+git clone https://github.com/ZhangGroup-MITChemistry/OpenNucleome.git
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+
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+
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+
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+## configs_generation  
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+
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+cd ./OpenNucleome/tutorials/init_configs/configs_generation/
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+
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+jupyter.opennucleome nbconvert --to script  ConfigsGeneration.ipynb
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+
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+python.opennucleome ./ConfigsGeneration.py
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+
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+
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+
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+## configs_relaxation  
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+
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+cd ../configs_relaxation/
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+
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+jupyter.opennucleome nbconvert --to script ConfigsRelaxation.ipynb
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+
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+python.opennucleome ./ConfigsRelaxation.py
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+
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+
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+
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+## configs_selection
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+
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+cd ../configs_selection
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+
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+jupyter.opennucleome nbconvert --to script ConfigsSelection.ipynb
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+python.opennucleome ./ConfigsSelection.py
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+```
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\ No newline at end of file