diff --git a/examples/3D-example/input/1WCM.fasta.txt b/broken-examples/3D-example/input/1WCM.fasta.txt
similarity index 100%
rename from examples/3D-example/input/1WCM.fasta.txt
rename to broken-examples/3D-example/input/1WCM.fasta.txt
diff --git a/examples/3D-example/input/1WCM.pdb b/broken-examples/3D-example/input/1WCM.pdb
similarity index 100%
rename from examples/3D-example/input/1WCM.pdb
rename to broken-examples/3D-example/input/1WCM.pdb
diff --git a/examples/3D-example/input/bayesian_em_restraint/C.mrc b/broken-examples/3D-example/input/bayesian_em_restraint/C.mrc
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/C.mrc
rename to broken-examples/3D-example/input/bayesian_em_restraint/C.mrc
diff --git a/examples/3D-example/input/bayesian_em_restraint/C.txt b/broken-examples/3D-example/input/bayesian_em_restraint/C.txt
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/C.txt
rename to broken-examples/3D-example/input/bayesian_em_restraint/C.txt
diff --git a/examples/3D-example/input/bayesian_em_restraint/K.mrc b/broken-examples/3D-example/input/bayesian_em_restraint/K.mrc
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/K.mrc
rename to broken-examples/3D-example/input/bayesian_em_restraint/K.mrc
diff --git a/examples/3D-example/input/bayesian_em_restraint/K.txt b/broken-examples/3D-example/input/bayesian_em_restraint/K.txt
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/K.txt
rename to broken-examples/3D-example/input/bayesian_em_restraint/K.txt
diff --git a/examples/3D-example/input/bayesian_em_restraint/gmm_data/10_2.0.mrc b/broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/10_2.0.mrc
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/gmm_data/10_2.0.mrc
rename to broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/10_2.0.mrc
diff --git a/examples/3D-example/input/bayesian_em_restraint/gmm_data/10_2.0.txt b/broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/10_2.0.txt
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/gmm_data/10_2.0.txt
rename to broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/10_2.0.txt
diff --git a/examples/3D-example/input/bayesian_em_restraint/gmm_data/15_2.0.mrc b/broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/15_2.0.mrc
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/gmm_data/15_2.0.mrc
rename to broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/15_2.0.mrc
diff --git a/examples/3D-example/input/bayesian_em_restraint/gmm_data/15_2.0.txt b/broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/15_2.0.txt
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/gmm_data/15_2.0.txt
rename to broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/15_2.0.txt
diff --git a/examples/3D-example/input/bayesian_em_restraint/gmm_data/25_2.0.mrc b/broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/25_2.0.mrc
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/gmm_data/25_2.0.mrc
rename to broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/25_2.0.mrc
diff --git a/examples/3D-example/input/bayesian_em_restraint/gmm_data/25_2.0.txt b/broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/25_2.0.txt
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/gmm_data/25_2.0.txt
rename to broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/25_2.0.txt
diff --git a/examples/3D-example/input/bayesian_em_restraint/gmm_data/3_2.0.mrc b/broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/3_2.0.mrc
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/gmm_data/3_2.0.mrc
rename to broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/3_2.0.mrc
diff --git a/examples/3D-example/input/bayesian_em_restraint/gmm_data/3_2.0.txt b/broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/3_2.0.txt
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/gmm_data/3_2.0.txt
rename to broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/3_2.0.txt
diff --git a/examples/3D-example/input/bayesian_em_restraint/gmm_data/5_2.0.mrc b/broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/5_2.0.mrc
