id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16723 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.2-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Current thread 0x00000001f6ad4100 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, 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scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, 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All rights reserved. How to cite UCSF ChimeraX > open /Users/nezakoritnik/Desktop/HCPro-struktura/monomerhcpro.cif Summary of feedback from opening /Users/nezakoritnik/Desktop/HCPro- struktura/monomerhcpro.cif --- warnings | Unknown polymer entity '1' on line 131 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for monomerhcpro.cif #1 --- Chain | Description Ab | No description available > set bgColor white > open ""/Users/nezakoritnik/Documents/REZULTATI/Bioinformatske > analize/AlphaFold/ALFAFOLD3/PVA- > HCPro_2024_05_09_pva_hcpro/fold_2024_05_09_pva_hcpro_model_0.cif"" Chain information for fold_2024_05_09_pva_hcpro_model_0.cif #2 --- Chain | Description A | . Computing secondary structure > ui tool show Matchmaker > matchmaker #2 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 1127.3 RMSD between 151 pruned atom pairs is 0.771 angstroms; (across all 261 pairs: 36.016) > ui tool show Matchmaker > ui tool show ""Show Sequence Viewer"" > sequence chain #1/Ab Alignment identifier is 1/Ab > select #1/Ab:102 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/Ab:102-174 584 atoms, 594 bonds, 73 residues, 1 model selected > ui tool show Matchmaker > matchmaker #2 to #1 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 342 RMSD between 63 pruned atom pairs is 0.737 angstroms; (across all 73 pairs: 2.555) > matchmaker #2 to #1 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 342 RMSD between 63 pruned atom pairs is 0.737 angstroms; (across all 73 pairs: 2.555) > matchmaker #2 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 1127.3 RMSD between 151 pruned atom pairs is 0.771 angstroms; (across all 261 pairs: 36.016) > ui tool show ""Command Line Interface"" > lighting intensity 0.45 ambientIntensity 0.14 fillIntensity 1 depthCue true > shadows true multiShadow 64 > cartoon style (sel & coil) xsection oval > cartoon style sel xsection barbell modeHelix default > select add #2 4180 atoms, 4262 bonds, 530 residues, 2 models selected > hide #!1 models > color (#2 & sel) dim gray > color (#2 & sel) gray > color (#2 & sel) light gray > hide #2 models > select subtract #2 584 atoms, 594 bonds, 73 residues, 1 model selected > show #2 models > show #!1 models > select add #2 4180 atoms, 4262 bonds, 530 residues, 2 models selected > select subtract #2 584 atoms, 594 bonds, 73 residues, 1 model selected > hide #2 models > show #2 models > select add #2 4180 atoms, 4262 bonds, 530 residues, 2 models selected > hide #!1 models > show #!1 models > ui tool show ""Color Actions"" > color sel pale violet red > undo > select subtract #2 584 atoms, 594 bonds, 73 residues, 1 model selected > select add #1 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > select subtract #1 Nothing selected > select add #1 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > color sel pale violet red > select clear > save ""/Users/nezakoritnik/Desktop/Alphafold C.png"" width 3000 height 2487 > supersample 3 transparentBackground true > save /Users/nezakoritnik/Desktop/alphafoldC.cxs > save ""/Users/nezakoritnik/Desktop/AlphaFold C2.png"" width 3000 height 2487 > supersample 3 transparentBackground true No reference and/or match structure/chain chosen > matchmaker #2 to #1 & sel No 'to' model specified > select #1/Ab:102 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/Ab:102-186 673 atoms, 684 bonds, 85 residues, 1 model selected > matchmaker #2 to #1 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 397.4 RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs: 11.855) > matchmaker #2 to #1 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 397.4 RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs: 11.855) > matchmaker #2 to #1 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 397.4 RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs: 11.855) > matchmaker #2 to #1 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 397.4 RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs: 11.855) > matchmaker #2 to #1 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 397.4 RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs: 11.855) > matchmaker #2 to #1 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 397.4 RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs: 11.855) > matchmaker #2 to #1 & sel Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 397.4 RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs: 11.855) > select clear > save ""/Users/nezakoritnik/Desktop/Alphafold N.png"" width 3000 height 2487 > supersample 3 transparentBackground true > save ""/Users/nezakoritnik/Desktop/Alphafold N2.png"" width 3000 height 2487 > supersample 3 transparentBackground true > hide #2 models > show #2 models > save /Users/nezakoritnik/Desktop/alphafoldN.cxs > hide #2 models > save /Users/nezakoritnik/Desktop/monomer.cxs > save ""/Users/nezakoritnik/Desktop/monomer 1.png"" width 3000 height 2435 > supersample 3 transparentBackground true > lighting intensity 0.45 ambientIntensity 0.14 fillIntensity 1 depthCue true > shadows true multiShadow 0 > lighting intensity 0.45 ambientIntensity 0.14 fillIntensity 1 depthCue true > shadows true multiShadow 64 > save ""/Users/nezakoritnik/Desktop/monomer 2.png"" width 3000 height 2435 > supersample 3 transparentBackground true > show #2 models > matchmaker #2 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 1127.3 RMSD between 151 pruned atom pairs is 0.771 angstroms; (across all 261 pairs: 36.016) > hide #!1 models > show #!1 models > select add #1 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > ui tool show ""Color Actions"" > color sel pink > hide #2 models > select clear > save ""/Users/nezakoritnik/Desktop/monomer 1.1.png"" width 3000 height 2435 > supersample 3 transparentBackground true > save ""/Users/nezakoritnik/Desktop/monomer 2.1.png"" width 3000 height 2435 > supersample 3 transparentBackground true > select #1/Ab:410-411 18 atoms, 18 bonds, 2 residues, 1 model selected > select #1/Ab:410-457 386 atoms, 393 bonds, 48 residues, 1 model selected Drag select of 1 residues > select #1/Ab:343 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/Ab:343-457 904 atoms, 922 bonds, 115 residues, 1 model selected > select #1/Ab:342 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/Ab:342-343 18 atoms, 18 bonds, 2 residues, 1 model selected > select #1/Ab:342 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/Ab:342-457 916 atoms, 935 bonds, 116 residues, 1 model selected > rainbow sel > select clear > rainbow #!1 > save ""/Users/nezakoritnik/Desktop/monomer 1.png"" width 3000 height 2435 > supersample 3 > save ""/Users/nezakoritnik/Desktop/monomer 1.png"" width 3000 height 2435 > supersample 3 transparentBackground true > rotate 180 Unknown command: rotate 180 > rot 180 Unknown command: rot 180 > turn z 180 > turn y 180 > save ""/Users/nezakoritnik/Desktop/monomer 2.png"" width 3000 height 2435 > supersample 3 transparentBackground true > select #1/Ab:293 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #1/Ab:279 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > disulphides Unknown command: disulphides > show disulfides Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show /ss > select #1/Ab:279@CA 1 atom, 1 residue, 1 model selected > select #1/Ab:279@SG 1 atom, 1 residue, 1 model selected > select #1/Ab:290 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/Ab:279@SG 1 atom, 1 residue, 1 model selected > select add #1/Ab:293@SG 2 atoms, 2 residues, 1 model selected > bond sel Created 1 bond > ui tool show ""Side View"" > save /Users/nezakoritnik/Desktop/disulfid.png width 3000 height 2579 > supersample 3 transparentBackground true > select clear > save /Users/nezakoritnik/Desktop/disulfid.png width 3000 height 2579 > supersample 3 transparentBackground true > select #1/Ab:180 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/Ab:180 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > select #1/Ab:181 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #1/Ab:182 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #1/Ab:183 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select clear > color #1 byhetero > save /Users/nezakoritnik/Desktop/monomer.cxs > open /Users/nezakoritnik/Desktop/HCPro-struktura/NOVHCPro- > Andreja/Rigidbodyrefine16/chains_filament16_real_space_refined.pdb Summary of feedback from opening /Users/nezakoritnik/Desktop/HCPro- struktura/NOVHCPro- Andreja/Rigidbodyrefine16/chains_filament16_real_space_refined.pdb --- warnings | Ignored bad PDB record found on line 379 SSBOND 1 CYS Aa 279 CYS Aa 293 Ignored bad PDB record found on line 380 SSBOND 2 CYS Ab 279 CYS Ab 293 Ignored bad PDB record found on line 381 SSBOND 3 CYS Ac 279 CYS Ac 293 Ignored bad PDB record found on line 382 SSBOND 4 CYS Ad 279 CYS Ad 293 Ignored bad PDB record found on line 383 SSBOND 5 CYS Ae 279 CYS Ae 293 19 messages similar to the above omitted Chain information for chains_filament16_real_space_refined.pdb #3 --- Chain | Description Aa Ab Ac Ad Ae Af Ag Ah Ai Aj Ak Al Am An Ao Ap Aq Ar As At Au Av Aw Ax | No description available > hide #!1 models > show #!1 models > hide #!1 models > show #!3 surfaces > open /Users/nezakoritnik/Desktop/HCPro-struktura/NOVHCPro-Andreja/newPVA- > HCPro_P130_J481.mrc Opened newPVA-HCPro_P130_J481.mrc as #4, grid size 512,512,512, pixel 0.834, shown at level 0.0803, step 2, values float32 > transparency 50 > color #4 #ebebebff models > transparency 0 > transparency 50 > hide #!4 models > lighting soft > select #3/Aa 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > color (#!3 & sel) red > select clear > save /Users/nezakoritnik/Desktop/interakcije1.png width 3000 height 2871 > supersample 3 transparentBackground true > close #4 > save /Users/nezakoritnik/Desktop/interakcije.cxs > open /Users/nezakoritnik/Desktop/HCPro-struktura/NOVHCPro-Andreja/newPVA- > HCPro_P130_J481.mrc Opened newPVA-HCPro_P130_J481.mrc as #4, grid size 512,512,512, pixel 0.834, shown at level 0.0803, step 2, values float32 > select add #4 2 models selected > transparency sel 50 > color #4 white models > hide #!4 models > show #!4 models > select subtract #4 Nothing selected > lighting soft > color #4 #ebebebff models > volume #4 step 1 > surface dust #4 size 8.34 > select add #4 2 models selected > transparency sel 50 > select subtract #4 Nothing selected > hide #!4 models > show #!4 models > select add #4 3 models selected > color #4 #d6d6d6ff models > transparency #4.1 70 > select subtract #4 Nothing selected > save ""/Users/nezakoritnik/Desktop/HCPro-struktura/NOVHCPro- > Andreja/interakcije 1.1.cxs"" includeMaps true > save ""/Users/nezakoritnik/Desktop/HCPro-struktura/NOVHCPro- > Andreja/interakcije 1.1.png"" width 3000 height 2871 supersample 3 > transparentBackground true > hide #!4 models > show #!4 models > hide #!4 models > save ""/Users/nezakoritnik/Desktop/interakcije 2.png"" width 3000 height 2605 > supersample 3 transparentBackground true > show #!4 models > color #4 darkgrey models > save ""/Users/nezakoritnik/Desktop/interakcije 1.1.png"" width 3000 height > 2605 supersample 3 > hide #!3 models > hide #!4 models > show #!3 models > show #!4 models > hide #!4 models > hide #!3 surfaces > style #!3 stick Changed 49344 atom styles > show #!3 cartoons > hide #!3 atoms > cartoon style #3 modeHelix tube sides 20 > show #!3 surfaces > transparency #3 0 > ui tool show ""Command Line Interface"" > split Did not split monomerhcpro.cif, has only one piece Did not split fold_2024_05_09_pva_hcpro_model_0.cif, has only one piece Split chains_filament16_real_space_refined.pdb (#3) into 24 models Chain information for chains_filament16_real_space_refined.pdb Aa #3.1 --- Chain | Description Aa | No description available Chain information for chains_filament16_real_space_refined.pdb Ab #3.2 --- Chain | Description Ab | No description available Chain information for chains_filament16_real_space_refined.pdb Ac #3.3 --- Chain | Description Ac | No description available Chain information for chains_filament16_real_space_refined.pdb Ad #3.4 --- Chain | Description Ad | No description available Chain information for chains_filament16_real_space_refined.pdb Ae #3.5 --- Chain | Description Ae | No description available Chain information for chains_filament16_real_space_refined.pdb Af #3.6 --- Chain | Description Af | No description available Chain information for chains_filament16_real_space_refined.pdb Ag #3.7 --- Chain | Description Ag | No description available Chain information for chains_filament16_real_space_refined.pdb Ah #3.8 --- Chain | Description Ah | No description available Chain information for chains_filament16_real_space_refined.pdb Ai #3.9 --- Chain | Description Ai | No description available Chain information for chains_filament16_real_space_refined.pdb Aj #3.10 --- Chain | Description Aj | No description available Chain information for chains_filament16_real_space_refined.pdb Ak #3.11 --- Chain | Description Ak | No description available Chain information for chains_filament16_real_space_refined.pdb Al #3.12 --- Chain | Description Al | No description available Chain information for chains_filament16_real_space_refined.pdb Am #3.13 --- Chain | Description Am | No description available Chain information for chains_filament16_real_space_refined.pdb An #3.14 --- Chain | Description An | No description available Chain information for chains_filament16_real_space_refined.pdb Ao #3.15 --- Chain | Description Ao | No description available Chain information for chains_filament16_real_space_refined.pdb Ap #3.16 --- Chain | Description Ap | No description available Chain information for chains_filament16_real_space_refined.pdb Aq #3.17 --- Chain | Description Aq | No description available Chain information for chains_filament16_real_space_refined.pdb Ar #3.18 --- Chain | Description Ar | No description available Chain information for chains_filament16_real_space_refined.pdb As #3.19 --- Chain | Description As | No description available Chain information for chains_filament16_real_space_refined.pdb At #3.20 --- Chain | Description At | No description available Chain information for chains_filament16_real_space_refined.pdb Au #3.21 --- Chain | Description Au | No description available Chain information for chains_filament16_real_space_refined.pdb Av #3.22 --- Chain | Description Av | No description available Chain information for chains_filament16_real_space_refined.pdb Aw #3.23 --- Chain | Description Aw | No description available Chain information for chains_filament16_real_space_refined.pdb Ax #3.24 --- Chain | Description Ax | No description available > show #!3.1-24 surfaces > hide #!3 models > show #!3 models > hide #!3.2 models > hide #!3.3 models > hide #!3.4 models > show #!3.4 models > hide #!3.4 models > hide #!3.5 models > hide #!3.6 models > hide #!3.7 models > show #!3.7 models > hide #!3.8 models > hide #!3.7 models > hide #!3.9 models > hide #!3.10 models > hide #!3.11 models > hide #!3.12 models > hide #!3.13 models > hide #!3.14 models > hide #!3.15 models > hide #!3.16 models > hide #!3.17 models > hide #!3.18 models > hide #!3.19 models > hide #!3.20 models > hide #!3.21 models > hide #!3.22 models > hide #!3.23 models > hide #!3.24 models > show #!3.7 models > hide #!3.7 models > show #!3.3 models > hide #!3.3 models > show #!3.4 models > hide #!3.1,4 surfaces > show #!3.1,4 surfaces > hide #!3.1,4 surfaces > hide #!3.4 models > show #!3.3 models > show #!3.1,3 surfaces > hide #!3.3 models > show #!3.8 models > hide #!3.8 models > show #!3.21 models > hide #!3.21 models > show #!3.2 models > show #!3.11 models > hide #!3.11 models > show #!3.17 models > hide #!3.17 models > show #!3.17 models > hide #!3.17 models > hide #!3.2 models > hide #!3.1 models > show #!3.3 models > show #!3.1 models > show #!3.4 models > hide #!3.3 models > hide #!3.1,4 surfaces > cartoon style #3.1,4#!3 modeHelix tube sides 20 > cartoon style (#3.1,4#!3 & coil) xsection oval > cartoon style #3.1,4#!3 xsection barbell modeHelix default > lighting intensity 0.45 ambientIntensity 0.14 fillIntensity 1 depthCue true > shadows true multiShadow 64 > select add #3.1 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > ui tool show ""Color Actions"" > color sel pink > select clear > show #!3.1,4 atoms > color #3.1,4#!3 byhetero > ui mousemode right distance > distance #3.4/Ad:135@OE1 #3.1/Aa:455@NH1 Distance between chains_filament16_real_space_refined.pdb Ad #3.4/Ad GLU 135 OE1 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 455 NH1: 5.036Å > hide #!3.1,4 atoms > select #3.4/Ad:135 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:455 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > ui tool show ""Color Actions"" > color sel lime > select #3.4/Ad:126 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:413 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > distance #3.1/Aa:413@NZ #3.4/Ad:126@OG1 Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa LYS 413 NZ and chains_filament16_real_space_refined.pdb Ad #3.4/Ad THR 126 OG1: 3.203Å > select clear > hide #5.1 models > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/od-cd.png"" width 3000 height > 2435 supersample 3 transparentBackground true > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/od-cd.cxs"" > close #4 > hide #!3.1,4 atoms > select #3.1/Aa:450 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:127 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:128 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > show sel atoms > select clear > hide #!3.1,4 atoms > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select #2/A:109 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:109-220 889 atoms, 905 bonds, 112 residues, 1 model selected > select #2/A:260-261 13 atoms, 12 bonds, 2 residues, 1 model selected > select #2/A:260-325 506 atoms, 515 bonds, 66 residues, 1 model selected > select #2/A:321-322 15 atoms, 15 bonds, 2 residues, 1 model selected > select #2/A:209-322 892 atoms, 910 bonds, 114 residues, 1 model selected > select #2/A:5 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:5-423 3296 atoms, 3363 bonds, 419 residues, 1 model selected > select #2/A:158 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:158-260 831 atoms, 845 bonds, 103 residues, 1 model selected > select #2/A:52-102 414 atoms, 421 bonds, 51 residues, 1 model selected > select #2/A:1-102 805 atoms, 821 bonds, 102 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #3.1/Aa Alignment identifier is 3.1/Aa > ui tool show ""Show Sequence Viewer"" > sequence chain #3.4/Ad Alignment identifier is 3.4/Ad > select #3.4/Ad:457 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3.4/Ad:298-457 994 atoms, 1015 bonds, 1 pseudobond, 126 residues, 2 models selected > select #3.4/Ad:267-268 13 atoms, 12 bonds, 2 residues, 1 model selected > select #3.4/Ad:267-457 1226 atoms, 1250 bonds, 1 pseudobond, 157 residues, 2 models selected > select #3.4/Ad:170 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.4/Ad:170-457 1502 atoms, 1527 bonds, 2 pseudobonds, 192 residues, 2 models selected > select #3.4/Ad:146 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3.4/Ad:146-457 1689 atoms, 1717 bonds, 2 pseudobonds, 216 residues, 2 models selected > cartoon hide (#!3.4 & sel) > select #3.1/Aa:101-102 23 atoms, 24 bonds, 2 residues, 1 model selected > select #3.1/Aa:101-145 367 atoms, 375 bonds, 45 residues, 1 model selected > hide (#!3.1 & sel) target a > cartoon hide (#!3.1 & sel) > select #3.1/Aa:457 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3.1/Aa:298-457 994 atoms, 1015 bonds, 1 pseudobond, 126 residues, 2 models selected > select #3.1/Aa:170-171 16 atoms, 15 bonds, 2 residues, 1 model selected > select #3.1/Aa:170-457 1502 atoms, 1527 bonds, 2 pseudobonds, 192 residues, 2 models selected > hide (#!3.1 & sel) target a > cartoon hide (#!3.1 & sel) > show sel atoms > hide sel atoms > select clear > show #!3.1,4 atoms > undo > select #3.4/Ad:117 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:163 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > distance #3.1/Aa:163@NH1 #3.4/Ad:117@OE1 Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 163 NH1 and chains_filament16_real_space_refined.pdb Ad #3.4/Ad GLU 117 OE1: 4.957Å > ui tool show ""Color Actions"" > color sel lime > select #3.1/Aa:166 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:169 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:127 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:168 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:166 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3.1/Aa:167 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.1/Aa:168 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3.1/Aa:168-297 526 atoms, 529 bonds, 1 pseudobond, 68 residues, 2 models selected > select #3.4/Ad:160 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3.4/Ad:160-252 253 atoms, 254 bonds, 1 pseudobond, 31 residues, 2 models selected > cartoon (#!3.4 & sel) > select #3.4/Ad:160 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3.4/Ad:101-160 473 atoms, 483 bonds, 60 residues, 1 model selected > select > #3.1/Aa:112-122,128-141,143-145,148-166,177-179,258-265,289-291,345-354,363-369,371-375,381-394,436-443,451-453 863 atoms, 865 bonds, 108 residues, 1 model selected > select #3.1/Aa:168-297 526 atoms, 529 bonds, 1 pseudobond, 68 residues, 2 models selected > select #3.1/Aa:146 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3.1/Aa:146-297 695 atoms, 701 bonds, 1 pseudobond, 90 residues, 2 models selected > show sel cartoons > select #3.4/Ad:457 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3.4/Ad 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > show sel cartoons > select clear > select #3.1/Aa:101 12 atoms, 12 bonds, 1 residue, 1 model selected > select #3.1/Aa:101-252 717 atoms, 729 bonds, 1 pseudobond, 90 residues, 2 models selected > cartoon (#!3.1 & sel) > select #3.4/Ad:169 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #3.4/Ad:170 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.4/Ad:170 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.4/Ad:168 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:171 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:170 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:170 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > hide #!3.1,4 atoms > select #3.4/Ad:170 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:171 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:170 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:170 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:168 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:171 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > distance #3.4/Ad:170@OD1 #3.1/Aa:168@NH1 Distance