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nilshof01 · May 10, 2023 · 9b7df58 · 9b7df58
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Showing 30 changed files with 16 additions and 181 deletions.
diff --git a/cabsflex_visualization.py → Cabsflex/cabsflex_visualization.py b/cabsflex_visualization.py → Cabsflex/cabsflex_visualization.py
diff --git a/Cabsflex/command_cabsflex.sh b/Cabsflex/command_cabsflex.sh
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+$CABSflex --input-protein *.pdb -k 10 -y 30 -a 10 -v 3 -z 10 -A
diff --git a/felxibility_plot.py → Cabsflex/felxibility_plot.py b/felxibility_plot.py → Cabsflex/felxibility_plot.py
diff --git a/heatmap_free_energies.py → mutatex/heatmap_free_energies.py b/heatmap_free_energies.py → mutatex/heatmap_free_energies.py
diff --git a/mutatex/individual_list.txt b/mutatex/individual_list.txt
diff --git a/mutatex/mutatex_commands.sh b/mutatex/mutatex_commands.sh
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+#!/bin/bash
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+$cp /home/projects/22117_proteins/lecture4_exercise/group0/mutatex_templates/mutatex/templates/foldxsuite5/repair_runfile_template.txt .
+$cp /home/projects/22117_proteins/lecture4_exercise/group0/mutatex_templates/mutatex/templates/foldxsuite5/mutate_runfile_template.txt .
+$cp /home/projects/22117_proteins/lecture4_exercise/group0/mutatex_templates/mutatex/templates/mutation_list.txt .
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+$/home/ctools/foldx-5.2023/foldx --command=RepairPDB --pdb=bx116_RBD_correct.pdb --ionStrength=0.05 --pH=7 -vdwDesign=2 --out-pdb=1 --pdbHydrogens=False
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+$mutatex bx116_RBD__Repair.pdb -p 10 -m mutation_list.txt -x /home/ctools/foldx-5.2023/foldx -f suite5 -R repair_runfile_template.txt -M mutate_runfile_template.txt -q poslist.txt -c -L -l -v &
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+$/home/ctools/anaconda3_2021.11/bin/ddg2excel -p RBD_BX116__Repair.pdb  -l mutation_list.txt -q poslist.txt -d results/mutation_ddgs/final_averages/ -F csv
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diff --git a/mutatex/mutatex_input.txt b/mutatex/mutatex_input.txt
diff --git a/plots/417_residue.png b/plots/417_residue.png
diff --git a/plots/6M0J_WT_CABSflexENERGY.png b/plots/6M0J_WT_CABSflexENERGY.png
diff --git a/plots/6M0J_WT_CABSflexRMSF.png b/plots/6M0J_WT_CABSflexRMSF.png
diff --git a/plots/6m0j.png b/plots/6m0j.png
diff --git a/plots/6vxx.png b/plots/6vxx.png
diff --git a/plots/7qo7.jpg b/plots/7qo7.jpg
diff --git a/plots/7u0n.png b/plots/7u0n.png
diff --git a/plots/Dock_aling.png b/plots/Dock_aling.png
diff --git a/plots/Newest_ACE2_CABSflexENERGY.png b/plots/Newest_ACE2_CABSflexENERGY.png
diff --git a/plots/Newest_ACE2_CABSflexRMSF.png b/plots/Newest_ACE2_CABSflexRMSF.png
diff --git a/plots/Omi_ACE2_CABSflexENERGY.png b/plots/Omi_ACE2_CABSflexENERGY.png
diff --git a/plots/Omi_ACE2_CABSflexRMSF.png b/plots/Omi_ACE2_CABSflexRMSF.png
diff --git a/plots/PBDsum_XBB116.png b/plots/PBDsum_XBB116.png
diff --git a/plots/PDBsum_Omi.png b/plots/PDBsum_Omi.png
diff --git a/plots/PDBsum_WT.png b/plots/PDBsum_WT.png
diff --git a/plots/aligned.png b/plots/aligned.png
diff --git a/plots/all_aligned.png b/plots/all_aligned.png
diff --git a/plots/binding.png b/plots/binding.png
diff --git a/plots/flexibilities.png b/plots/flexibilities.png
diff --git a/plots/multisequence_alignment_RBD.png b/plots/multisequence_alignment_RBD.png
diff --git a/plots/spike.png b/plots/spike.png
diff --git a/plots/triagnle_residues.png b/plots/triagnle_residues.png
diff --git a/plots/tyr449.png b/plots/tyr449.png
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		$CABSflex --input-protein *.pdb -k 10 -y 30 -a 10 -v 3 -z 10 -A