examples.md
... ...
@@ -9,6 +9,7 @@ The following pages provide usage info and examples for select applications in t
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- [Arp/Warp registration](examples/arpwarp_registration)
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- [CARELESS](examples/careless)
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- [DiffDock](examples/diffdock)
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+- [DomainSeeker](examples/DomainSeeker)
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- [EMAN2 with Theano for Neural Network Particle Picking](examples/EMAN2_w_theano)
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- [EMBuild](examples/embuild)
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- [GTalign](examples/gtalign)
examples/DomainSeeker.md
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@@ -0,0 +1,47 @@
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+DomainSeeker Example
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+Feb 26, 2025
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+
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+```
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+#!/usr/bin/env bash
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+
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+## SBGrid DomainSeeker example
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+## Args: none
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+##
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+## James Vincent - help@sbgrid.org
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+## Feb 26, 2025
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+
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+# ACKNOWLEDGE
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+
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+# If your use of SBGrid compiled software was an important element in
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+# your publication, please include the following statement in your work:
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+# "Software used in the project was installed and configured by SBGrid
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+# (cite: eLife 2013;2:e01456, Collaboration gets the most out of software.)
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+
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+
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+source /programs/sbgrid.shrc
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+export DOMAINSEEKER_X=20250204
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+
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+echo -e "\n## domainseeker version info ##\n"
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+sbgrid-info -l domainseeker
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+
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+echo -e "\n## domainseeker callable programs##\n"
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+sbgrid-list domainseeker
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+
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+## Copy DomainSeeker provided Example directory to local dir
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+cp -r /programs//x86_64-linux//domainseeker/20250204/DomainSeeker/Example ./
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+
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+## Run test from the DomainSeeker provided Example directory
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+cd Example
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+
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+echo -e "\n## domainseeker sample call##\n"
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+fetch_pdb_pae.py protein_list.txt .
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+
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+parse_with_pae.py pdb_files pae_files domain_files
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+fit_with_chimerax.py domain_files em_data fit_out 0.001 7 200 16
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+score_rank.py domain_files em_data fit_out 0.001 -0.0001 0.0001 7 16 10 50
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+
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+#get_fitted_domain.py domain_dir fitout_dir domain_list
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+
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+
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+
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+```