between chains_filament16_real_space_refined.pdb Ad #3.4/Ad ASP 170 OD1 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 168 NH1: 4.754Å > color sel lime > select clear > ui tool show ""Side View"" > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/zanka-zanka.cxs"" > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/zanka-zanka.png"" width 3000 > height 2435 supersample 3 transparentBackground true > open ""/Users/nezakoritnik/Desktop/INTERFACE 1/od-cd.cxs"" Opened newPVA-HCPro_P130_J481.mrc as #4, grid size 512,512,512, pixel 0.834, shown at level 0.0803, step 1, values float32 opened ChimeraX session > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/od-cd.png"" width 3000 height > 2435 supersample 3 transparentBackground true > hide #!3.1,4 atoms > ui tool show ""Show Sequence Viewer"" > sequence chain #3.1/Aa Alignment identifier is 3.1/Aa > select #3.1/Aa:457 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3.1/Aa:377-457 635 atoms, 649 bonds, 81 residues, 1 model selected > select #3.1/Aa:273 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3.1/Aa:273-457 1181 atoms, 1205 bonds, 1 pseudobond, 151 residues, 2 models selected > select #3.1/Aa:253 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.1/Aa:253-457 1339 atoms, 1363 bonds, 1 pseudobond, 171 residues, 2 models selected > select #3.1/Aa:167 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.1/Aa:167-457 1528 atoms, 1553 bonds, 2 pseudobonds, 195 residues, 2 models selected > select #3.1/Aa:175 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3.1/Aa:175-457 1460 atoms, 1485 bonds, 2 pseudobonds, 187 residues, 2 models selected > cartoon hide (#!3.1 & sel) > select #3.1/Aa:101 12 atoms, 12 bonds, 1 residue, 1 model selected > select #3.1/Aa:101-140 333 atoms, 341 bonds, 40 residues, 1 model selected > select #3.1/Aa:145 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3.1/Aa:101-145 367 atoms, 375 bonds, 45 residues, 1 model selected > cartoon hide (#!3.1 & sel) > ui tool show ""Show Sequence Viewer"" > sequence chain #3.4/Ad Alignment identifier is 3.4/Ad > select #3.4/Ad:457 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3.4/Ad:253-457 1339 atoms, 1363 bonds, 1 pseudobond, 171 residues, 2 models selected > select #3.4/Ad:167 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.4/Ad:167-457 1528 atoms, 1553 bonds, 2 pseudobonds, 195 residues, 2 models selected > select #3.4/Ad:148 7 atoms, 7 bonds, 1 residue, 1 model selected > select #3.4/Ad:148-457 1677 atoms, 1705 bonds, 2 pseudobonds, 214 residues, 2 models selected > hide sel cartoons > select #3.1/Aa:166 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:130 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > distance #3.1/Aa:166@NH1 #3.4/Ad:130@OH Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 166 NH1 and chains_filament16_real_space_refined.pdb Ad #3.4/Ad TYR 130 OH: 3.848Å > select clear > select #3.1/Aa:163 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:117 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:169 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > distance #3.1/Aa:169@OG1 #3.4/Ad:130@OH Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa THR 169 OG1 and chains_filament16_real_space_refined.pdb Ad #3.4/Ad TYR 130 OH: 2.497Å > select #3.1/Aa:170 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.1/Aa:171 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:127 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > show sel atoms > distance #3.1/Aa:171@OD1 #3.4/Ad:127@NE2 Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ASN 171 OD1 and chains_filament16_real_space_refined.pdb Ad #3.4/Ad GLN 127 NE2: 6.116Å > hide sel atoms > select #3.1/Aa:171 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:159 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:133 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:118 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:114 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:162 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:155 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:141 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3.4/Ad:140 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.1/Aa:158 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:137 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.4/Ad:140 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:154 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:137 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.4/Ad:137 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.4/Ad:111 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.4/Ad:136 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:161 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.4/Ad:136@CA 1 atom, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.4/Ad:136 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:162 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3.1/Aa:161 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.1/Aa:165 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:129 7 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:137 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:137 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.4/Ad:136 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:137 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.1/Aa:151 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/od-od.cxs"" > ui tool show ""Side View"" > select #3.4/Ad:109 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > distance #3.4/Ad:109@OD1 #3.1/Aa:163@NH1 Distance between chains_filament16_real_space_refined.pdb Ad #3.4/Ad ASN 109 OD1 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 163 NH1: 14.827Å > ~distance #3.4/Ad:109@OD1 #3.1/Aa:163@NH1 > distance #3.1/Aa:163@NH1 #3.4/Ad:117@OE1 Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 163 NH1 and chains_filament16_real_space_refined.pdb Ad #3.4/Ad GLU 117 OE1: 4.957Å > distance #3.4/Ad:109@OD1 #3.1/Aa:155@OG Distance between chains_filament16_real_space_refined.pdb Ad #3.4/Ad ASN 109 OD1 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa SER 155 OG: 3.725Å > turn y 180 > select #3.4/Ad:129 7 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > turn y 180 > select clear > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/od-od1.png"" width 3000 height > 2435 supersample 3 transparentBackground true > turn y 180 > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/od-od1.png"" width 3000 height > 2435 supersample 3 transparentBackground true > undo > select clear > color sel lime > select clear > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/od-od1.png"" width 3000 height > 2435 supersample 3 transparentBackground true > turn y 180 > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/od-od2.png"" width 3000 height > 2435 supersample 3 transparentBackground true > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/od-od.cxs"" > hide #!5 models > select #3.4/Ad:101 12 atoms, 12 bonds, 1 residue, 1 model selected > select #3.4/Ad 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > show sel cartoons > hide sel atoms > select #3.1/Aa:456-457 12 atoms, 11 bonds, 2 residues, 1 model selected > select #3.1/Aa 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > show sel cartoons > hide sel atoms > select clear > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/celoten.cxs"" > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/celoten.png"" width 3000 height > 2435 supersample 3 > show #!3.3 models > hide #!3.4 models > hide #!3.1,3 surfaces > select add #3.3 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > ui tool show ""Color Actions"" > color sel aquamarine > color sel medium aquamarine > color sel mint cream > color sel pale turquoise > show #!3.4 models > ui tool show ""Color Actions"" > color #3.3 #a4c4b3ff > color #3.3 #dbfdefff > color #3.3 #cdf4e1ff > hide #!3.4 models > select clear > save ""/Users/nezakoritnik/Desktop/INTERFACE 2/celoten.png"" width 3000 height > 2435 supersample 3 > show #!3.4 models > hide #!3.3 models > select clear > select #3.4/Ad:450 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:126 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:127 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #3.1/Aa:128 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:453 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:164 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:157 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:132 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > show #!3.3 models > hide #!3.4 models > select #3.1/Aa:457 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3.1/Aa:169-457 1509 atoms, 1534 bonds, 2 pseudobonds, 193 residues, 2 models selected > hide sel cartoons > ui tool show ""Show Sequence Viewer"" > sequence chain #3.3/Ac Alignment identifier is 3.3/Ac > select #3.3/Ac:101 12 atoms, 12 bonds, 1 residue, 1 model selected > select #3.3/Ac:101-183 666 atoms, 678 bonds, 83 residues, 1 model selected > hide sel cartoons > hide sel atoms > select clear > hide #!3.1,3 atoms > select #3.1/Aa:113 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.1/Aa:106 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:362 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > color #3.1,3#!3 byhetero > distance #3.1/Aa:106@NH1 #3.3/Ac:362@OD2 Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 106 NH1 and chains_filament16_real_space_refined.pdb Ac #3.3/Ac ASP 362 OD2: 2.728Å > distance #3.3/Ac:362@OD2 #3.1/Aa:106@NH1 Distance already exists; modify distance properties with 'distance style' > show #!5 models > color sel lime > select #3.1/Aa:145 11 atoms, 10 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected models"" > show sel atoms > select #3.3/Ac:357 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:358 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:359 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:360 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select clear > select #3.3/Ac:358 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:145 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.3/Ac:359 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.3/Ac:357 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:115 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:389 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > ui mousemode right distance > distance #3.1/Aa:115@OH #3.3/Ac:389@OG Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa TYR 115 OH and chains_filament16_real_space_refined.pdb Ac #3.3/Ac SER 389 OG: 2.696Å > select #3.1/Aa:116 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:374 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > distance #3.1/Aa:116@NH1 #3.3/Ac:374@OD2 Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 116 NH1 and chains_filament16_real_space_refined.pdb Ac #3.3/Ac ASP 374 OD2: 3.301Å > color sel lime > select #3.1/Aa:120 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:445 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > distance #3.1/Aa:120@NZ #3.3/Ac:445@OD1 Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa LYS 120 NZ and chains_filament16_real_space_refined.pdb Ac #3.3/Ac ASN 445 OD1: 3.904Å > select #3.1/Aa:138 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:437 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:135 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:440 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.3/Ac:437 