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/gmm_data/5_2.0.mrc
rename to broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/5_2.0.mrc
diff --git a/examples/3D-example/input/bayesian_em_restraint/gmm_data/5_2.0.txt b/broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/5_2.0.txt
similarity index 100%
rename from examples/3D-example/input/bayesian_em_restraint/gmm_data/5_2.0.txt
rename to broken-examples/3D-example/input/bayesian_em_restraint/gmm_data/5_2.0.txt
diff --git a/examples/3D-example/input/session.py b/broken-examples/3D-example/input/session.py
similarity index 100%
rename from examples/3D-example/input/session.py
rename to broken-examples/3D-example/input/session.py
diff --git a/examples/3D-example/test_bayesian_gaussian_em_restraint.py b/broken-examples/3D-example/test_bayesian_gaussian_em_restraint.py
similarity index 100%
rename from examples/3D-example/test_bayesian_gaussian_em_restraint.py
rename to broken-examples/3D-example/test_bayesian_gaussian_em_restraint.py
diff --git a/examples/3D-example_2/input/1WCM.fasta.txt b/broken-examples/3D-example_2/input/1WCM.fasta.txt
similarity index 100%
rename from examples/3D-example_2/input/1WCM.fasta.txt
rename to broken-examples/3D-example_2/input/1WCM.fasta.txt
diff --git a/examples/3D-example_2/input/1WCM.pdb b/broken-examples/3D-example_2/input/1WCM.pdb
similarity index 100%
rename from examples/3D-example_2/input/1WCM.pdb
rename to broken-examples/3D-example_2/input/1WCM.pdb
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/C.mrc b/broken-examples/3D-example_2/input/bayesian_em_restraint/C.mrc
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/C.mrc
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/C.mrc
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/C.txt b/broken-examples/3D-example_2/input/bayesian_em_restraint/C.txt
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/C.txt
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/C.txt
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/J.mrc b/broken-examples/3D-example_2/input/bayesian_em_restraint/J.mrc
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/J.mrc
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/J.mrc
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/J.txt b/broken-examples/3D-example_2/input/bayesian_em_restraint/J.txt
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/J.txt
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/J.txt
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/K.mrc b/broken-examples/3D-example_2/input/bayesian_em_restraint/K.mrc
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/K.mrc
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/K.mrc
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/K.txt b/broken-examples/3D-example_2/input/bayesian_em_restraint/K.txt
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/K.txt
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/K.txt
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/L.mrc b/broken-examples/3D-example_2/input/bayesian_em_restraint/L.mrc
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/L.mrc
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/L.mrc
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/L.txt b/broken-examples/3D-example_2/input/bayesian_em_restraint/L.txt
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/L.txt
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/L.txt
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/analysis/cluster.0/0.1.pdb b/broken-examples/3D-example_2/input/bayesian_em_restraint/analysis/cluster.0/0.1.pdb
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/analysis/cluster.0/0.1.pdb
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/analysis/cluster.0/0.1.pdb
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/analysis/cluster.0/0.1.rmf3 b/broken-examples/3D-example_2/input/bayesian_em_restraint/analysis/cluster.0/0.1.rmf3