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3.3/Ac:437 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:135 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.3/Ac:393 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3.1/Aa:142 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:394 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:142 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:141 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:390 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:142 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:119 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:386 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:390 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.3/Ac:440 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.3/Ac:443 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > cartoon style (#!3.3 & sel) modeHelix tube sides 20 > cartoon style (#!3.3 & sel & coil) xsection oval > cartoon style (#!3.3 & sel) xsection barbell modeHelix default > select clear > select #3.1/Aa:138 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > turn y 180 > save ""/Users/nezakoritnik/Desktop/INTERFACE 2/interface1.png"" width 3000 > height 2435 supersample 3 transparentBackground true > turn y 180 > save ""/Users/nezakoritnik/Desktop/INTERFACE 2/interface2.png"" width 3000 > height 2435 supersample 3 transparentBackground true > save ""/Users/nezakoritnik/Desktop/INTERFACE 2/interface.cxs"" > turn y 180 > save ""/Users/nezakoritnik/Desktop/INTERFACE 2/interface11.png"" width 3000 > height 2435 supersample 3 transparentBackground true > turn y 180 > save ""/Users/nezakoritnik/Desktop/INTERFACE 2/interface 21.png"" width 3000 > height 2435 supersample 3 transparentBackground true > open ""/Users/nezakoritnik/Desktop/INTERFACE 2/interface.cxs"" Opened newPVA-HCPro_P130_J481.mrc as #4, grid size 512,512,512, pixel 0.834, shown at level 0.0803, step 1, values float32 opened ChimeraX session > close #4 > show #!3.2 models > ui tool show ""Side View"" > hide #!3.1 models > show #!3.1 models > hide #!3.2 models > show #!3.5 models > hide #!3.5 models > show #!3.5 models > hide #!3.5 models > show #!3.7 models > hide #!3.7 models > show #!3.9 models > show #!3.8 models > hide #!3.8 models > hide #!3.9 models > show #!3.10 models > hide #!3.10 models > show #!3.11 models > show #!3.12 models > hide #!3.11 models > hide #!3.12 models > show #!3.14 models > hide #!3.14 models > show #!3.15 models > hide #!3.15 models > show #!3.16 models > hide #!3.16 models > show #!3.17 models > hide #!3.17 models > show #!3.20 models > hide #!3.20 models > show #!3.20 models > hide #!3.20 models > show #!3.20 models > hide #!3.20 models > show #!3.20 models > hide #!3.20 models > show #!3.21 models > hide #!3.21 models > show #!3.21 models > hide #!3.21 models > show #!3.22 models > hide #!3.22 models > show #!3.21 models > hide #!3.21 models > select #3.3/Ac:407-457 409 atoms, 416 bonds, 51 residues, 1 model selected > select #3.3/Ac 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > show sel cartoons > select #3.1/Aa:457 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3.1/Aa 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > show sel cartoons > show #!3.21 models > hide sel surfaces > select clear > hide #!3.1,3,21 surfaces > color #3.21 #e0fef3ff > color #3.21 #c8e7d8ff > cartoon style (#3.1,3,21#!3,5 & coil) xsection oval > cartoon style #3.1,3,21#!3,5 xsection barbell modeHelix default > hide #!3.3 models > hide #!3.1,21 atoms > save ""/Users/nezakoritnik/Desktop/INTERFACE 3/celotna.png"" width 3000 height > 2435 supersample 3 transparentBackground true > save ""/Users/nezakoritnik/Desktop/INTERFACE 3/celotna.cxs"" > select #3.1/Aa:265 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:261 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:258 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.21/Au:254 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:254 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3.21/Au:258 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.21/Au:261 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.21/Au:265 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:457 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3.1/Aa:298-457 994 atoms, 1015 bonds, 1 pseudobond, 126 residues, 2 models selected > cartoon hide (#!3.1 & sel) > select #3.1/Aa:297 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.1/Aa:270-297 213 atoms, 215 bonds, 28 residues, 1 model selected > select #3.1/Aa:272 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3.1/Aa:272-297 196 atoms, 198 bonds, 26 residues, 1 model selected > surface hidePatches (#!3.1 & sel) > ui tool show ""Show Sequence Viewer"" > sequence chain #3.21/Au Alignment identifier is 3.21/Au > select #3.21/Au:449-457 77 atoms, 78 bonds, 9 residues, 1 model selected > select #3.21/Au:272-457 1190 atoms, 1214 bonds, 1 pseudobond, 152 residues, 2 models selected > cartoon hide (#!3.21 & sel) > select #3.21/Au:189 10 atoms, 10 bonds, 1 residue, 1 model selected > select #3.21/Au:101-189 709 atoms, 722 bonds, 89 residues, 1 model selected > cartoon hide (#!3.21 & sel) > select #3.1/Aa:189 10 atoms, 10 bonds, 1 residue, 1 model selected > select #3.1/Aa:101-189 709 atoms, 722 bonds, 89 residues, 1 model selected > cartoon hide (#!3.1 & sel) > select #3.1/Aa:281-282 14 atoms, 13 bonds, 2 residues, 1 model selected > select #3.1/Aa:281-297 132 atoms, 134 bonds, 17 residues, 1 model selected > select #3.1/Aa:272 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3.1/Aa:272-297 196 atoms, 198 bonds, 26 residues, 1 model selected > cartoon hide (#!3.1 & sel) > select #3.1/Aa:266 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3.1/Aa:266-271 45 atoms, 44 bonds, 6 residues, 1 model selected > hide (#!3.1 & sel) target a > select #3.21/Au:266 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3.21/Au:266-275 75 atoms, 74 bonds, 10 residues, 1 model selected > select #3.21/Au:267-268 13 atoms, 12 bonds, 2 residues, 1 model selected > select #3.21/Au:267-284 128 atoms, 127 bonds, 18 residues, 1 model selected > cartoon hide (#!3.21 & sel) > select #3.1/Aa:267 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3.1/Aa:267-278 87 atoms, 86 bonds, 12 residues, 1 model selected > cartoon hide (#!3.1 & sel) > save ""/Users/nezakoritnik/Desktop/INTERFACE 3/interface.cxs"" > save ""/Users/nezakoritnik/Desktop/INTERFACE 3/interface.png"" width 3000 > height 2435 supersample 3 transparentBackground true > undo > surface hidePatches (#!3.1 & sel) > select #3.1/Aa:457 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3.1/Aa 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > show sel cartoons > select #3.21/Au:457 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3.21/Au 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > show sel cartoons > ui tool show ""Model Panel"" > show #!3.2 models > show sel surfaces > select clear > show #!3.1-2,21 surfaces > hide #!3.1-2,21 surfaces > ui tool show ""Show Sequence Viewer"" > sequence chain #3.2/Ab Alignment identifier is 3.2/Ab > select #3.2/Ab:105 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3.2/Ab:105-386 1462 atoms, 1484 bonds, 2 pseudobonds, 186 residues, 2 models selected > select #3.2/Ab:386-387 13 atoms, 12 bonds, 2 residues, 1 model selected > select #3.2/Ab:101-387 1507 atoms, 1532 bonds, 2 pseudobonds, 191 residues, 2 models selected > select #3.2/Ab:101 12 atoms, 12 bonds, 1 residue, 1 model selected > select #3.2/Ab:101 12 atoms, 12 bonds, 1 residue, 1 model selected > color #3.2 #daf6e9ff > color #3.2 #d4efe3ff > select add #3.2 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 5 models selected > select subtract #3.2 1 model selected > hide #!3.21 models > hide #!3.1-2 atoms > select #3.1/Aa:173 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.2/Ab:285 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > hide #!3.1-2 atoms > cartoon style (#3.1-2#!3,5 & coil) xsection oval > cartoon style #3.1-2#!3,5 xsection barbell modeHelix default > ui tool show ""Side View"" > save ""/Users/nezakoritnik/Desktop/INTERFACE 4/celotna.png"" width 3000 height > 2435 supersample 3 transparentBackground true > save ""/Users/nezakoritnik/Desktop/INTERFACE 4/celotna.cxs"" > select #3.1/Aa:173 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.2/Ab:284 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > show sel atoms > select clear > color #3.1-2#!3,5 byhetero > select #3.2/Ab:285 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:163 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.2/Ab:120 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3.2/Ab:117 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > distance #3.2/Ab:117@OE2 #3.1/Aa:163@NH1 Distance between chains_filament16_real_space_refined.pdb Ab #3.2/Ab GLU 117 OE2 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 163 NH1: 5.233Å > show #5.1 models > hide #5.1 models > ui tool show ""Color Actions"" > color sel lime > select #3.1/Aa:173@NZ 1 atom, 1 residue, 1 model selected > select clear > select #3.1/Aa:173@NZ 1 atom, 1 residue, 1 model selected > select #3.2/Ab:284@OD2 1 atom, 1 residue, 1 model selected > select #3.1/Aa:173@NZ 1 atom, 1 residue, 1 model selected > select clear > select #3.2/Ab:284@OD2 1 atom, 1 residue, 1 model selected > select #3.1/Aa:173@NZ 1 atom, 1 residue, 1 model selected > select #3.2/Ab:284@OD2 1 atom, 1 residue, 1 model selected > select add #3.1/Aa:173@NZ 2 atoms, 2 residues, 3 models selected > select subtract #3.2/Ab:284@OD2 1 atom, 1 residue, 3 models selected > select #3.1/Aa:173@NZ 1 atom, 1 residue, 1 model selected Drag select of 1 atoms > select #3.1/Aa:173@NZ 1 atom, 1 residue, 1 model selected > select #3.2/Ab:284@OD2 1 atom, 1 residue, 1 model selected > select #3.1/Aa:173@NZ 1 atom, 1 residue, 1 model selected > select clear > select #3.1/Aa:173@NZ 1 atom, 1 residue, 1 model selected > select #3.2/Ab:284@OD2 1 atom, 1 residue, 1 model selected > select clear > select #3.1/Aa:173@NZ 1 atom, 1 residue, 1 model selected > distance #3.1/Aa:173@NZ #3.2/Ab:284@OD2 Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa LYS 173 NZ and chains_filament16_real_space_refined.pdb Ab #3.2/Ab ASP 284 OD2: 3.248Å > distance #3.1/Aa:173@NZ #3.2/Ab:285@OD1 Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa LYS 173 NZ and chains_filament16_real_space_refined.pdb Ab #3.2/Ab ASN 285 OD1: 3.099Å > color sel lime > select #3.2/Ab:187 9 atoms, 8 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected models"" > show sel atoms > select #3.1/Aa:268 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > ui mousemode right distance > distance #3.1/Aa:268@OE2 #3.2/Ab:187@NZ Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa GLU 268 OE2 and chains_filament16_real_space_refined.pdb Ab #3.2/Ab LYS 187 NZ: 5.543Å > select clear > color sel lime > select #3.2/Ab:286 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:276 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:275 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:274 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:273 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:277 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:273 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3.1/Aa:272 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:271 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:272 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3.2/Ab:287 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > select #3.2/Ab:288 