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/analysis/cluster.0/0.1.rmf3
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/analysis/cluster.0/0.1.rmf3
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/analysis/clustering.py b/broken-examples/3D-example_2/input/bayesian_em_restraint/analysis/clustering.py
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/analysis/clustering.py
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/analysis/clustering.py
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/gmm_data/10_2.0.mrc b/broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/10_2.0.mrc
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/gmm_data/10_2.0.mrc
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/10_2.0.mrc
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/gmm_data/10_2.0.txt b/broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/10_2.0.txt
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/gmm_data/10_2.0.txt
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/10_2.0.txt
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/gmm_data/15_2.0.mrc b/broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/15_2.0.mrc
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/gmm_data/15_2.0.mrc
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/15_2.0.mrc
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/gmm_data/15_2.0.txt b/broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/15_2.0.txt
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/gmm_data/15_2.0.txt
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/15_2.0.txt
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/gmm_data/25_2.0.mrc b/broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/25_2.0.mrc
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/gmm_data/25_2.0.mrc
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/25_2.0.mrc
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/gmm_data/25_2.0.txt b/broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/25_2.0.txt
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/gmm_data/25_2.0.txt
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/25_2.0.txt
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/gmm_data/30_2.0.mrc b/broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/30_2.0.mrc
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/gmm_data/30_2.0.mrc
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/30_2.0.mrc
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/gmm_data/30_2.0.txt b/broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/30_2.0.txt
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/gmm_data/30_2.0.txt
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/30_2.0.txt
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/gmm_data/3_2.0.mrc b/broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/3_2.0.mrc
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/gmm_data/3_2.0.mrc
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/3_2.0.mrc
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/gmm_data/3_2.0.txt b/broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/3_2.0.txt
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/gmm_data/3_2.0.txt
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/3_2.0.txt
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/gmm_data/5_2.0.mrc b/broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/5_2.0.mrc
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/gmm_data/5_2.0.mrc
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/5_2.0.mrc
diff --git a/examples/3D-example_2/input/bayesian_em_restraint/gmm_data/5_2.0.txt b/broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/5_2.0.txt
similarity index 100%
rename from examples/3D-example_2/input/bayesian_em_restraint/gmm_data/5_2.0.txt
rename to broken-examples/3D-example_2/input/bayesian_em_restraint/gmm_data/5_2.0.txt
diff --git a/examples/3D-example_2/input/session.py b/broken-examples/3D-example_2/input/session.py
similarity index 100%
rename from examples/3D-example_2/input/session.py
rename to broken-examples/3D-example_2/input/session.py
diff --git a/examples/3D-example_2/test_bayesian_gaussian_em_restraint.py b/broken-examples/3D-example_2/test_bayesian_gaussian_em_restraint.py
similarity index 100%
rename from examples/3D-example_2/test_bayesian_gaussian_em_restraint.py
rename to broken-examples/3D-example_2/test_bayesian_gaussian_em_restraint.py
diff --git a/examples/exosome/analysis/analysis_xl.py b/broken-examples/exosome/analysis/analysis_xl.py
similarity index 100%
rename from examples/exosome/analysis/analysis_xl.py
rename to broken-examples/exosome/analysis/analysis_xl.py
diff --git a/examples/exosome/analysis/clustering.py b/broken-examples/exosome/analysis/clustering.py
similarity index 100%
rename from examples/exosome/analysis/clustering.py
rename to broken-examples/exosome/analysis/clustering.py
diff --git a/examples/exosome/analysis/get_data.py b/broken-examples/exosome/analysis/get_data.py
similarity index 100%
rename from examples/exosome/analysis/get_data.py
rename to broken-examples/exosome/analysis/get_data.py
diff --git a/examples/exosome/analysis/make_table.py b/broken-examples/exosome/analysis/make_table.py
similarity index 100%
rename from examples/exosome/analysis/make_table.py
rename to broken-examples/exosome/analysis/make_table.py
diff --git a/examples/exosome/data/1_imp.gmm b/broken-examples/exosome/data/1_imp.gmm
similarity index 100%
rename from examples/exosome/data/1_imp.gmm
rename to broken-examples/exosome/data/1_imp.gmm
diff --git a/examples/exosome/data/2_imp.gmm b/broken-examples/exosome/data/2_imp.gmm
similarity index 100%
rename from examples/exosome/data/2_imp.gmm
rename to broken-examples/exosome/data/2_imp.gmm
diff --git a/examples/exosome/data/3_imp.gmm b/broken-examples/exosome/data/3_imp.gmm
similarity index 100%
rename from examples/exosome/data/3_imp.gmm
rename to broken-examples/exosome/data/3_imp.gmm
diff --git a/examples/exosome/data/4IFD.pdb b/broken-examples/exosome/data/4IFD.pdb
similarity index 100%
rename from examples/exosome/data/4IFD.pdb
rename to broken-examples/exosome/data/4IFD.pdb
diff --git a/examples/exosome/data/4_imp.gmm b/broken-examples/exosome/data/4_imp.gmm
similarity index 100%
rename from examples/exosome/data/4_imp.gmm
rename to broken-examples/exosome/data/4_imp.gmm
diff --git a/examples/exosome/data/5_imp.gmm b/broken-examples/exosome/data/5_imp.gmm
similarity index 100%
rename from examples/exosome/data/5_imp.gmm
rename to broken-examples/exosome/data/5_imp.gmm
diff --git a/examples/exosome/data/5g06_align_2.pdb b/broken-examples/exosome/data/5g06_align_2.pdb
similarity index 100%
rename from examples/exosome/data/5g06_align_2.pdb
rename to broken-examples/exosome/data/5g06_align_2.pdb
diff --git a/examples/exosome/data/6_imp.gmm b/broken-examples/exosome/data/6_imp.gmm
similarity index 100%
rename from examples/exosome/data/6_imp.gmm
rename to broken-examples/exosome/data/6_imp.gmm
diff --git a/examples/exosome/data/7_imp.gmm b/broken-examples/exosome/data/7_imp.gmm
similarity index 100%
rename from examples/exosome/data/7_imp.gmm
rename to broken-examples/exosome/data/7_imp.gmm
diff --git a/examples/exosome/data/8_imp.gmm b/broken-examples/exosome/data/8_imp.gmm
similarity index 100%
rename from examples/exosome/data/8_imp.gmm
rename to broken-examples/exosome/data/8_imp.gmm
diff --git a/examples/exosome/data/9_imp.gmm b/broken-examples/exosome/data/9_imp.gmm
similarity index 100%
rename from examples/exosome/data/9_imp.gmm
rename to broken-examples/exosome/data/9_imp.gmm
diff --git a/examples/exosome/data/GFP_1GFL.pdb b/broken-examples/exosome/data/GFP_1GFL.pdb
similarity index 100%
rename from examples/exosome/data/GFP_1GFL.pdb
rename to broken-examples/exosome/data/GFP_1GFL.pdb
diff --git a/examples/exosome/data/exosome.fasta b/broken-examples/exosome/data/exosome.fasta
similarity index 100%
rename from examples/exosome/data/exosome.fasta