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.2/Ab:289 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms Drag select of 1 residues > select #3.2/Ab:290 7 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.2/Ab:289 12 atoms, 12 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select #3.2/Ab:288 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.2/Ab:287 12 atoms, 12 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.2/Ab:286@CA 1 atom, 1 residue, 1 model selected > hide sel atoms > select #3.2/Ab:286 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:277 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:276 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:275 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:274 5 atoms, 4 bonds, 1 residue, 1 model selected > hide sel atoms > show sel atoms > hide sel atoms > select #3.2/Ab:437 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:271 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:272 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select #3.1/Aa:411 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:273 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:271 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.2/Ab:288 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.2/Ab:289 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.2/Ab:286 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > show sel atoms > select #3.2/Ab:289 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > select #3.2/Ab:288 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.2/Ab:287 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.2/Ab:288 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.2/Ab:289 12 atoms, 12 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.2/Ab:286 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > distance #3.2/Ab:437@NH2 #3.1/Aa:411@OD2 Distance between chains_filament16_real_space_refined.pdb Ab #3.2/Ab ARG 437 NH2 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa ASP 411 OD2: 7.180Å > show #5.1 models > hide #5.1 models > select clear > color sel lime > select #3.1/Aa:277 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.1/Aa:413 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > show sel atoms > hide sel atoms > select #3.1/Aa:271 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > save ""/Users/nezakoritnik/Desktop/INTERFACE 4/interakcijska površina.cxs"" > save ""/Users/nezakoritnik/Desktop/INTERFACE 4/interakcijska povrina.png"" > width 3000 height 2435 supersample 3 transparentBackground true ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/nezakoritnik/Desktop/INTERFACE 4/interakcijska površina.cxs"" Log from Wed Jan 29 07:29:35 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/nezakoritnik/Desktop/INTERFACE 2/interface.cxs"" Opened newPVA-HCPro_P130_J481.mrc as #4, grid size 512,512,512, pixel 0.834, shown at level 0.0803, step 1, values float32 Log from Tue Jan 28 14:16:05 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/nezakoritnik/Desktop/INTERFACE 1/od-cd.cxs"" Opened newPVA-HCPro_P130_J481.mrc as #4, grid size 512,512,512, pixel 0.834, shown at level 0.0803, step 1, values float32 Log from Tue Jan 28 10:12:17 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/nezakoritnik/Desktop/HCPro-struktura/monomerhcpro.cif Summary of feedback from opening /Users/nezakoritnik/Desktop/HCPro- struktura/monomerhcpro.cif --- warnings | Unknown polymer entity '1' on line 131 Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for monomerhcpro.cif #1 --- Chain | Description Ab | No description available > set bgColor white > open ""/Users/nezakoritnik/Documents/REZULTATI/Bioinformatske > analize/AlphaFold/ALFAFOLD3/PVA- > HCPro_2024_05_09_pva_hcpro/fold_2024_05_09_pva_hcpro_model_0.cif"" Chain information for fold_2024_05_09_pva_hcpro_model_0.cif #2 --- Chain | Description A | . Computing secondary structure > ui tool show Matchmaker > matchmaker #2 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 1127.3 RMSD between 151 pruned atom pairs is 0.771 angstroms; (across all 261 pairs: 36.016) > ui tool show Matchmaker > ui tool show ""Show Sequence Viewer"" > sequence chain #1/Ab Alignment identifier is 1/Ab > select #1/Ab:102 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/Ab:102-174 584 atoms, 594 bonds, 73 residues, 1 model selected > ui tool show Matchmaker > matchmaker #2 to #1 & sel Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 342 RMSD between 63 pruned atom pairs is 0.737 angstroms; (across all 73 pairs: 2.555) > matchmaker #2 to #1 & sel Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 342 RMSD between 63 pruned atom pairs is 0.737 angstroms; (across all 73 pairs: 2.555) > matchmaker #2 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 1127.3 RMSD between 151 pruned atom pairs is 0.771 angstroms; (across all 261 pairs: 36.016) > ui tool show ""Command Line Interface"" > lighting intensity 0.45 ambientIntensity 0.14 fillIntensity 1 depthCue true > shadows true multiShadow 64 > cartoon style (sel & coil) xsection oval > cartoon style sel xsection barbell modeHelix default > select add #2 4180 atoms, 4262 bonds, 530 residues, 2 models selected > hide #!1 models > color (#2 & sel) dim gray > color (#2 & sel) gray > color (#2 & sel) light gray > hide #2 models > select subtract #2 584 atoms, 594 bonds, 73 residues, 1 model selected > show #2 models > show #!1 models > select add #2 4180 atoms, 4262 bonds, 530 residues, 2 models selected > select subtract #2 584 atoms, 594 bonds, 73 residues, 1 model selected > hide #2 models > show #2 models > select add #2 4180 atoms, 4262 bonds, 530 residues, 2 models selected > hide #!1 models > show #!1 models > ui tool show ""Color Actions"" > color sel pale violet red > undo > select subtract #2 584 atoms, 594 bonds, 73 residues, 1 model selected > select add #1 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > select subtract #1 Nothing selected > select add #1 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > color sel pale violet red > select clear > save ""/Users/nezakoritnik/Desktop/Alphafold C.png"" width 3000 height 2487 > supersample 3 transparentBackground true > save /Users/nezakoritnik/Desktop/alphafoldC.cxs > save ""/Users/nezakoritnik/Desktop/AlphaFold C2.png"" width 3000 height 2487 > supersample 3 transparentBackground true No reference and/or match structure/chain chosen > matchmaker #2 to #1 & sel No 'to' model specified > select #1/Ab:102 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/Ab:102-186 673 atoms, 684 bonds, 85 residues, 1 model selected > matchmaker #2 to #1 & sel Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 397.4 RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs: 11.855) > matchmaker #2 to #1 & sel Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 397.4 RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs: 11.855) > matchmaker #2 to #1 & sel Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 397.4 RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs: 11.855) > matchmaker #2 to #1 & sel Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 397.4 RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs: 11.855) > matchmaker #2 to #1 & sel Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 397.4 RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs: 11.855) > matchmaker #2 to #1 & sel Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 397.4 RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs: 11.855) > matchmaker #2 to #1 & sel Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 397.4 RMSD between 60 pruned atom pairs is 0.699 angstroms; (across all 85 pairs: 11.855) > select clear > save ""/Users/nezakoritnik/Desktop/Alphafold N.png"" width 3000 height 2487 > supersample 3 transparentBackground true > save ""/Users/nezakoritnik/Desktop/Alphafold N2.png"" width 3000 height 2487 > supersample 3 transparentBackground true > hide #2 models > show #2 models > save /Users/nezakoritnik/Desktop/alphafoldN.cxs > hide #2 models > save /Users/nezakoritnik/Desktop/monomer.cxs > save ""/Users/nezakoritnik/Desktop/monomer 1.png"" width 3000 height 2435 > supersample 3 transparentBackground true > lighting intensity 0.45 ambientIntensity 0.14 fillIntensity 1 depthCue true > shadows true multiShadow 0 > lighting intensity 0.45 ambientIntensity 0.14 fillIntensity 1 depthCue true > shadows true multiShadow 64 > save ""/Users/nezakoritnik/Desktop/monomer 2.png"" width 3000 height 2435 > supersample 3 transparentBackground true > show #2 models > matchmaker #2 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker monomerhcpro.cif, chain Ab (#1) with fold_2024_05_09_pva_hcpro_model_0.cif, chain A (#2), sequence alignment score = 1127.3 RMSD between 151 pruned atom pairs is 0.771 angstroms; (across all 261 pairs: 36.016) > hide #!1 models > show #!1 models > select add #1 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > ui tool show ""Color Actions"" > color sel pink > hide #2 models > select clear > save ""/Users/nezakoritnik/Desktop/monomer 1.1.png"" width 3000 height 2435 > supersample 3 transparentBackground true > save ""/Users/nezakoritnik/Desktop/monomer 2.1.png"" width 3000 height 2435 > supersample 3 transparentBackground true > select #1/Ab:410-411 18 atoms, 18 bonds, 2 residues, 1 model selected > select #1/Ab:410-457 386 atoms, 393 bonds, 48 residues, 1 model selected Drag select of 1 residues > select #1/Ab:343 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/Ab:343-457 904 atoms, 922 bonds, 115 residues, 1 model selected > select #1/Ab:342 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/Ab:342-343 18 atoms, 18 bonds, 2 residues, 1 model selected > select #1/Ab:342 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/Ab:342-457 916 atoms, 935 bonds, 116 residues, 1 model selected > rainbow sel > select clear > rainbow #!1 > save ""/Users/nezakoritnik/Desktop/monomer 1.png"" width 3000 height 2435 > supersample 3 > save ""/Users/nezakoritnik/Desktop/monomer 1.png"" width 3000 height 2435 > supersample 3 transparentBackground true > rotate 180 Unknown command: rotate 180 > rot 180 Unknown command: rot 180 > turn z 180 [Repeated 1 time(s)] > turn y 180 > save ""/Users/nezakoritnik/Desktop/monomer 2.png"" width 3000 height 2435 > supersample 3 transparentBackground true > select #1/Ab:293 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #1/Ab:279 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms [Repeated 2 time(s)] > color sel byhetero > disulphides Unknown command: disulphides > show disulfides Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show /ss > select #1/Ab:279@CA 1 atom, 1 residue, 1 model selected > select #1/Ab:279@SG 1 atom, 1 residue, 1 model selected > select #1/Ab:290 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/Ab:279@SG 1 atom, 1 residue, 1 model selected > select add #1/Ab:293@SG 2 atoms, 2 residues, 1 model selected > bond sel Created 1 bond > ui tool show ""Side View"" > save /Users/nezakoritnik/Desktop/disulfid.png width 3000 height 2579 > supersample 3 transparentBackground true > select clear > save /Users/nezakoritnik/Desktop/disulfid.png width 3000 height 2579 > supersample 3 transparentBackground true > select #1/Ab:180 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/Ab:180 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > select #1/Ab:181 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #1/Ab:182 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #1/Ab:183 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select clear > color #1 