rename to broken-examples/exosome/data/exosome.fasta
diff --git a/examples/exosome/data/exosome_XLMS_column07012014.csv b/broken-examples/exosome/data/exosome_XLMS_column07012014.csv
similarity index 100%
rename from examples/exosome/data/exosome_XLMS_column07012014.csv
rename to broken-examples/exosome/data/exosome_XLMS_column07012014.csv
diff --git a/examples/exosome/modeling/get_seeds.py b/broken-examples/exosome/modeling/get_seeds.py
similarity index 100%
rename from examples/exosome/modeling/get_seeds.py
rename to broken-examples/exosome/modeling/get_seeds.py
diff --git a/examples/exosome/modeling/get_seeds.sh b/broken-examples/exosome/modeling/get_seeds.sh
similarity index 100%
rename from examples/exosome/modeling/get_seeds.sh
rename to broken-examples/exosome/modeling/get_seeds.sh
diff --git a/examples/exosome/modeling/init.py b/broken-examples/exosome/modeling/init.py
similarity index 100%
rename from examples/exosome/modeling/init.py
rename to broken-examples/exosome/modeling/init.py
diff --git a/examples/exosome/modeling/job.sh b/broken-examples/exosome/modeling/job.sh
similarity index 100%
rename from examples/exosome/modeling/job.sh
rename to broken-examples/exosome/modeling/job.sh
diff --git a/examples/exosome/modeling/model.py b/broken-examples/exosome/modeling/model.py
similarity index 100%
rename from examples/exosome/modeling/model.py
rename to broken-examples/exosome/modeling/model.py
diff --git a/examples/exosome/modeling/submit.sh b/broken-examples/exosome/modeling/submit.sh
similarity index 100%
rename from examples/exosome/modeling/submit.sh
rename to broken-examples/exosome/modeling/submit.sh
diff --git a/examples/modeling.py b/broken-examples/modeling.py
similarity index 100%
rename from examples/modeling.py
rename to broken-examples/modeling.py
diff --git a/examples/rnapolii/analysis/Makefile b/broken-examples/rnapolii/analysis/Makefile
similarity index 100%
rename from examples/rnapolii/analysis/Makefile
rename to broken-examples/rnapolii/analysis/Makefile
diff --git a/examples/rnapolii/analysis/analysis_xl.py b/broken-examples/rnapolii/analysis/analysis_xl.py
similarity index 100%
rename from examples/rnapolii/analysis/analysis_xl.py
rename to broken-examples/rnapolii/analysis/analysis_xl.py
diff --git a/examples/rnapolii/analysis/clustering_new.py b/broken-examples/rnapolii/analysis/clustering_new.py
similarity index 100%
rename from examples/rnapolii/analysis/clustering_new.py
rename to broken-examples/rnapolii/analysis/clustering_new.py
diff --git a/examples/rnapolii/analysis/get_data.py b/broken-examples/rnapolii/analysis/get_data.py
similarity index 100%
rename from examples/rnapolii/analysis/get_data.py
rename to broken-examples/rnapolii/analysis/get_data.py
diff --git a/examples/rnapolii/analysis/get_stat_or_rmf3.sh b/broken-examples/rnapolii/analysis/get_stat_or_rmf3.sh
similarity index 100%
rename from examples/rnapolii/analysis/get_stat_or_rmf3.sh
rename to broken-examples/rnapolii/analysis/get_stat_or_rmf3.sh
diff --git a/examples/rnapolii/analysis/make_table_new.py b/broken-examples/rnapolii/analysis/make_table_new.py
similarity index 100%
rename from examples/rnapolii/analysis/make_table_new.py
rename to broken-examples/rnapolii/analysis/make_table_new.py
diff --git a/examples/rnapolii/data/1WCM.fasta.txt b/broken-examples/rnapolii/data/1WCM.fasta.txt
similarity index 100%
rename from examples/rnapolii/data/1WCM.fasta.txt
rename to broken-examples/rnapolii/data/1WCM.fasta.txt
diff --git a/examples/rnapolii/data/1WCM.pdb b/broken-examples/rnapolii/data/1WCM.pdb
similarity index 100%
rename from examples/rnapolii/data/1WCM.pdb
rename to broken-examples/rnapolii/data/1WCM.pdb
diff --git a/examples/rnapolii/data/1WCM_map_fitted.pdb b/broken-examples/rnapolii/data/1WCM_map_fitted.pdb
similarity index 100%
rename from examples/rnapolii/data/1WCM_map_fitted.pdb
rename to broken-examples/rnapolii/data/1WCM_map_fitted.pdb
diff --git a/examples/rnapolii/data/1WCM_new.fasta.txt b/broken-examples/rnapolii/data/1WCM_new.fasta.txt
similarity index 100%
rename from examples/rnapolii/data/1WCM_new.fasta.txt
rename to broken-examples/rnapolii/data/1WCM_new.fasta.txt
diff --git a/examples/rnapolii/data/1_imp.gmm b/broken-examples/rnapolii/data/1_imp.gmm
similarity index 100%
rename from examples/rnapolii/data/1_imp.gmm
rename to broken-examples/rnapolii/data/1_imp.gmm
diff --git a/examples/rnapolii/data/2_imp.gmm b/broken-examples/rnapolii/data/2_imp.gmm
similarity index 100%
rename from examples/rnapolii/data/2_imp.gmm
rename to broken-examples/rnapolii/data/2_imp.gmm
diff --git a/examples/rnapolii/data/3_imp.gmm b/broken-examples/rnapolii/data/3_imp.gmm
similarity index 100%
rename from examples/rnapolii/data/3_imp.gmm
rename to broken-examples/rnapolii/data/3_imp.gmm
diff --git a/examples/rnapolii/data/4_imp.gmm b/broken-examples/rnapolii/data/4_imp.gmm
similarity index 100%
rename from examples/rnapolii/data/4_imp.gmm
rename to broken-examples/rnapolii/data/4_imp.gmm
diff --git a/examples/rnapolii/data/5_imp.gmm b/broken-examples/rnapolii/data/5_imp.gmm
similarity index 100%
rename from examples/rnapolii/data/5_imp.gmm
rename to broken-examples/rnapolii/data/5_imp.gmm
diff --git a/examples/rnapolii/data/6_imp.gmm b/broken-examples/rnapolii/data/6_imp.gmm
similarity index 100%
rename from examples/rnapolii/data/6_imp.gmm
rename to broken-examples/rnapolii/data/6_imp.gmm
diff --git a/examples/rnapolii/data/7_imp.gmm b/broken-examples/rnapolii/data/7_imp.gmm
similarity index 100%
rename from examples/rnapolii/data/7_imp.gmm
rename to broken-examples/rnapolii/data/7_imp.gmm
diff --git a/examples/rnapolii/data/8_imp.gmm b/broken-examples/rnapolii/data/8_imp.gmm
similarity index 100%
rename from examples/rnapolii/data/8_imp.gmm
rename to broken-examples/rnapolii/data/8_imp.gmm
diff --git a/examples/rnapolii/data/9_imp.gmm b/broken-examples/rnapolii/data/9_imp.gmm
similarity index 100%
rename from examples/rnapolii/data/9_imp.gmm
rename to broken-examples/rnapolii/data/9_imp.gmm
diff --git a/examples/rnapolii/data/native.rmf3 b/broken-examples/rnapolii/data/native.rmf3
similarity index 100%
rename from examples/rnapolii/data/native.rmf3
rename to broken-examples/rnapolii/data/native.rmf3
diff --git a/examples/rnapolii/data/polii_juri.csv b/broken-examples/rnapolii/data/polii_juri.csv
similarity index 100%
rename from examples/rnapolii/data/polii_juri.csv
rename to broken-examples/rnapolii/data/polii_juri.csv
diff --git a/examples/rnapolii/data/polii_xlinks.csv b/broken-examples/rnapolii/data/polii_xlinks.csv
similarity index 100%
rename from examples/rnapolii/data/polii_xlinks.csv
rename to broken-examples/rnapolii/data/polii_xlinks.csv
diff --git a/examples/rnapolii/data/topology.txt b/broken-examples/rnapolii/data/topology.txt
similarity index 100%
rename from examples/rnapolii/data/topology.txt
rename to broken-examples/rnapolii/data/topology.txt
diff --git a/examples/rnapolii/modeling/get_seeds.py b/broken-examples/rnapolii/modeling/get_seeds.py
similarity index 100%
rename from examples/rnapolii/modeling/get_seeds.py
rename to broken-examples/rnapolii/modeling/get_seeds.py
diff --git a/examples/rnapolii/modeling/get_seeds.sh b/broken-examples/rnapolii/modeling/get_seeds.sh
similarity index 100%
rename from examples/rnapolii/modeling/get_seeds.sh
rename to broken-examples/rnapolii/modeling/get_seeds.sh
diff --git a/examples/rnapolii/modeling/job.sh b/broken-examples/rnapolii/modeling/job.sh
similarity index 100%
rename from examples/rnapolii/modeling/job.sh
rename to broken-examples/rnapolii/modeling/job.sh
diff --git a/examples/rnapolii/modeling/modeling.py b/broken-examples/rnapolii/modeling/modeling.py
similarity index 100%
rename from examples/rnapolii/modeling/modeling.py
rename to broken-examples/rnapolii/modeling/modeling.py
diff --git a/examples/rnapolii/modeling/submit.sh b/broken-examples/rnapolii/modeling/submit.sh
similarity index 100%
rename from examples/rnapolii/modeling/submit.sh
rename to broken-examples/rnapolii/modeling/submit.sh