byhetero > save /Users/nezakoritnik/Desktop/monomer.cxs > open /Users/nezakoritnik/Desktop/HCPro-struktura/NOVHCPro- > Andreja/Rigidbodyrefine16/chains_filament16_real_space_refined.pdb Summary of feedback from opening /Users/nezakoritnik/Desktop/HCPro- struktura/NOVHCPro- Andreja/Rigidbodyrefine16/chains_filament16_real_space_refined.pdb --- warnings | Ignored bad PDB record found on line 379 SSBOND 1 CYS Aa 279 CYS Aa 293 Ignored bad PDB record found on line 380 SSBOND 2 CYS Ab 279 CYS Ab 293 Ignored bad PDB record found on line 381 SSBOND 3 CYS Ac 279 CYS Ac 293 Ignored bad PDB record found on line 382 SSBOND 4 CYS Ad 279 CYS Ad 293 Ignored bad PDB record found on line 383 SSBOND 5 CYS Ae 279 CYS Ae 293 19 messages similar to the above omitted Chain information for chains_filament16_real_space_refined.pdb #3 --- Chain | Description Aa Ab Ac Ad Ae Af Ag Ah Ai Aj Ak Al Am An Ao Ap Aq Ar As At Au Av Aw Ax | No description available > hide #!1 models > show #!1 models > hide #!1 models > show #!3 surfaces > open /Users/nezakoritnik/Desktop/HCPro-struktura/NOVHCPro-Andreja/newPVA- > HCPro_P130_J481.mrc Opened newPVA-HCPro_P130_J481.mrc as #4, grid size 512,512,512, pixel 0.834, shown at level 0.0803, step 2, values float32 > transparency 50 > color #4 #ebebebff models > transparency 0 > transparency 50 > hide #!4 models > lighting soft > select #3/Aa 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > color (#!3 & sel) red > select clear > save /Users/nezakoritnik/Desktop/interakcije1.png width 3000 height 2871 > supersample 3 transparentBackground true > close #4 > save /Users/nezakoritnik/Desktop/interakcije.cxs > open /Users/nezakoritnik/Desktop/HCPro-struktura/NOVHCPro-Andreja/newPVA- > HCPro_P130_J481.mrc Opened newPVA-HCPro_P130_J481.mrc as #4, grid size 512,512,512, pixel 0.834, shown at level 0.0803, step 2, values float32 > select add #4 2 models selected > transparency sel 50 > color #4 white models > hide #!4 models > show #!4 models > select subtract #4 Nothing selected > lighting soft > color #4 #ebebebff models > volume #4 step 1 > surface dust #4 size 8.34 > select add #4 2 models selected > transparency sel 50 > select subtract #4 Nothing selected > hide #!4 models > show #!4 models > select add #4 3 models selected > color #4 #d6d6d6ff models > transparency #4.1 70 > select subtract #4 Nothing selected > save ""/Users/nezakoritnik/Desktop/HCPro-struktura/NOVHCPro- > Andreja/interakcije 1.1.cxs"" includeMaps true > save ""/Users/nezakoritnik/Desktop/HCPro-struktura/NOVHCPro- > Andreja/interakcije 1.1.png"" width 3000 height 2871 supersample 3 > transparentBackground true > hide #!4 models > show #!4 models > hide #!4 models > save ""/Users/nezakoritnik/Desktop/interakcije 2.png"" width 3000 height 2605 > supersample 3 transparentBackground true > show #!4 models > color #4 darkgrey models > save ""/Users/nezakoritnik/Desktop/interakcije 1.1.png"" width 3000 height > 2605 supersample 3 > hide #!3 models > hide #!4 models > show #!3 models > show #!4 models > hide #!4 models > hide #!3 surfaces > style #!3 stick Changed 49344 atom styles > show #!3 cartoons > hide #!3 atoms > cartoon style #3 modeHelix tube sides 20 > show #!3 surfaces [Repeated 5 time(s)] > transparency #3 0 > ui tool show ""Command Line Interface"" > split Did not split monomerhcpro.cif, has only one piece Did not split fold_2024_05_09_pva_hcpro_model_0.cif, has only one piece Split chains_filament16_real_space_refined.pdb (#3) into 24 models Chain information for chains_filament16_real_space_refined.pdb Aa #3.1 --- Chain | Description Aa | No description available Chain information for chains_filament16_real_space_refined.pdb Ab #3.2 --- Chain | Description Ab | No description available Chain information for chains_filament16_real_space_refined.pdb Ac #3.3 --- Chain | Description Ac | No description available Chain information for chains_filament16_real_space_refined.pdb Ad #3.4 --- Chain | Description Ad | No description available Chain information for chains_filament16_real_space_refined.pdb Ae #3.5 --- Chain | Description Ae | No description available Chain information for chains_filament16_real_space_refined.pdb Af #3.6 --- Chain | Description Af | No description available Chain information for chains_filament16_real_space_refined.pdb Ag #3.7 --- Chain | Description Ag | No description available Chain information for chains_filament16_real_space_refined.pdb Ah #3.8 --- Chain | Description Ah | No description available Chain information for chains_filament16_real_space_refined.pdb Ai #3.9 --- Chain | Description Ai | No description available Chain information for chains_filament16_real_space_refined.pdb Aj #3.10 --- Chain | Description Aj | No description available Chain information for chains_filament16_real_space_refined.pdb Ak #3.11 --- Chain | Description Ak | No description available Chain information for chains_filament16_real_space_refined.pdb Al #3.12 --- Chain | Description Al | No description available Chain information for chains_filament16_real_space_refined.pdb Am #3.13 --- Chain | Description Am | No description available Chain information for chains_filament16_real_space_refined.pdb An #3.14 --- Chain | Description An | No description available Chain information for chains_filament16_real_space_refined.pdb Ao #3.15 --- Chain | Description Ao | No description available Chain information for chains_filament16_real_space_refined.pdb Ap #3.16 --- Chain | Description Ap | No description available Chain information for chains_filament16_real_space_refined.pdb Aq #3.17 --- Chain | Description Aq | No description available Chain information for chains_filament16_real_space_refined.pdb Ar #3.18 --- Chain | Description Ar | No description available Chain information for chains_filament16_real_space_refined.pdb As #3.19 --- Chain | Description As | No description available Chain information for chains_filament16_real_space_refined.pdb At #3.20 --- Chain | Description At | No description available Chain information for chains_filament16_real_space_refined.pdb Au #3.21 --- Chain | Description Au | No description available Chain information for chains_filament16_real_space_refined.pdb Av #3.22 --- Chain | Description Av | No description available Chain information for chains_filament16_real_space_refined.pdb Aw #3.23 --- Chain | Description Aw | No description available Chain information for chains_filament16_real_space_refined.pdb Ax #3.24 --- Chain | Description Ax | No description available > show #!3.1-24 surfaces > hide #!3 models > show #!3 models > hide #!3.2 models > hide #!3.3 models > hide #!3.4 models > show #!3.4 models > hide #!3.4 models > hide #!3.5 models > hide #!3.6 models > hide #!3.7 models > show #!3.7 models > hide #!3.8 models > hide #!3.7 models > hide #!3.9 models > hide #!3.10 models > hide #!3.11 models > hide #!3.12 models > hide #!3.13 models > hide #!3.14 models > hide #!3.15 models > hide #!3.16 models > hide #!3.17 models > hide #!3.18 models > hide #!3.19 models > hide #!3.20 models > hide #!3.21 models > hide #!3.22 models > hide #!3.23 models > hide #!3.24 models > show #!3.7 models > hide #!3.7 models > show #!3.3 models > hide #!3.3 models > show #!3.4 models > hide #!3.1,4 surfaces > show #!3.1,4 surfaces > hide #!3.1,4 surfaces > hide #!3.4 models > show #!3.3 models > show #!3.1,3 surfaces > hide #!3.3 models > show #!3.8 models > hide #!3.8 models > show #!3.21 models > hide #!3.21 models > show #!3.2 models > show #!3.11 models > hide #!3.11 models > show #!3.17 models > hide #!3.17 models > show #!3.17 models > hide #!3.17 models > hide #!3.2 models > hide #!3.1 models > show #!3.3 models > show #!3.1 models > show #!3.4 models > hide #!3.3 models > hide #!3.1,4 surfaces > cartoon style #3.1,4#!3 modeHelix tube sides 20 > cartoon style (#3.1,4#!3 & coil) xsection oval > cartoon style #3.1,4#!3 xsection barbell modeHelix default > lighting intensity 0.45 ambientIntensity 0.14 fillIntensity 1 depthCue true > shadows true multiShadow 64 > select add #3.1 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > ui tool show ""Color Actions"" > color sel pink > select clear > show #!3.1,4 atoms > color #3.1,4#!3 byhetero > ui mousemode right distance > distance #3.4/Ad:135@OE1 #3.1/Aa:455@NH1 Distance between chains_filament16_real_space_refined.pdb Ad #3.4/Ad GLU 135 OE1 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 455 NH1: 5.036Å > hide #!3.1,4 atoms > select #3.4/Ad:135 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:455 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > ui tool show ""Color Actions"" > color sel lime > select #3.4/Ad:126 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:413 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > distance #3.1/Aa:413@NZ #3.4/Ad:126@OG1 Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa LYS 413 NZ and chains_filament16_real_space_refined.pdb Ad #3.4/Ad THR 126 OG1: 3.203Å > select clear > hide #5.1 models > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/od-cd.png"" width 3000 height > 2435 supersample 3 transparentBackground true > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/od-cd.cxs"" ——— End of log from Tue Jan 28 10:12:17 2025 ——— opened ChimeraX session > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/od-cd.png"" width 3000 height > 2435 supersample 3 transparentBackground true > hide #!3.1,4 atoms > ui tool show ""Show Sequence Viewer"" > sequence chain #3.1/Aa Alignment identifier is 3.1/Aa > select #3.1/Aa:457 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3.1/Aa:377-457 635 atoms, 649 bonds, 81 residues, 1 model selected > select #3.1/Aa:273 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3.1/Aa:273-457 1181 atoms, 1205 bonds, 1 pseudobond, 151 residues, 2 models selected > select #3.1/Aa:253 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.1/Aa:253-457 1339 atoms, 1363 bonds, 1 pseudobond, 171 residues, 2 models selected > select #3.1/Aa:167 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.1/Aa:167-457 1528 atoms, 1553 bonds, 2 pseudobonds, 195 residues, 2 models selected > select #3.1/Aa:175 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3.1/Aa:175-457 1460 atoms, 1485 bonds, 2 pseudobonds, 187 residues, 2 models selected > cartoon hide (#!3.1 & sel) > select #3.1/Aa:101 12 atoms, 12 bonds, 1 residue, 1 model selected > select #3.1/Aa:101-140 333 atoms, 341 bonds, 40 residues, 1 model selected > select #3.1/Aa:145 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3.1/Aa:101-145 367 atoms, 375 bonds, 45 residues, 1 model selected > cartoon hide (#!3.1 & sel) > ui tool show ""Show Sequence Viewer"" > sequence chain #3.4/Ad Alignment identifier is 3.4/Ad > select #3.4/Ad:457 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3.4/Ad:253-457 1339 atoms, 1363 bonds, 1 pseudobond, 171 residues, 2 models selected > select #3.4/Ad:167 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.4/Ad:167-457 1528 atoms, 1553 bonds, 2 pseudobonds, 195 residues, 2 models selected > select #3.4/Ad:148 7 atoms, 7 bonds, 1 residue, 1 model selected > select #3.4/Ad:148-457 1677 atoms, 1705 bonds, 2 pseudobonds, 214 residues, 2 models selected > hide sel cartoons > select #3.1/Aa:166 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:130 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > distance #3.1/Aa:166@NH1 #3.4/Ad:130@OH Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 166 NH1 and chains_filament16_real_space_refined.pdb Ad #3.4/Ad TYR 130 OH: 3.848Å > select clear > select #3.1/Aa:163 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:117 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:169 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > distance #3.1/Aa:169@OG1 #3.4/Ad:130@OH Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa THR 169 OG1 and chains_filament16_real_space_refined.pdb Ad #3.4/Ad TYR 130 OH: 2.497Å > select #3.1/Aa:170 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.1/Aa:171 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:127 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > show sel atoms > distance #3.1/Aa:171@OD1 #3.4/Ad:127@NE2 Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ASN 171 OD1 and chains_filament16_real_space_refined.pdb Ad #3.4/Ad GLN 127 NE2: 6.116Å > hide sel atoms > select #3.1/Aa:171 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:159 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:133 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:118 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:114 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:162 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:155 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:141 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3.4/Ad:140 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.1/Aa:158 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:137 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.4/Ad:140 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:154 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:137 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.4/Ad:137 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.4/Ad:111 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.4/Ad:136 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:161 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.4/Ad:136@CA 1 atom, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.4/Ad:136 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:162 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3.1/Aa:161 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.1/Aa:165 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:129 7 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:137 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:137 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.4/Ad:136 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:137 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.1/Aa:151 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/od-od.cxs"" > ui tool show ""Side View"" > select #3.4/Ad:109 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > distance #3.4/Ad:109@OD1 #3.1/Aa:163@NH1 Distance between chains_filament16_real_space_refined.pdb Ad #3.4/Ad ASN 109 OD1 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 163 NH1: 14.827Å > ~distance #3.4/Ad:109@OD1 #3.1/Aa:163@NH1 > distance #3.1/Aa:163@NH1 #3.4/Ad:117@OE1 Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 163 NH1 and chains_filament16_real_space_refined.pdb Ad #3.4/Ad GLU 117 OE1: 4.957Å > distance #3.4/Ad:109@OD1 #3.1/Aa:155@OG Distance between chains_filament16_real_space_refined.pdb Ad #3.4/Ad ASN 109 OD1 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa SER 155 OG: 3.725Å > turn y 180 [Repeated 18 time(s)] > select #3.4/Ad:129 7 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > turn y 180 [Repeated 4 time(s)] > select clear > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/od-od1.png"" width 3000 height > 2435 supersample 3 transparentBackground true > turn y 180 > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/od-od1.png"" width 3000 height > 2435 supersample 3 transparentBackground true > undo [Repeated 1 time(s)] > select clear > color sel lime > select clear > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/od-od1.png"" width 3000 height > 2435 supersample 3 transparentBackground true > turn y 180 > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/od-od2.png"" width 3000 height > 2435 supersample 3 transparentBackground true > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/od-od.cxs"" > hide #!5 models > select #3.4/Ad:101 12 atoms, 12 bonds, 1 residue, 1 model selected > select #3.4/Ad 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > show sel cartoons > hide sel atoms > select #3.1/Aa:456-457 12 atoms, 11 bonds, 2 residues, 1 model selected > select #3.1/Aa 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > show sel cartoons > hide sel atoms > select clear > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/celoten.cxs"" > save ""/Users/nezakoritnik/Desktop/INTERFACE 1/celoten.png"" width 3000 height > 2435 supersample 3 > show #!3.3 models > hide #!3.4 models > hide #!3.1,3 surfaces > select add #3.3 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > ui tool show ""Color Actions"" > color sel aquamarine > color sel medium aquamarine > color sel mint cream > color sel pale turquoise > show #!3.4 models > ui tool show ""Color Actions"" > color #3.3 #a4c4b3ff > color #3.3 #dbfdefff > color #3.3 #cdf4e1ff > hide #!3.4 models > select clear > save ""/Users/nezakoritnik/Desktop/INTERFACE 2/celoten.png"" width 3000 height > 2435 supersample 3 > show #!3.4 models > hide #!3.3 models > select clear > select #3.4/Ad:450 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:126 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:127 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms [Repeated 1 time(s)] > select clear > select #3.1/Aa:128 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select #3.4/Ad:453 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:164 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:157 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:132 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > show #!3.3 models > hide #!3.4 models > select #3.1/Aa:457 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3.1/Aa:169-457 1509 atoms, 1534 bonds, 2 pseudobonds, 193 residues, 2 models selected > hide sel cartoons > ui tool show ""Show Sequence Viewer"" > sequence chain #3.3/Ac Alignment identifier is 3.3/Ac > select #3.3/Ac:101 12 atoms, 12 bonds, 1 residue, 1 model selected > select #3.3/Ac:101-183 666 atoms, 678 bonds, 83 residues, 1 model selected > hide sel cartoons [Repeated 1 time(s)] > hide sel atoms [Repeated 1 time(s)] > select clear > hide #!3.1,3 atoms > select #3.1/Aa:113 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.1/Aa:106 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:362 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > color #3.1,3#!3 byhetero > distance #3.1/Aa:106@NH1 #3.3/Ac:362@OD2 Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 106 NH1 and chains_filament16_real_space_refined.pdb Ac #3.3/Ac ASP 362 OD2: 2.728Å > distance #3.3/Ac:362@OD2 #3.1/Aa:106@NH1 Distance already exists; modify distance properties with 'distance style' > show #!5 models > color sel lime > select #3.1/Aa:145 11 atoms, 10 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected models"" [Repeated 1 time(s)] > show sel atoms > select #3.3/Ac:357 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:358 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:359 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms [Repeated 1 time(s)] > select #3.3/Ac:360 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select clear > select #3.3/Ac:358 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:145 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.3/Ac:359 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.3/Ac:357 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:115 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:389 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > ui mousemode right distance > distance #3.1/Aa:115@OH #3.3/Ac:389@OG Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa TYR 115 OH and chains_filament16_real_space_refined.pdb Ac #3.3/Ac SER 389 OG: 2.696Å > select #3.1/Aa:116 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:374 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > distance #3.1/Aa:116@NH1 #3.3/Ac:374@OD2 Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 116 NH1 and chains_filament16_real_space_refined.pdb Ac #3.3/Ac ASP 374 OD2: 3.301Å > color sel lime > select #3.1/Aa:120 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:445 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > distance #3.1/Aa:120@NZ #3.3/Ac:445@OD1 Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa LYS 120 NZ and chains_filament16_real_space_refined.pdb Ac #3.3/Ac ASN 445 OD1: 3.904Å > select #3.1/Aa:138 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:437 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:135 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:440 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.3/Ac:437 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3.3/Ac:437 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:135 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.3/Ac:393 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3.1/Aa:142 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:394 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:142 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:141 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:390 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:142 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms [Repeated 1 time(s)] > select #3.1/Aa:119 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:386 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3.3/Ac:390 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.3/Ac:440 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.3/Ac:443 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms [Repeated 1 time(s)] > hide sel atoms > cartoon style (#!3.3 & sel) modeHelix tube sides 20 [Repeated 1 time(s)] > cartoon style (#!3.3 & sel & coil) xsection oval > cartoon style (#!3.3 & sel) xsection barbell modeHelix default > select clear > select #3.1/Aa:138 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > turn y 180 [Repeated 1 time(s)] > save ""/Users/nezakoritnik/Desktop/INTERFACE 2/interface1.png"" width 3000 > height 2435 supersample 3 transparentBackground true > turn y 180 > save ""/Users/nezakoritnik/Desktop/INTERFACE 2/interface2.png"" width 3000 > height 2435 supersample 3 transparentBackground true > save ""/Users/nezakoritnik/Desktop/INTERFACE 2/interface.cxs"" ——— End of log from Tue Jan 28 14:16:05 2025 ——— opened ChimeraX session > close #4 > show #!3.2 models > ui tool show ""Side View"" > hide #!3.1 models > show #!3.1 models > hide #!3.2 models > show #!3.5 models > hide #!3.5 models > show #!3.5 models > hide #!3.5 models > show #!3.7 models > hide #!3.7 models > show #!3.9 models > show #!3.8 models > hide #!3.8 models > hide #!3.9 models > show #!3.10 models > hide #!3.10 models > show #!3.11 models > show #!3.12 models > hide #!3.11 models > hide #!3.12 models > show #!3.14 models > hide #!3.14 models > show #!3.15 models > hide #!3.15 models > show #!3.16 models > hide #!3.16 models > show #!3.17 models > hide #!3.17 models > show #!3.20 models > hide #!3.20 models > show #!3.20 models > hide #!3.20 models > show #!3.20 models > hide #!3.20 models > show #!3.20 models > hide #!3.20 models > show #!3.21 models > hide #!3.21 models > show #!3.21 models > hide #!3.21 models > show #!3.22 models > hide #!3.22 models > show #!3.21 models > hide #!3.21 models > select #3.3/Ac:407-457 409 atoms, 416 bonds, 51 residues, 1 model selected > select #3.3/Ac 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > show sel cartoons > select #3.1/Aa:457 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3.1/Aa 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > show sel cartoons > show #!3.21 models > hide sel surfaces > select clear > hide #!3.1,3,21 surfaces > color #3.21 #e0fef3ff > color #3.21 #c8e7d8ff > cartoon style (#3.1,3,21#!3,5 & coil) xsection oval > cartoon style #3.1,3,21#!3,5 xsection barbell modeHelix default > hide #!3.3 models > hide #!3.1,21 atoms > save ""/Users/nezakoritnik/Desktop/INTERFACE 3/celotna.png"" width 3000 height > 2435 supersample 3 transparentBackground true > save ""/Users/nezakoritnik/Desktop/INTERFACE 3/celotna.cxs"" > select #3.1/Aa:265 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:261 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:258 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.21/Au:254 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:254 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3.21/Au:258 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.21/Au:261 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.21/Au:265 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:457 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3.1/Aa:298-457 994 atoms, 1015 bonds, 1 pseudobond, 126 residues, 2 models selected > cartoon hide (#!3.1 & sel) > select #3.1/Aa:297 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3.1/Aa:270-297 213 atoms, 215 bonds, 28 residues, 1 model selected > select #3.1/Aa:272 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3.1/Aa:272-297 196 atoms, 198 bonds, 26 residues, 1 model selected > surface hidePatches (#!3.1 & sel) > ui tool show ""Show Sequence Viewer"" > sequence chain #3.21/Au Alignment identifier is 3.21/Au > select #3.21/Au:449-457 77 atoms, 78 bonds, 9 residues, 1 model selected > select #3.21/Au:272-457 1190 atoms, 1214 bonds, 1 pseudobond, 152 residues, 2 models selected > cartoon hide (#!3.21 & sel) > select #3.21/Au:189 10 atoms, 10 bonds, 1 residue, 1 model selected > select #3.21/Au:101-189 709 atoms, 722 bonds, 89 residues, 1 model selected > cartoon hide (#!3.21 & sel) > select #3.1/Aa:189 10 atoms, 10 bonds, 1 residue, 1 model selected > select #3.1/Aa:101-189 709 atoms, 722 bonds, 89 residues, 1 model selected > cartoon hide (#!3.1 & sel) > select #3.1/Aa:281-282 14 atoms, 13 bonds, 2 residues, 1 model selected > select #3.1/Aa:281-297 132 atoms, 134 bonds, 17 residues, 1 model selected > select #3.1/Aa:272 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3.1/Aa:272-297 196 atoms, 198 bonds, 26 residues, 1 model selected > cartoon hide (#!3.1 & sel) > select #3.1/Aa:266 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3.1/Aa:266-271 45 atoms, 44 bonds, 6 residues, 1 model selected > hide (#!3.1 & sel) target a > select #3.21/Au:266 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3.21/Au:266-275 75 atoms, 74 bonds, 10 residues, 1 model selected > select #3.21/Au:267-268 13 atoms, 12 bonds, 2 residues, 1 model selected > select #3.21/Au:267-284 128 atoms, 127 bonds, 18 residues, 1 model selected > cartoon hide (#!3.21 & sel) > select #3.1/Aa:267 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3.1/Aa:267-278 87 atoms, 86 bonds, 12 residues, 1 model selected > cartoon hide (#!3.1 & sel) > save ""/Users/nezakoritnik/Desktop/INTERFACE 3/interface.cxs"" > save ""/Users/nezakoritnik/Desktop/INTERFACE 3/interface.png"" width 3000 > height 2435 supersample 3 transparentBackground true [Repeated 1 time(s)] > undo > surface hidePatches (#!3.1 & sel) > select #3.1/Aa:457 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3.1/Aa 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > show sel cartoons > select #3.21/Au:457 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3.21/Au 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 2 models selected > show sel cartoons > ui tool show ""Model Panel"" > show #!3.2 models > show sel surfaces > select clear > show #!3.1-2,21 surfaces > hide #!3.1-2,21 surfaces > ui tool show ""Show Sequence Viewer"" > sequence chain #3.2/Ab Alignment identifier is 3.2/Ab > select #3.2/Ab:105 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3.2/Ab:105-386 1462 atoms, 1484 bonds, 2 pseudobonds, 186 residues, 2 models selected > select #3.2/Ab:386-387 13 atoms, 12 bonds, 2 residues, 1 model selected > select #3.2/Ab:101-387 1507 atoms, 1532 bonds, 2 pseudobonds, 191 residues, 2 models selected > select #3.2/Ab:101 12 atoms, 12 bonds, 1 residue, 1 model selected > select #3.2/Ab:101 12 atoms, 12 bonds, 1 residue, 1 model selected > color #3.2 #daf6e9ff > color #3.2 #d4efe3ff > select add #3.2 2056 atoms, 2093 bonds, 2 pseudobonds, 261 residues, 5 models selected > select subtract #3.2 1 model selected > hide #!3.21 models > hide #!3.1-2 atoms > select #3.1/Aa:173 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.2/Ab:285 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear [Repeated 1 time(s)] > hide #!3.1-2 atoms > cartoon style (#3.1-2#!3,5 & coil) xsection oval > cartoon style #3.1-2#!3,5 xsection barbell modeHelix default > ui tool show ""Side View"" > save ""/Users/nezakoritnik/Desktop/INTERFACE 4/celotna.png"" width 3000 height > 2435 supersample 3 transparentBackground true > save ""/Users/nezakoritnik/Desktop/INTERFACE 4/celotna.cxs"" > select #3.1/Aa:173 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.2/Ab:284 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > show sel atoms > select clear > color #3.1-2#!3,5 byhetero > select #3.2/Ab:285 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:163 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.2/Ab:120 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3.2/Ab:117 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > distance #3.2/Ab:117@OE2 #3.1/Aa:163@NH1 Distance between chains_filament16_real_space_refined.pdb Ab #3.2/Ab GLU 117 OE2 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa ARG 163 NH1: 5.233Å > show #5.1 models > hide #5.1 models > ui tool show ""Color Actions"" > color sel lime > select #3.1/Aa:173@NZ 1 atom, 1 residue, 1 model selected > select clear > select #3.1/Aa:173@NZ 1 atom, 1 residue, 1 model selected > select #3.2/Ab:284@OD2 1 atom, 1 residue, 1 model selected > select #3.1/Aa:173@NZ 1 atom, 1 residue, 1 model selected > select clear [Repeated 1 time(s)] > select #3.2/Ab:284@OD2 1 atom, 1 residue, 1 model selected > select #3.1/Aa:173@NZ 1 atom, 1 residue, 1 model selected > select #3.2/Ab:284@OD2 1 atom, 1 residue, 1 model selected > select add #3.1/Aa:173@NZ 2 atoms, 2 residues, 3 models selected > select subtract #3.2/Ab:284@OD2 1 atom, 1 residue, 3 models selected > select #3.1/Aa:173@NZ 1 atom, 1 residue, 1 model selected Drag select of 1 atoms > select #3.1/Aa:173@NZ 1 atom, 1 residue, 1 model selected > select #3.2/Ab:284@OD2 1 atom, 1 residue, 1 model selected > select #3.1/Aa:173@NZ 1 atom, 1 residue, 1 model selected > select clear > select #3.1/Aa:173@NZ 1 atom, 1 residue, 1 model selected > select #3.2/Ab:284@OD2 1 atom, 1 residue, 1 model selected > select clear > select #3.1/Aa:173@NZ 1 atom, 1 residue, 1 model selected > distance #3.1/Aa:173@NZ #3.2/Ab:284@OD2 Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa LYS 173 NZ and chains_filament16_real_space_refined.pdb Ab #3.2/Ab ASP 284 OD2: 3.248Å > distance #3.1/Aa:173@NZ #3.2/Ab:285@OD1 Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa LYS 173 NZ and chains_filament16_real_space_refined.pdb Ab #3.2/Ab ASN 285 OD1: 3.099Å > color sel lime > select #3.2/Ab:187 9 atoms, 8 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected models"" > show sel atoms > select #3.1/Aa:268 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > ui mousemode right distance > distance #3.1/Aa:268@OE2 #3.2/Ab:187@NZ Distance between chains_filament16_real_space_refined.pdb Aa #3.1/Aa GLU 268 OE2 and chains_filament16_real_space_refined.pdb Ab #3.2/Ab LYS 187 NZ: 5.543Å > select clear > color sel lime > select #3.2/Ab:286 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:276 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:275 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:274 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:273 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:277 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:273 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3.1/Aa:272 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:271 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:272 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3.2/Ab:287 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > select #3.2/Ab:288 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.2/Ab:289 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms Drag select of 1 residues > select #3.2/Ab:290 7 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.2/Ab:289 12 atoms, 12 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select #3.2/Ab:288 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.2/Ab:287 12 atoms, 12 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.2/Ab:286@CA 1 atom, 1 residue, 1 model selected > hide sel atoms > select #3.2/Ab:286 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:277 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:276 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:275 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:274 5 atoms, 4 bonds, 1 residue, 1 model selected > hide sel atoms > show sel atoms > hide sel atoms > select #3.2/Ab:437 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:271 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:272 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select #3.1/Aa:411 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3.1/Aa:273 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.1/Aa:271 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.2/Ab:288 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.2/Ab:289 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.2/Ab:286 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > show sel atoms > select #3.2/Ab:289 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > select #3.2/Ab:288 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3.2/Ab:287 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.2/Ab:288 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.2/Ab:289 12 atoms, 12 bonds, 1 residue, 1 model selected > hide sel atoms > select #3.2/Ab:286 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > distance #3.2/Ab:437@NH2 #3.1/Aa:411@OD2 Distance between chains_filament16_real_space_refined.pdb Ab #3.2/Ab ARG 437 NH2 and chains_filament16_real_space_refined.pdb Aa #3.1/Aa ASP 411 OD2: 7.180Å > show #5.1 models > hide #5.1 models > select clear [Repeated 2 time(s)] > color sel lime > select #3.1/Aa:277 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #3.1/Aa:413 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > show sel atoms > hide sel atoms > select #3.1/Aa:271 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > save ""/Users/nezakoritnik/Desktop/INTERFACE 4/interakcijska površina.cxs"" ——— End of log from Wed Jan 29 07:29:35 2025 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir10,1 Model Number: Z128000N6ZE/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 8419.80.7 OS Loader Version: 8419.80.7 Software: System Software Overview: System Version: macOS 13.2 (22D49) Kernel Version: Darwin 22.3.0 Time since boot: 16 days, 19 hours, 49 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal HP E243i: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX