id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20165 Crash on Mac waking from sleep a.fasemire@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.7.4-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: Bus error Thread 0x000000030e1b3000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030d1a7000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File 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""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030715f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000306153000 (most 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start ===== UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/ayomidefasemire/Documents/Doctoral/Main > Project/ClpP/Probac1_Figures/figures_prep.cxs"" Opened ClpP_volume_map_1_95A_bfactor_77_flip.mrc as #9, grid size 256,256,256, pixel 0.84, shown at level 0.042, step 1, values float32 Log from Thu Apr 9 16:14:06 2026UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/ayomidefasemire/Downloads/ClpP structures comparison .cxs"" Log from Sun Mar 22 14:55:57 2026 Startup Messages --- warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:/Users/Majka/Downloads/16Mar26_flip_KHS_QMR_refined.pdb Chain information for 16Mar26_flip_KHS_QMR_refined.pdb #1 --- Chain | Description A B C D E F G H I J K L M N | No description available > hide surfaces > select add #1 41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 2 models selected > hide sel surfaces > show sel atoms [Repeated 2 time(s)] > show sel cartoons [Repeated 1 time(s)] > hide sel surfaces > style sel sphere Changed 41972 atom styles > style sel sphere Changed 41972 atom styles > style sel stick Changed 41972 atom styles > select subtract #1 Nothing selected > ui tool show ""Show Sequence Viewer"" [Repeated 1 time(s)] > sequence chain /A Alignment identifier is 1/A > open 6NB1 fromDatabase pdb format mmcif Summary of feedback from opening 6NB1 fetched from pdb --- note | Fetching compressed mmCIF 6nb1 from http://files.rcsb.org/download/6nb1.cif 6nb1 title: Crystal structure of Escherichia coli ClpP protease complexed with small molecule activator, ACP1-06 [more info...] Chain information for 6nb1 #2 --- Chain | Description | UniProt A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | CLPP_ECOLI 1-207 2-207 Non-standard residues in 6nb1 #2 --- GOL — glycerol (glycerin; propane-1,2,3-triol) KHS — N-{2-[(2-chlorophenyl)sulfanyl]ethyl}-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]sulfonyl}propanamide > ui tool show Matchmaker > matchmaker #!2 to #1 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 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A (#2), sequence alignment score = 958.6 RMSD between 183 pruned atom pairs is 0.392 angstroms; (across all 187 pairs: 0.581) > open 1TYF fromDatabase pdb format mmcif Summary of feedback from opening 1TYF fetched from pdb --- note | Fetching compressed mmCIF 1tyf from http://files.rcsb.org/download/1tyf.cif 1tyf title: The structure of CLPP At 2.3 angstrom resolution suggests A model for atp- dependent proteolysis [more info...] Chain information for 1tyf #3 --- Chain | Description | UniProt A B C D E F G H I J K L M N | CLP PEPTIDASE | CLPP_ECOLI 1-193 > ui tool show Matchmaker > matchmaker #3#!2 to #1 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 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 1tyf, chain J (#3), sequence alignment score = 937.6 RMSD between 175 pruned atom pairs is 0.316 angstroms; (across all 181 pairs: 2.425) Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A (#2), sequence alignment score = 958.6 RMSD between 183 pruned atom pairs is 0.392 angstroms; (across all 187 pairs: 0.581) > select add #3 21308 atoms, 20384 bonds, 3808 residues, 1 model selected > style sel stick Changed 21308 atom styles > hide sel surfaces > show sel atoms > hide #!2 models > select subtract #3 Nothing selected > show #!2 models > hide surfaces > show atoms > select add #2 21442 atoms, 20839 bonds, 12 pseudobonds, 3512 residues, 2 models selected > hide sel surfaces > show sel atoms > style sel stick Changed 21442 atom styles > select subtract #2 Nothing selected > hide #3 models > show #3 models > hide #!2 models > show #!2 models > hide #!2 models > hide #3 models > hide #!1 atoms > show #!1 cartoons > show #!2 models > select add #2 21442 atoms, 20839 bonds, 12 pseudobonds, 3512 residues, 2 models selected > hide sel atoms > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > show sel cartoons > select subtract #2 Nothing selected > open 1YG6 fromDatabase pdb format mmcif Summary of feedback from opening 1YG6 fetched from pdb --- note | Fetching compressed mmCIF 1yg6 from http://files.rcsb.org/download/1yg6.cif 1yg6 title: ClpP [more info...] Chain information for 1yg6 #4 --- Chain | Description | UniProt A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | CLPP_ECOLI 1-193 Non-standard residues in 1yg6 #4 --- MPD — (4S)-2-methyl-2,4-pentanediol > ui tool show Matchmaker > matchmaker #3-4#!2 to #1 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 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 1tyf, chain J (#3), sequence alignment score = 937.6 RMSD between 175 pruned atom pairs is 0.316 angstroms; (across all 181 pairs: 2.425) Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 1yg6, chain I (#4), sequence alignment score = 934.6 RMSD between 176 pruned atom pairs is 0.252 angstroms; (across all 181 pairs: 2.818) Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A (#2), sequence alignment score = 958.6 RMSD between 183 pruned atom pairs is 0.392 angstroms; (across all 187 pairs: 0.581) > select add #4 21540 atoms, 20901 bonds, 3585 residues, 1 model selected > hide sel surfaces > show sel cartoons > style sel stick Changed 21540 atom styles > hide sel atoms > show sel cartoons > select subtract #4 Nothing selected > show #3 models > hide atoms > show cartoons > color #1 #ff55ffff > color #2 #55007fff > color #3 #ffaaffff > color #4 #aaaaffff > hide #!2 models > hide #!1 models > hide #3 models > hide #4 models > show #!1 models > show #!2 models > show #3 models > show #4 models > open 3MT6 fromDatabase pdb format mmcif Summary of feedback from opening 3MT6 fetched from pdb --- note | Fetching compressed mmCIF 3mt6 from http://files.rcsb.org/download/3mt6.cif 3mt6 title: Structure of ClpP from Escherichia coli in complex with ADEP1 [more info...] Chain information for 3mt6 #5 --- Chain | Description | UniProt 1 2 3 4 c d e f g h i j k l m n o p q r s t u v w x y z | ACYLDEPSIPEPTIDE 1 | A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b | ATP-dependent Clp protease proteolytic subunit | CLPP_ECOLI -13-193 Non-standard residues in 3mt6 #5 --- MAA — N-methyl-L-alanine MP8 — (4R)-4-methyl-L-proline MPD — (4S)-2-methyl-2,4-pentanediol OTT — (2E,4E,6E)-octa-2,4,6-trienoic acid (2,4,6-octatrienoic acid) 3mt6 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > ui tool show Matchmaker > matchmaker #3-4#!2,5 to #1 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 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 1tyf, chain J (#3), sequence alignment score = 937.6 RMSD between 175 pruned atom pairs is 0.316 angstroms; (across all 181 pairs: 2.425) Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 1yg6, chain I (#4), sequence alignment score = 934.6 RMSD between 176 pruned atom pairs is 0.252 angstroms; (across all 181 pairs: 2.818) Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A (#2), sequence alignment score = 958.6 RMSD between 183 pruned atom pairs is 0.392 angstroms; (across all 187 pairs: 0.581) Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 3mt6, chain E (#5), sequence alignment score = 954.4 RMSD between 181 pruned atom pairs is 0.466 angstroms; (across all 186 pairs: 0.661) > select add #5 46272 atoms, 43362 bonds, 19 pseudobonds, 9074 residues, 2 models selected > hide sel atoms > show sel cartoons > hide sel surfaces > select subtract #5 Nothing selected > select add #5 46272 atoms, 43362 bonds, 19 pseudobonds, 9074 residues, 2 models selected > select #5/O 1613 atoms, 1511 bonds, 314 residues, 1 model selected > hide sel cartoons > hide sel atoms > hide sel surfaces > hide #3 models > hide #4 models > hide #!1 models > show #!1 models > hide #!5 models > show #!5 models > hide #!1 models > hide #!2 models > show #!2 models > show #!1 models > hide #!1 models > show #!1 models > save ""C:/Users/Majka/Downloads/ClpP structures comparison .cxs"" > show #4 models > show #3 models > hide #4 models > hide #!2 models > hide #!1 models > show #!2 models > show #!1 models > select #5/1 52 atoms, 55 bonds, 7 residues, 1 model selected > select #2/N 1516 atoms, 1467 bonds, 1 pseudobond, 254 residues, 2 models selected > style sel stick Changed 1516 atom styles > show sel atoms > undo [Repeated 2 time(s)] > select #5/V 1548 atoms, 1461 bonds, 1 pseudobond, 293 residues, 2 models selected > undo > select ::name=""KHS"" 1064 atoms, 1092 bonds, 28 residues, 2 models selected > show sel atoms > save ""C:/Users/Majka/Downloads/ClpP structures comparison .cxs"" ——— End of log from Sun Mar 22 14:55:57 2026 ——— opened ChimeraX session > set bgColor white > select add #2 22100 atoms, 21511 bonds, 12 pseudobonds, 3526 residues, 3 models selected > select add #1 63414 atoms, 63147 bonds, 26 pseudobonds, 6158 residues, 4 models selected > select subtract #1 21442 atoms, 20839 bonds, 12 pseudobonds, 3512 residues, 2 models selected > select subtract #2 Nothing selected > show #4 models > hide #!2 models > hide #!5 models > set bgColor black > hide #3 models > show #3 models > hide #3 models > hide #4 models > show #3 models > hide #!1 models > show #!2 models > hide #3 models > set bgColor white > show #3 models > show #4 models > hide #3 models > show #3 models > hide #4 models > show #4 models > hide #4 models > show #!5 models > hide #!2 models > open ""/Users/ayomidefasemire/Documents/Doctoral/Main > Project/ClpP/Map/ClpP_volume_map_1_95A_bfactor_77_flip.mrc"" Opened ClpP_volume_map_1_95A_bfactor_77_flip.mrc as #6, grid size 256,256,256, pixel 0.84, shown at level 0.0426, step 1, values float32 > volume #6 level 0.037 > ui tool show ""Segment Map"" Segmenting ClpP_volume_map_1_95A_bfactor_77_flip.mrc, density threshold 0.037000 Only showing 60 of 174 regions. Showing 60 of 174 region surfaces 2757 watershed regions, grouped to 174 regions Showing ClpP_volume_map_1_95A_bfactor_77_flip.seg - 174 regions, 60 surfaces Smoothing and grouping, standard deviation 5 voxels Only showing 60 of 100 regions. Showing 60 of 100 region surfaces Got 100 regions after smoothing 5 voxels. > show #!1 models > hide #!7 models > show #!7 models > hide #!7 models > hide #!6 models > show #!6 models > hide #!6 models > hide #3 models > hide #!5 models > hide #!1 models > show #!2 models > show #!6 models > show #!7 models > hide #!6 models > show #!6 models > hide #!6 models > close #7 > show #!1 models > select #1/A:75 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1/A:75-76 40 atoms, 40 bonds, 2 residues, 1 model selected > select #1/A:75 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1/A:75 19 atoms, 18 bonds, 1 residue, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/B #1/C #1/D #1/E #1/F #1/G #1/H #1/I #1/J #1/K #1/L > #1/M #1/N Alignment identifier is 1 > select #1/A-N:75 266 atoms, 252 bonds, 14 residues, 1 model selected > select #1/A-N:75 266 atoms, 252 bonds, 14 residues, 1 model selected > select #1/A-N:58 224 atoms, 210 bonds, 14 residues, 1 model selected > select #1/A-N:58 224 atoms, 210 bonds, 14 residues, 1 model selected > select #1/A-N:83 224 atoms, 210 bonds, 14 residues, 1 model selected > select #1/A-N:83 224 atoms, 210 bonds, 14 residues, 1 model selected > select #1/A-N:42 224 atoms, 210 bonds, 14 residues, 1 model selected > select #1/A-N:42 224 atoms, 210 bonds, 14 residues, 1 model selected > select #1/A-N:28 210 atoms, 196 bonds, 14 residues, 1 model selected > select #1/A-N:28 210 atoms, 196 bonds, 14 residues, 1 model selected > select #1/A-N:32 168 atoms, 154 bonds, 14 residues, 1 model selected > select #1/A-N:32 168 atoms, 154 bonds, 14 residues, 1 model selected > select add #1 41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 2 models selected > select subtract #1 Nothing selected > hide #!2 models > show #!2 models > hide #!2 models > show #3 models > hide #!1 models > show #!1 models > hide #3 models > show #!5 models > hide #!5 models > show #!6 models > select #1/I,J,K,L,M 14990 atoms, 15110 bonds, 5 pseudobonds, 945 residues, 2 models selected > color zone #1 near sel distance 5.0 color forestgreen Expected a keyword > color zone #1 near sel distance 5.0 forestgreen Expected a keyword > color zone #6 near sel distance 5.0 farColor forestgreen > color zone #6 near sel distance 3.0 farColor forestgreen > ui tool show ""Color Actions"" > color sel cornflower blue > select #1/H,I,J,K,L,M,N 20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected > color (#!1 & sel) cornflower blue > color zone #6 near sel & #1 distance 5.04 > select #1/A,B,C,D,E,F,G 20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected > color zone #6 near sel & #1 distance 5.04 > ui tool show ""Color Actions"" > color sel deep sky blue > select #1/H,I,J,K,L,M,N 20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected > color sel cyan > select clear > color zone #6 near #1 distance 5.04 > select #1/H,I,J,K,L,M,N 20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light gray > select #1/A,B,C,D,E,F,G 20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected > ui tool show ""Color Actions"" > color sel dim gray > select clear > color zone #6 near #1 distance 5.04 > select #1/H,I,J,K,L,M,N 20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected > ui tool show ""Color Actions"" > color sel dark gray > select clear > color zone #6 near #1 distance 5.04 > select #1/H,I,J,K,L,M,N 20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected > ui tool show ""Color Actions"" > color sel lavender > select #1/A,B,C,D,E,F,G 20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected > color sel indigo > select clear > color zone #6 near #1 distance 5.04 > select #1/H,I,J,K,L,M,N 20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected > ui tool show ""Color Actions"" > color sel orchid > select clear > color zone #6 near #1 distance 5.04 > select #1/H,I,J,K,L,M,N 20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected > color sel light steel blue > select clear > color zone #6 near #1 distance 5.04 > select #1/H,I,J,K,L,M,N 20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected > color sel pale turquoise > select clear > color zone #6 near #1 distance 5.04 > select #1/H,I,J,K,L,M,N 20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected > color sel light slate gray > select clear > color zone #6 near #1 distance 5.04 > select ::name=""KHS"" 1064 atoms, 1092 bonds, 28 residues, 2 models selected > color sel teal > color sel green > select clear > color zone #6 near #1 distance 5.04 > select clear > select #1/A-N:16 252 atoms, 238 bonds, 14 residues, 1 model selected > select #1/A-N:16-22 1610 atoms, 1610 bonds, 98 residues, 1 model selected > hide #!6 models > select #1/A-N:35 154 atoms, 140 bonds, 14 residues, 1 model selected > select #1/A-N:16-35 3556 atoms, 3570 bonds, 14 pseudobonds, 224 residues, 2 models selected > color sel magenta > show #!6 models > select clear > color zone #6 near #1 distance 5.04 > select #1/A-N:16-35 3556 atoms, 3570 bonds, 14 pseudobonds, 224 residues, 2 models selected > volume style surface > hide #!6 models > surface sel > show #!6 models > color surface magenta Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel magenta > transparency (#!1 & sel) 80 > select clear [Repeated 1 time(s)] > select ::name=""KHS"" 1064 atoms, 1092 bonds, 28 residues, 2 models selected > color sel dark goldenrod > select clear > color zone #6 near #1 distance 5.04 > open 6nb1 structureFactors true Summary of feedback from opening 6nb1 fetched from pdb --- notes | Fetching compressed 6nb1 structure factors from http://files.rcsb.org/download/6nb1-sf.cif Resolution: 1.9000085448470343 Launching live xmap mgr took 1.6232528686523438 seconds. Opened (LIVE) 2mFo-DFc as #7.1.1.2, grid size 50,38,40, pixel 0.589,0.632,0.621, shown at level 0.705, step 1, values float32 Opened (LIVE) mFo-DFc as #7.1.1.3, grid size 50,38,40, pixel 0.589,0.632,0.621, shown at level -0.203,0.203, step 1, values float32 Opened (LIVE) 2mFo-DFc_smooth_17 as #7.1.1.4, grid size 50,38,40, pixel 0.589,0.632,0.621, shown at level 0.206, step 1, values float32 6nb1 title: Crystal structure of Escherichia coli ClpP protease complexed with small molecule activator, ACP1-06 [more info...] Chain information for 6nb1 --- Chain | Description | UniProt 7.2/A 7.2/B 7.2/C 7.2/D 7.2/E 7.2/F 7.2/G 7.2/H 7.2/I 7.2/J 7.2/K 7.2/L 7.2/M 7.2/N | ATP-dependent Clp protease proteolytic subunit | CLPP_ECOLI 1-207 2-207 Non-standard residues in 6nb1 #7.2 --- GOL — glycerol (glycerin; propane-1,2,3-triol) KHS — N-{2-[(2-chlorophenyl)sulfanyl]ethyl}-2-methyl-2-{[5-(trifluoromethyl)pyridin-2-yl]sulfonyl}propanamide 406 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #!7.1 models > show #!7.1 models > hide #!7.2 models > show #!7.2 models > hide #!7.2 models > show #!7.2 models > hide #!7.2 models > show #!7.2 models > hide #7.3 models > close #7 Deleting Crystallographic maps(6nb1-sf.cif) Deleting (LIVE) 2mFo-DFc Deleting (LIVE) mFo-DFc Deleting (LIVE) 2mFo-DFc_smooth_17 > hide #!6 models > select add #1 41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 2 models selected > show surfaces sel Expected ',' or a keyword > show sel surfaces > select ::name=""KHS"" 1064 atoms, 1092 bonds, 28 residues, 2 models selected > show sel & #!1 atoms > hide sel & #!1 atoms > show sel & #!1 atoms > style sel & #!1 sphere Changed 658 atom styles > select clear > select #1/A-N:16-35 3556 atoms, 3570 bonds, 14 pseudobonds, 224 residues, 2 models selected > transparency (#!1 & sel) 60 > select clear > show #3 models > hide #!1 models > select add #3 21308 atoms, 20384 bonds, 3808 residues, 1 model selected > show sel surfaces > hide sel atoms > undo [Repeated 2 time(s)] > show #!3 cartoons > select add #3 21308 atoms, 20384 bonds, 3808 residues, 1 model selected > hide sel atoms > show sel cartoons > surface hidePatches (#!3 & sel) > select clear > select #3/H,I,J,K,L,M,N 10653 atoms, 10192 bonds, 1903 residues, 1 model selected > color sel indigo > select #3/A,B,C,D,E,F,G 10655 atoms, 10192 bonds, 1905 residues, 1 model selected > color sel light slate gray > select #3/A-N:16-35 2352 atoms, 2380 bonds, 280 residues, 1 model selected > color sel magenta > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A #3/B #3/C #3/D #3/E #3/F #3/G #3/H #3/I #3/J #3/K #3/L > #3/M #3/N #4/A #4/B #4/C #4/D #4/E #4/F #4/G #4/H #4/I #4/J #4/K #4/L #4/M > #4/N Alignment identifier is 2 > select #3/A-N:19 #4/A-N:19 224 atoms, 196 bonds, 28 residues, 2 models selected > select #3/A-N:11-19 > #4/A,D-F:1-19/B,G:2-19/C:5-19/H:8-19/I-J:10-19/K:16-19/L-M:12-19/N:17-19 2499 atoms, 2505 bonds, 308 residues, 2 models selected CLP PEPTIDASE [ID: 2] region 28 chains [1-19] RMSD: 1.096 > select clear > select #3/A,B,C,D,E,F,G 10655 atoms, 10192 bonds, 1905 residues, 1 model selected > color sel light slate gray > select #3/H,I,J,K,L,M,N 10653 atoms, 10192 bonds, 1903 residues, 1 model selected > color sel indigo > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A #3/B #3/C #3/D #3/E #3/F #3/G #3/H #3/I #3/J #3/K #3/L > #3/M #3/N #4/A #4/B #4/C #4/D #4/E #4/F #4/G #4/H #4/I #4/J #4/K #4/L #4/M > #4/N Alignment identifier is 2 > select #3/A-N:19 #4/A-N:19 224 atoms, 196 bonds, 28 residues, 2 models selected > select #3/A-N:11-19 > #4/A,D-F:1-19/B,G:2-19/C:5-19/H:8-19/I-J:10-19/K:16-19/L-M:12-19/N:17-19 2499 atoms, 2505 bonds, 308 residues, 2 models selected CLP PEPTIDASE [ID: 2] region 28 chains [1-19] RMSD: 1.096 > color sel magenta > select clear > select add #3 21308 atoms, 20384 bonds, 3808 residues, 1 model selected > surface (#!3 & sel) > select clear > select #3/A-N:1-19 1036 atoms, 1036 bonds, 126 residues, 1 model selected > transparency (#!3 & sel) 70 > select clear > show #!1 models > hide #!3 models > hide #!1 models > show #!3 models > hide #!3 models > show #!1 models > hide #!1 models > show #!3 models > hide #!3 models > show #!1 models > hide #!1 models > show #!3 models > cd ""/Users/ayomidefasemire/Documents/Doctoral/Main > Project/ClpP/Probac1_Figures"" Current working directory is: /Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Probac1_Figures > save 1TYF_1 width 2000 supersample 4 Cannot determine format for '1TYF_1' > save 1TYF_1.png width 2000 supersample 4 > save 1TYF_2.png width 2000 supersample 4 > show #!1 models > hide #!3 models > save data_1.png width 2000 supersample 4 > save data_2.png width 2000 supersample 4 [Repeated 1 time(s)] > show #!3 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > select #3/A-N:1-19 1036 atoms, 1036 bonds, 126 residues, 1 model selected > transparency (#!3 & sel) 0 > select clear > save 1TYF_3.png width 2000 supersample 4 > show #!1 models > hide #!3 models > select #1/A-N:16-35 3556 atoms, 3570 bonds, 14 pseudobonds, 224 residues, 2 models selected > transparency (#!1 & sel) 0 > select clear > save data_3.png width 2000 supersample 4 > save data_4.png width 2000 supersample 4 > open ""/Users/ayomidefasemire/Documents/Doctoral/Main > Project/docking/ClpP_DHFR_Probac1/clpP_DHFR_PRBC_frank.pdb"" Chain information for clpP_DHFR_PRBC_frank.pdb #7 --- Chain | Description A B | No description available H | No description available I | No description available Computing secondary structure > select #1 41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 2 models selected > surface hidePatches (#!1 & sel) > select ::name=""KHS"" 1064 atoms, 1092 bonds, 28 residues, 2 models selected > style sel & #!1 stick Changed 658 atom styles > select clear > hide #!1 models > show #!1 models > ui tool show Matchmaker > matchmaker #7 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 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with clpP_DHFR_PRBC_frank.pdb, chain I (#7), sequence alignment score = 881.1 RMSD between 176 pruned atom pairs is 0.362 angstroms; (across all 176 pairs: 0.362) > select ::name=""PRB"" 69 atoms, 72 bonds, 1 residue, 1 model selected > color sel light sea green > select clear > hide #7 models > show #!6 models > hide #!1 models > show #!1 models > open ""/Users/ayomidefasemire/Documents/Doctoral/Main > Project/ClpP/Map/test_asymmetric_map.mrc"" Opened test_asymmetric_map.mrc as #8, grid size 256,256,256, pixel 0.84, shown at level 0.0428, step 1, values float32 > hide #!6 models > hide #!1 models > show #!6 models > hide #!8 models > show #!8 models > fitmap #6 inMap #8 Fit map ClpP_volume_map_1_95A_bfactor_77_flip.mrc in map test_asymmetric_map.mrc using 195735 points correlation = 0.9974, correlation about mean = 0.9758, overlap = 894.8 steps = 152, shift = 1.67, angle = 17.7 degrees Position of ClpP_volume_map_1_95A_bfactor_77_flip.mrc (#6) relative to test_asymmetric_map.mrc (#8) coordinates: Matrix rotation and translation 0.96361098 -0.23397631 -0.12926315 41.50325809 0.25065052 0.95892918 0.13277476 -37.24829245 0.09288806 -0.16034310 0.98268098 9.90778098 Axis -0.48179659 -0.36514900 0.79657909 Axis point 171.62206310 153.77425141 0.00000000 Rotation angle (degrees) 17.70959179 Shift along axis 1.49737967 > hide #!6 models > show #!1 models > fitmap #1 inMap #8 Fit molecule 16Mar26_flip_KHS_QMR_refined.pdb (#1) to map test_asymmetric_map.mrc (#8) using 41972 atoms average map value = 0.05091, steps = 148 shifted from previous position = 1.68 rotated from previous position = 17.7 degrees atoms outside contour = 19244, contour level = 0.042842 Position of 16Mar26_flip_KHS_QMR_refined.pdb (#1) relative to test_asymmetric_map.mrc (#8) coordinates: Matrix rotation and translation 0.96361310 -0.23401205 -0.12918263 41.49555884 0.25065054 0.95896209 0.13253685 -37.23739034 0.09286603 -0.16009394 0.98272368 9.88457216 Axis -0.48118856 -0.36512657 0.79695681 Axis point 171.54046910 153.74748158 0.00000000 Rotation angle (degrees) 17.70226995 Shift along axis 1.50674939 > show #!6 models > hide #!1 models > open ""/Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic > Models/Pdb/28Mar_flip_KHS_QMR_refined.pdb"" Chain information for 28Mar_flip_KHS_QMR_refined.pdb #9 --- Chain | Description A B C D E F G H I J K L M N | No description available > hide #!9 models > show #!9 models > select add #9 41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 2 models selected > show sel cartoons > hide sel atoms > select clear Must specify one map, got 0 > fitmap #9 inMap #8 Fit molecule 28Mar_flip_KHS_QMR_refined.pdb (#9) to map test_asymmetric_map.mrc (#8) using 41972 atoms average map value = 0.05091, steps = 148 shifted from previous position = 1.68 rotated from previous position = 17.7 degrees atoms outside contour = 19251, contour level = 0.042842 Position of 28Mar_flip_KHS_QMR_refined.pdb (#9) relative to test_asymmetric_map.mrc (#8) coordinates: Matrix rotation and translation 0.96361171 -0.23400654 -0.12920295 41.49833440 0.25064935 0.95896094 0.13254739 -37.23776800 0.09288363 -0.16010885 0.98271959 9.88275255 Axis -0.48121400 -0.36517646 0.79691859 Axis point 171.54789170 153.75638342 0.00000000 Rotation angle (degrees) 17.70289406 Shift along axis 1.50452585 > undo [Repeated 2 time(s)] > close #9 > close #6 > open ""/Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic > Models/Pdb/28Mar_flip_KHS_QMR_refined.pdb"" Chain information for 28Mar_flip_KHS_QMR_refined.pdb #6 --- Chain | Description A B C D E F G H I J K L M N | No description available > hide #!6 atoms > show #!6 cartoons > open ""/Users/ayomidefasemire/Documents/Doctoral/Main > Project/ClpP/Map/ClpP_volume_map_1_95A_bfactor_77_flip.mrc"" Opened ClpP_volume_map_1_95A_bfactor_77_flip.mrc as #9, grid size 256,256,256, pixel 0.84, shown at level 0.0426, step 1, values float32 > hide #!6 models > fitmap #8 inMap #9 Fit map test_asymmetric_map.mrc in map ClpP_volume_map_1_95A_bfactor_77_flip.mrc using 167708 points correlation = 0.9987, correlation about mean = 0.982, overlap = 849.7 steps = 136, shift = 1.67, angle = 17.7 degrees Position of test_asymmetric_map.mrc (#8) relative to ClpP_volume_map_1_95A_bfactor_77_flip.mrc (#9) coordinates: Matrix rotation and translation 0.96361431 0.25061912 0.09293821 -31.57671855 -0.23396910 0.95897005 -0.16010905 46.99198765 -0.12925135 0.13253870 0.98271440 0.59004779 Axis 0.48121617 0.36535804 -0.79683405 Axis point 171.53066021 153.78511267 0.00000000 Rotation angle (degrees) 17.70228062 Shift along axis 1.50350289 > show #!6 models > volume #9 level 0.042 > hide #!9 models > hide #!8 models > show #!9 models > hide #!9 models > show #!8 models > select add #8 2 models selected > hide #!6 models No model chosen to save relative to > save ""/Users/ayomidefasemire/Documents/Doctoral/Main > Project/ClpP/Map/ClpP_asym_shift_2_17_flip.mrc"" models #8 > select clear > open ""/Users/ayomidefasemire/Documents/Doctoral/Main > Project/ClpP/Map/ClpP_asym_shift_2_17_flip.mrc"" Opened ClpP_asym_shift_2_17_flip.mrc as #10, grid size 256,256,256, pixel 0.84, shown at level 0.0428, step 1, values float32 > close #10 > select add #8 2 models selected > show #!6 models > close #8 > open ""/Users/ayomidefasemire/Documents/Doctoral/Main > Project/ClpP/Map/test_asymmetric_map.mrc"" Opened test_asymmetric_map.mrc as #8, grid size 256,256,256, pixel 0.84, shown at level 0.0428, step 1, values float32 > fitmap #6 inMap #8 Fit molecule 28Mar_flip_KHS_QMR_refined.pdb (#6) to map test_asymmetric_map.mrc (#8) using 41972 atoms average map value = 0.05091, steps = 148 shifted from previous position = 1.68 rotated from previous position = 17.7 degrees atoms outside contour = 19251, contour level = 0.042842 Position of 28Mar_flip_KHS_QMR_refined.pdb (#6) relative to test_asymmetric_map.mrc (#8) coordinates: Matrix rotation and translation 0.96361171 -0.23400654 -0.12920295 41.49833440 0.25064935 0.95896094 0.13254739 -37.23776800 0.09288363 -0.16010885 0.98271959 9.88275255 Axis -0.48121400 -0.36517646 0.79691859 Axis point 171.54789170 153.75638342 0.00000000 Rotation angle (degrees) 17.70289406 Shift along axis 1.50452585 > select add #6 41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 2 models selected > save ""/Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic > Models/Pdb/28Mar_Final_shift_asym.pdb"" selectedOnly true > close #6 > open ""/Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic > Models/Pdb/28Mar_Final_shift_asym.pdb"" Chain information for 28Mar_Final_shift_asym.pdb #6 --- Chain | Description A B C D E F G H I J K L M N | No description available > hide #!6 atoms > show #!6 cartoons Computing secondary structure > hide #!8 models > hide #!6 models > show #!8 models > open ""/Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic > Models/Pdb/28Mar_flip_KHS_QMR_refined.pdb"" Chain information for 28Mar_flip_KHS_QMR_refined.pdb #10 --- Chain | Description A B C D E F G H I J K L M N | No description available > hide #!10 atoms > show #!10 cartoons > hide #!10 models > show #!6 models > select ::name=""KHS"" 2380 atoms, 2436 bonds, 56 residues, 4 models selected > show sel & #!6 atoms > select clear > close #8 > hide #!6 models > show #!1 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > select #1 41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 2 models selected > show surfaces sel Expected ',' or a keyword > surface sel > hide sel atoms > show sel atoms > hide sel surfaces > hide sel atoms > select ::name=""KHS"" 2380 atoms, 2436 bonds, 56 residues, 4 models selected > show sel & #!1 atoms > select clear > select #1/A-N:16-35 3556 atoms, 3570 bonds, 14 pseudobonds, 224 residues, 2 models selected > color sel light steel blue > color sel light slate gray > select clear > select #1/H,I,J,K,L,M,N 20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected > select #1/A,B,C,D,E,F,G 20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected > color sel indigo > select clear > select add #1 41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 2 models selected > surface (#!1 & sel) > select #1/H,I,J,K,L,M,N 20986 atoms, 21154 bonds, 7 pseudobonds, 1323 residues, 2 models selected > select #1/H-N:16-35 1778 atoms, 1785 bonds, 7 pseudobonds, 112 residues, 2 models selected > color sel light 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blue > color sel silver > color sel light gray > color sel thistle > color sel dark olive green > color sel dark slate gray > color sel midnight blue > color sel pale violet red > color sel medium purple > color sel light gray > color sel gray > color sel dark gray > color sel dim gray > color sel dark slate gray > color sel midnight blue > color sel pale violet red > color sel medium purple > color sel slate gray > color sel light slate gray > color sel cadet blue > color sel steel blue > color sel teal > color sel medium aquamarine > color sel dark cyan > color sel cornflower blue > color sel light sea green > color sel medium turquoise > color sel turquoise > color sel dodger blue > color sel medium spring green > color sel dark turquoise > color (#!1 & sel) #fbfff6ff [Repeated 1 time(s)] > color (#!1 & sel) #fefeffff > color (#!1 & sel) #f7f1ffff > color (#!1 & sel) #f6eeffff > color (#!1 & sel) #f5edffff > color (#!1 & sel) #f3e9ffff > color (#!1 & sel) #ebdeffff > color (#!1 & 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> color (#!1 & sel) #a56dffff > color (#!1 & sel) #a975ffff > color (#!1 & sel) #ac7cffff > color (#!1 & sel) #ad7fffff > color (#!1 & sel) #ae81ffff > color (#!1 & sel) #ae82ffff > color (#!1 & sel) #b086ffff > color (#!1 & sel) #b189ffff > color (#!1 & sel) #b28effff > color (#!1 & sel) #b392ffff > color (#!1 & sel) #b495ffff > color (#!1 & sel) #b397ffff > color (#!1 & sel) #b398ffff > color (#!1 & sel) #b298ffff > color (#!1 & sel) #b098ffff > color (#!1 & sel) #ae97ffff > color (#!1 & sel) #ac97ffff > color (#!1 & sel) #a996ffff > color (#!1 & sel) #a795ffff > color (#!1 & sel) #a294ffff > color (#!1 & sel) #9f93ffff > color (#!1 & sel) #9e93ffff > color (#!1 & sel) #9d92ffff > color (#!1 & sel) #9a91ffff > color (#!1 & sel) #9790ffff > color (#!1 & sel) #958fffff > color (#!1 & sel) #938fffff [Repeated 1 time(s)] > color (#!1 & sel) #948fffff > color (#!1 & sel) #958fffff > color (#!1 & sel) #9790ffff > color (#!1 & sel) #9890ffff > color (#!1 & sel) #9991ffff > color (#!1 & sel) #9a91ffff > color (#!1 & sel) #9b92ffff > color (#!1 & sel) #9d92ffff [Repeated 1 time(s)] > color (#!1 & sel) #9a91ffff > color (#!1 & sel) #9991ffff > color (#!1 & sel) #9890ffff > color (#!1 & sel) #9790ffff > color (#!1 & sel) #9690ffff > color (#!1 & sel) #938fffff > color (#!1 & sel) #8c8dffff > color (#!1 & sel) #8c8effff > color (#!1 & sel) #8b8effff > color (#!1 & sel) #8b8fffff > color (#!1 & sel) #8a8fffff > color (#!1 & sel) #8691ffff > color (#!1 & sel) #8492ffff > color (#!1 & sel) #8392ffff > color (#!1 & sel) #8293ffff > color (#!1 & sel) #8094ffff > color (#!1 & sel) #7f94ffff > color (#!1 & sel) #7e94ffff > color (#!1 & sel) #7c94ffff > color (#!1 & sel) #7a95ffff [Repeated 1 time(s)] > color (#!1 & sel) #7995ffff > color (#!1 & sel) #7896ffff > color (#!1 & sel) #7696ffff [Repeated 1 time(s)] > color (#!1 & sel) #7596ffff > color (#!1 & sel) #7497ffff > color (#!1 & sel) #7297ffff > color (#!1 & sel) #7197ffff > color (#!1 & sel) #7097ffff > color (#!1 & sel) #6e98ffff > color (#!1 & sel) #6c99ffff > color (#!1 & sel) #6b9affff > color (#!1 & sel) #6a9bffff [Repeated 1 time(s)] > color (#!1 & sel) #6a9cffff > color (#!1 & sel) #699effff > color (#!1 & sel) #68a0ffff > color (#!1 & sel) #68a1ffff > color (#!1 & sel) #69a3ffff > color (#!1 & sel) #69a7ffff > color (#!1 & sel) #69a8ffff > color (#!1 & sel) #6aa9ffff > color (#!1 & sel) #6bacffff > color (#!1 & sel) #6baeffff > color (#!1 & sel) #6cafffff > color (#!1 & sel) #6cb0ffff > color (#!1 & sel) #6db2ffff > color (#!1 & sel) #6fb3ffff > color (#!1 & sel) #70b4ffff > color (#!1 & sel) #73b6ffff > color (#!1 & sel) #76b8ffff > color (#!1 & sel) #82beffff > color (#!1 & sel) #8ac1ffff > color (#!1 & sel) #8dc3ffff > color (#!1 & sel) #8ec3ffff > color (#!1 & sel) #90c4ffff > color (#!1 & sel) #93c5ffff > color (#!1 & sel) #9bc9ffff > color (#!1 & sel) #9ccaffff > color (#!1 & sel) #9dcaffff > color (#!1 & sel) #a0caffff > color (#!1 & sel) #a4cbffff > color (#!1 & sel) #a5cbffff > color (#!1 & sel) #a5caffff > color (#!1 & sel) #a5c9ffff > color (#!1 & sel) #a6c6ffff > color (#!1 & sel) #a5c4ffff > color (#!1 & sel) #a4beffff > color (#!1 & sel) #a3baffff > color (#!1 & sel) #a2b7ffff > color (#!1 & sel) #a0b3ffff > color (#!1 & sel) #9cacffff > color (#!1 & sel) #9baaffff > color (#!1 & sel) #99a7ffff > color (#!1 & sel) #99a6ffff > color (#!1 & sel) #97a4ffff > color (#!1 & sel) #97a3ffff > color (#!1 & sel) #95a1ffff > color (#!1 & sel) #939dffff > color (#!1 & sel) #939cffff > color (#!1 & sel) #929bffff > color (#!1 & sel) #919affff > color (#!1 & sel) #8e96ffff > color (#!1 & sel) #8c93ffff > color (#!1 & sel) #8c92ffff > color (#!1 & sel) #8a90ffff > color (#!1 & sel) #8a8fffff > color (#!1 & sel) #898effff > color (#!1 & sel) #888dffff > color (#!1 & sel) #888cffff > color (#!1 & sel) #878bffff > color (#!1 & sel) #8689ffff > color (#!1 & sel) #8486ffff > color (#!1 & sel) #8485ffff > color (#!1 & sel) #8484ffff > color (#!1 & sel) #8383ffff > color (#!1 & sel) #8483ffff [Repeated 1 time(s)] > color (#!1 & sel) #8482ffff > color (#!1 & sel) #8582ffff > color (#!1 & sel) #8782ffff > color (#!1 & sel) #8781ffff > color (#!1 & sel) #8881ffff > color (#!1 & sel) #8981ffff > color (#!1 & sel) #8c80ffff > color (#!1 & sel) #8d80ffff > color (#!1 & sel) #8e80ffff [Repeated 2 time(s)] > color (#!1 & sel) #8f80ffff > color (#!1 & sel) #9180ffff > color (#!1 & sel) #9281ffff > color (#!1 & sel) #9482ffff > color (#!1 & sel) #9682ffff > color (#!1 & sel) #9883ffff > color (#!1 & sel) #9983ffff > color (#!1 & sel) #9a83ffff > color (#!1 & sel) #9b84ffff > color (#!1 & sel) #9c84ffff > color (#!1 & sel) #9d84ffff > color (#!1 & sel) #9e84ffff [Repeated 1 time(s)] > color (#!1 & sel) #8484ffff [Repeated 1 time(s)] > color (#!1 & sel) #8478ffff > color (#!1 & sel) #8478adff > select clear > select #1/H-N:16-35 1778 atoms, 1785 bonds, 7 pseudobonds, 112 residues, 2 models selected > color (#!1 & sel) #a878adff > color (#!1 & sel) #a897adff > color (#!1 & sel) #a897dcff [Repeated 1 time(s)] > color (#!1 & sel) #a897dbff > color (#!1 & sel) #a897daff > color (#!1 & sel) #a897d8ff > color (#!1 & sel) #a897d5ff > color (#!1 & sel) #a897d4ff > color (#!1 & sel) #a897d2ff > color (#!1 & sel) #a897d0ff > color (#!1 & sel) #a897ceff > color (#!1 & sel) #a897cdff > color (#!1 & sel) #a897cbff > color (#!1 & sel) #a897c6ff [Repeated 1 time(s)] > color (#!1 & sel) #a897c5ff [Repeated 1 time(s)] > color (#!1 & sel) #a897c3ff > color (#!1 & sel) #a897c0ff > color (#!1 & sel) #a897bfff > color (#!1 & sel) #a897beff [Repeated 1 time(s)] > color (#!1 & sel) #a897bcff > color (#!1 & sel) #a897bbff [Repeated 1 time(s)] > color (#!1 & sel) #a897bcff [Repeated 1 time(s)] > color (#!1 & sel) #a897beff > color (#!1 & sel) #a897bfff > color (#!1 & sel) #a897c1ff > color (#!1 & sel) #a897c3ff > color (#!1 & sel) #a897c7ff > color (#!1 & sel) #a897c8ff > color (#!1 & sel) #a897caff > color (#!1 & sel) #a897ceff > color (#!1 & sel) #a897d2ff > color (#!1 & sel) #a897d4ff > color (#!1 & sel) #a897d5ff [Repeated 1 time(s)] > color (#!1 & sel) #a897d6ff > color (#!1 & sel) #a897d7ff > color (#!1 & sel) #a897d8ff [Repeated 1 time(s)] > color (#!1 & sel) #a897d9ff [Repeated 1 time(s)] > color (#!1 & sel) #a897daff > color (#!1 & sel) #a897dbff > color (#!1 & sel) #a897dcff [Repeated 2 time(s)] > color (#!1 & sel) #a89bdcff > color (#!1 & sel) #a89edcff > color (#!1 & sel) #a89fdcff > color (#!1 & sel) #a8a0dcff > color (#!1 & sel) #a8a1dcff [Repeated 2 time(s)] > color (#!1 & sel) #a8a0dcff > color (#!1 & sel) #a89edcff > color (#!1 & sel) #a89ddcff > color (#!1 & sel) #a89cdcff > color (#!1 & sel) #a89adcff > color (#!1 & sel) #a898dcff > color (#!1 & sel) #a895dcff > color (#!1 & sel) #a891dcff > color (#!1 & sel) #a88fdcff > color (#!1 & sel) #a88bdcff > color (#!1 & sel) #a88adcff > color (#!1 & sel) #a887dcff > color (#!1 & sel) #a886dcff [Repeated 1 time(s)] > color (#!1 & sel) #a887dcff > color (#!1 & sel) #a888dcff [Repeated 1 time(s)] > color (#!1 & sel) #a88adcff > color (#!1 & sel) #a88bdcff > color (#!1 & sel) #a88cdcff > color (#!1 & sel) #a88edcff > color (#!1 & sel) #a88fdcff > color (#!1 & sel) #a891dcff > color (#!1 & sel) #a894dcff > color (#!1 & sel) #a895dcff [Repeated 1 time(s)] > color (#!1 & sel) #a896dcff [Repeated 1 time(s)] > color (#!1 & sel) #a897dcff [Repeated 2 time(s)] > color (#!1 & sel) #a697dcff > color (#!1 & sel) #a597dcff > color (#!1 & sel) #a397dcff > color (#!1 & sel) #a197dcff > color (#!1 & sel) #9f97dcff > color (#!1 & sel) #9d97dcff > color (#!1 & sel) #9c97dcff [Repeated 4 time(s)] > color (#!1 & sel) #9d97dcff > color (#!1 & sel) #9e97dcff > color (#!1 & sel) #9f97dcff [Repeated 2 time(s)] > color (#!1 & sel) #9e97dcff [Repeated 1 time(s)] > color (#!1 & sel) #9e96dcff > color (#!1 & sel) #9e94dcff > color (#!1 & sel) #9e93dcff > color (#!1 & sel) #9e92dcff > color (#!1 & sel) #9e91dcff > color (#!1 & sel) #9e8fdcff > color (#!1 & sel) #9e8edcff > color (#!1 & sel) #9e8ddcff [Repeated 1 time(s)] > color (#!1 & sel) #9e8edcff > color (#!1 & sel) #9e8fdcff > color (#!1 & sel) #9e90dcff > color (#!1 & sel) #9e91dcff > color (#!1 & sel) #9e92dcff [Repeated 1 time(s)] > color (#!1 & sel) #9e93dcff [Repeated 1 time(s)] > color (#!1 & sel) #9e92dcff > color (#!1 & sel) #9e91dcff > color (#!1 & sel) #9e90dcff > color (#!1 & sel) #9e8fdcff [Repeated 1 time(s)] > color (#!1 & sel) #9e8edcff [Repeated 1 time(s)] > color (#!1 & sel) #9e8ddcff [Repeated 2 time(s)] > color (#!1 & sel) #9e8dd9ff > color (#!1 & sel) #9e8dd8ff > color (#!1 & sel) #9e8dd6ff > color (#!1 & sel) #9e8dd3ff > color (#!1 & sel) #9e8dd2ff > color (#!1 & sel) #9e8dcfff > color (#!1 & sel) #9e8dccff > color (#!1 & sel) #9e8dc9ff > color (#!1 & sel) #9e8dc5ff > color (#!1 & sel) #9e8dc1ff > color (#!1 & sel) #9e8dbfff > color (#!1 & sel) #9e8dbeff > color (#!1 & sel) #9e8dbdff > color (#!1 & sel) #9e8dbbff > color (#!1 & sel) #9e8db9ff > color (#!1 & sel) #9e8db8ff > color (#!1 & sel) 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sel) #9e8dbfff [Repeated 2 time(s)] > color (#!1 & sel) #9e8dbeff > color (#!1 & sel) #9e8dbdff [Repeated 1 time(s)] > color (#!1 & sel) #9e8dbcff [Repeated 2 time(s)] > color (#!1 & sel) #9e8fbcff > color (#!1 & sel) #9e91bcff > color (#!1 & sel) #9e93bcff > color (#!1 & sel) #9e96bcff > color (#!1 & sel) #9e99bcff > color (#!1 & sel) #9e9abcff > color (#!1 & sel) #9e9bbcff > color (#!1 & sel) #9e9cbcff > color (#!1 & sel) #9e9ebcff [Repeated 1 time(s)] > color (#!1 & sel) #9e9dbcff > color (#!1 & sel) #9e99bcff > color (#!1 & sel) #9e97bcff > color (#!1 & sel) #9e95bcff > color (#!1 & sel) #9e93bcff > color (#!1 & sel) #9e91bcff > color (#!1 & sel) #9e8ebcff > color (#!1 & sel) #9e8cbcff > color (#!1 & sel) #9e8abcff > color (#!1 & sel) #9e88bcff > color (#!1 & sel) #9e86bcff [Repeated 1 time(s)] > color (#!1 & sel) #9e85bcff [Repeated 2 time(s)] > color (#!1 & sel) #9e86bcff > color (#!1 & sel) #9e88bcff > color (#!1 & sel) #9e89bcff > color (#!1 & sel) #9e8bbcff > color (#!1 & sel) #9e8cbcff > color (#!1 & sel) #9e8dbcff > color (#!1 & sel) #9e8ebcff > color (#!1 & sel) #9e8fbcff > color (#!1 & sel) #9e90bcff > color (#!1 & sel) #9e91bcff [Repeated 1 time(s)] > color (#!1 & sel) #9e92bcff [Repeated 1 time(s)] > color (#!1 & sel) #9f92bcff > color (#!1 & sel) #a192bcff > color (#!1 & sel) #a392bcff > color (#!1 & sel) #a592bcff > color (#!1 & sel) #a692bcff [Repeated 1 time(s)] > color (#!1 & sel) #a892bcff [Repeated 1 time(s)] > color (#!1 & sel) #a992bcff > color (#!1 & sel) #aa92bcff > color (#!1 & sel) #a992bcff > color (#!1 & sel) #a892bcff > color (#!1 & sel) #a692bcff > color (#!1 & sel) #a592bcff > color (#!1 & sel) #a492bcff > color (#!1 & sel) #a392bcff > color (#!1 & sel) #a292bcff > color (#!1 & sel) #a192bcff [Repeated 1 time(s)] > color (#!1 & sel) #a092bcff [Repeated 1 time(s)] > color (#!1 & sel) #9f92bcff [Repeated 1 time(s)] > color (#!1 & sel) #9e92bcff [Repeated 2 time(s)] > color (#!1 & sel) #9f92bcff [Repeated 2 time(s)] > color (#!1 & sel) #a092bcff [Repeated 1 time(s)] > color (#!1 & sel) #a192bcff [Repeated 1 time(s)] > color (#!1 & sel) #a292bcff [Repeated 3 time(s)] > color (#!1 & sel) #a092bcff > color (#!1 & sel) #9f92bcff > color (#!1 & sel) #9e92bcff > color (#!1 & sel) #9d92bcff [Repeated 2 time(s)] > color (#!1 & sel) #9d91bcff > color (#!1 & sel) #9d90bcff > color (#!1 & sel) #9d8fbcff > color (#!1 & sel) #9d8ebcff [Repeated 1 time(s)] > color (#!1 & sel) #9d8dbcff > color (#!1 & sel) #9d8cbcff [Repeated 1 time(s)] > color (#!1 & sel) #9d8dbcff > color (#!1 & sel) #9d8ebcff > color (#!1 & sel) #9d8fbcff > color (#!1 & sel) #9d90bcff > color (#!1 & sel) #9d91bcff > color (#!1 & sel) #9d92bcff [Repeated 3 time(s)] > color (#!1 & sel) #9d93bcff [Repeated 1 time(s)] > color (#!1 & sel) #9d92bcff [Repeated 1 time(s)] > color (#!1 & sel) #9d91bcff > color (#!1 & sel) #9d90bcff [Repeated 1 time(s)] > color (#!1 & sel) #9d91bcff [Repeated 2 time(s)] > color (#!1 & sel) #9d92bcff [Repeated 1 time(s)] > color (#!1 & sel) #9d93bcff [Repeated 1 time(s)] > color (#!1 & sel) #9d93bbff [Repeated 1 time(s)] > color (#!1 & sel) #9d93baff > color (#!1 & sel) #9d93b9ff > color (#!1 & sel) #9d93b8ff > color (#!1 & sel) #9d93b7ff [Repeated 2 time(s)] > color (#!1 & sel) #9d93b6ff [Repeated 1 time(s)] > color (#!1 & sel) #9d93b7ff > color (#!1 & sel) #9d93b8ff > color (#!1 & sel) #9d93b9ff > color (#!1 & sel) #9d93baff > color (#!1 & sel) #9d93bbff > color (#!1 & sel) #9d93bcff [Repeated 1 time(s)] > color (#!1 & sel) #9d93bdff [Repeated 1 time(s)] > color (#!1 & sel) #9d93beff > color (#!1 & sel) #9d93bfff [Repeated 1 time(s)] > select clear > select #1/H-N:16-35 1778 atoms, 1785 bonds, 7 pseudobonds, 112 residues, 2 models selected > color (#!1 & sel) #9d93bfff > color (#!1 & sel) #2093bfff [Repeated 1 time(s)] > color (#!1 & sel) #201ebfff > color (#!1 & sel) #201e2aff > color (#!1 & sel) #771e2aff > color (#!1 & sel) #776d2aff > color (#!1 & sel) #776d9cff [Repeated 1 time(s)] > color (#!1 & sel) #776d98ff [Repeated 1 time(s)] > color (#!1 & sel) #776d97ff > color (#!1 & sel) #776d96ff > color (#!1 & sel) #776d95ff > color (#!1 & sel) #776d94ff > color (#!1 & sel) #776d93ff > color (#!1 & sel) #776d92ff > color (#!1 & sel) #776d91ff [Repeated 1 time(s)] > color (#!1 & sel) #776d90ff [Repeated 1 time(s)] > color (#!1 & sel) #776d8fff [Repeated 1 time(s)] > color (#!1 & sel) #776e8fff [Repeated 1 time(s)] > color (#!1 & sel) #77708fff > color (#!1 & sel) #77728fff [Repeated 1 time(s)] > color (#!1 & sel) #77748fff [Repeated 1 time(s)] > color (#!1 & sel) #77738fff [Repeated 1 time(s)] > color (#!1 & sel) #77728fff > color (#!1 & sel) #77718fff > color (#!1 & sel) #77708fff [Repeated 2 time(s)] > color (#!1 & sel) #78708fff > color (#!1 & sel) #7a708fff [Repeated 1 time(s)] > color (#!1 & sel) #7b708fff > color (#!1 & sel) #7a708fff [Repeated 1 time(s)] > color (#!1 & sel) #79708fff [Repeated 1 time(s)] > color (#!1 & sel) #78708fff [Repeated 2 time(s)] > color (#!1 & sel) #77708fff [Repeated 1 time(s)] > color (#!1 & sel) #777090ff > color (#!1 & sel) #777092ff > color (#!1 & sel) #777093ff [Repeated 1 time(s)] > color (#!1 & sel) #777094ff [Repeated 1 time(s)] > color (#!1 & sel) #777095ff [Repeated 1 time(s)] > color (#!1 & sel) #777096ff [Repeated 2 time(s)] > color (#!1 & sel) #777097ff > color (#!1 & sel) #777098ff [Repeated 1 time(s)] > color (#!1 & sel) #777099ff [Repeated 3 time(s)] > color (#!1 & sel) #777097ff [Repeated 2 time(s)] > color (#!1 & sel) #777096ff > color (#!1 & sel) #777095ff [Repeated 1 time(s)] > color (#!1 & sel) #777094ff > color (#!1 & sel) #777093ff [Repeated 2 time(s)] > color (#!1 & sel) #777092ff [Repeated 1 time(s)] > color (#!1 & sel) #777091ff > color (#!1 & sel) #777090ff [Repeated 2 time(s)] > color (#!1 & sel) #777091ff > color (#!1 & sel) #777092ff [Repeated 1 time(s)] > color (#!1 & sel) #777093ff [Repeated 1 time(s)] > color (#!1 & sel) #777094ff [Repeated 1 time(s)] > color (#!1 & sel) #777095ff [Repeated 1 time(s)] > color (#!1 & sel) #777295ff > color (#!1 & sel) #777395ff > color (#!1 & sel) #777495ff > color (#!1 & sel) #777595ff [Repeated 2 time(s)] > color (#!1 & sel) #777495ff [Repeated 1 time(s)] > color (#!1 & sel) #777395ff [Repeated 1 time(s)] > color (#!1 & sel) #777295ff > color (#!1 & sel) #777195ff [Repeated 1 time(s)] > color (#!1 & sel) #777295ff [Repeated 2 time(s)] > color (#!1 & sel) #787295ff [Repeated 1 time(s)] > color (#!1 & sel) #7a7295ff > color (#!1 & sel) #7b7295ff > color (#!1 & sel) #7c7295ff [Repeated 1 time(s)] > color (#!1 & sel) #7d7295ff [Repeated 2 time(s)] > color (#!1 & sel) #7c7295ff > color (#!1 & sel) #7b7295ff > color (#!1 & sel) #7a7295ff [Repeated 3 time(s)] > select clear > select #1/H-N:16-35 1778 atoms, 1785 bonds, 7 pseudobonds, 112 residues, 2 models selected > color (#!1 & sel) #7a7295ff > color (#!1 & sel) #7a7294ff > color (#!1 & sel) #7a7293ff > color (#!1 & sel) #7a7292ff > color (#!1 & sel) #7a7291ff [Repeated 1 time(s)] > color (#!1 & sel) #7a728fff > color (#!1 & sel) #7a728eff > color (#!1 & sel) #7a728dff > color (#!1 & sel) #7a728bff > color (#!1 & sel) #7a728aff [Repeated 1 time(s)] > color (#!1 & sel) #7a7289ff [Repeated 2 time(s)] > color (#!1 & sel) #7a728aff > color (#!1 & sel) #7a728cff > color (#!1 & sel) #7a728dff > color (#!1 & sel) #7a728fff > color (#!1 & sel) #7a7290ff > color (#!1 & sel) #7a7292ff > color (#!1 & sel) #7a7293ff > color (#!1 & sel) #7a7294ff [Repeated 1 time(s)] > color (#!1 & sel) #7a7295ff [Repeated 1 time(s)] > color (#!1 & sel) #7a7296ff [Repeated 1 time(s)] > color (#!1 & sel) #7a7299ff > color (#!1 & sel) #7a729bff [Repeated 2 time(s)] > color (#!1 & sel) #7a729aff > color (#!1 & sel) #7a7299ff > color (#!1 & sel) #7a7298ff [Repeated 1 time(s)] > color (#!1 & sel) #7a7297ff [Repeated 1 time(s)] > color (#!1 & sel) #7a7296ff [Repeated 1 time(s)] > color (#!1 & sel) #7a7295ff [Repeated 1 time(s)] > color (#!1 & sel) #7a7296ff > color (#!1 & sel) #7a7297ff [Repeated 1 time(s)] > color (#!1 & sel) #7a7298ff [Repeated 2 time(s)] > color (#!1 & sel) #7a7297ff > color (#!1 & sel) #7a7296ff [Repeated 1 time(s)] > color (#!1 & sel) #7a7295ff > color (#!1 & sel) #7a7294ff [Repeated 1 time(s)] > color (#!1 & sel) #7a7295ff > color (#!1 & sel) #7a7296ff [Repeated 1 time(s)] > color (#!1 & sel) #7a7297ff [Repeated 2 time(s)] > select clear > select ::name=""KHS"" 2380 atoms, 2436 bonds, 56 residues, 4 models selected > style sel & #!1 sphere Changed 658 atom styles > style sel & #!1 ball Changed 658 atom styles > style sel & #!1 sphere Changed 658 atom styles > style sel & #!1 stick Changed 658 atom styles > style sel & #!1 sphere Changed 658 atom styles > color (#!1 & sel) forest green > color (#!1 & sel) lime > color (#!1 & sel) light sea green > color (#!1 & sel) forest green > select clear > save new_data_1.png width 2000 supersample 4 > graphics silhouettes true > save new_data_1.png width 2000 supersample 4 > show #!3 models > hide #!3 models > save new_data_2.png width 2000 supersample 4 > save new_data_3.png width 2000 supersample 4 > show #!3 models > ui tool show Matchmaker > matchmaker #4#!2-3,5 to #1 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 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 1yg6, chain I (#4), sequence alignment score = 934.6 RMSD between 176 pruned atom pairs is 0.252 angstroms; (across all 181 pairs: 2.818) Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A (#2), sequence alignment score = 958.6 RMSD between 183 pruned atom pairs is 0.392 angstroms; (across all 187 pairs: 0.581) Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 1tyf, chain J (#3), sequence alignment score = 937.6 RMSD between 175 pruned atom pairs is 0.316 angstroms; (across all 181 pairs: 2.425) Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 3mt6, chain E (#5), sequence alignment score = 954.4 RMSD between 181 pruned atom pairs is 0.466 angstroms; (across all 186 pairs: 0.661) > hide #!3 models > show #4 models > hide #!1 models > select add #4 21540 atoms, 20901 bonds, 3585 residues, 1 model selected > surface sel > show #!1 models > hide #!4 models > show #!4 models > hide #!4 models > select subtract #4 14 models selected > show #!4 models > select #3/H,I,J,K,L,M,N 10653 atoms, 10192 bonds, 1903 residues, 1 model selected > color sel #7A7297 > select #4/H,I,J,K,L,M,N 10526 atoms, 10173 bonds, 1787 residues, 1 model selected > color sel #7A7297 > hide #!1 models > show #!1 models > color sel INDIGO Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel Indigo Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel indigo > select #4/A-G 11014 atoms, 10728 bonds, 1798 residues, 1 model selected > color sel #7A7297 > select clear > hide #!1 models > save 1YG6_1.png width 2000 supersample 4 > show #!1 models > hide #!4 models > show #!4 models > hide #!1 models > save 1YG6_1.png width 2000 supersample 4 > hide #!4 models > show #!1 models > save new_data_1.png width 2000 supersample 4 > show #!3 models > hide #!1 models > select #3/A-G 10655 atoms, 10192 bonds, 1905 residues, 1 model selected > color sel indigo > select clear > show #!1 models > hide #!1 models > select #3/A-G 10655 atoms, 10192 bonds, 1905 residues, 1 model selected > color sel #7A7297 > select #3/H-N 10653 atoms, 10192 bonds, 1903 residues, 1 model selected > color sel indigo > select clear > show #!1 models > hide #!1 models > save 1TYF_1.png width 2000 supersample 4 > show #!5 models > hide #!3 models > select clear [Repeated 1 time(s)] > select #5/Q:16 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 30 atoms, 30 bonds, 4 residues, 1 model selected > select up 1391 atoms, 1414 bonds, 179 residues, 1 model selected > select up 1407 atoms, 1429 bonds, 181 residues, 1 model selected > select up 1453 atoms, 1476 bonds, 187 residues, 1 model selected > select up 1594 atoms, 1490 bonds, 314 residues, 1 model selected > select up 46272 atoms, 43362 bonds, 9074 residues, 1 model selected > select down 1594 atoms, 1490 bonds, 314 residues, 1 model selected > select up 46272 atoms, 43362 bonds, 9074 residues, 1 model selected > select down 1594 atoms, 1490 bonds, 314 residues, 1 model selected > delete sel [Repeated 1 time(s)]Drag select of 1000 residues, 6 pseudobonds > select clear Drag select of 661 residues, 3 pseudobonds > select #5/R:130 4 atoms, 3 bonds, 1 residue, 1 model selected Drag select of 2287 residues, 6 pseudobonds > delete atoms (#!5 & sel) > delete bonds (#!5 & sel) > select #5/P:9 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 16 atoms, 15 bonds, 2 residues, 1 model selected > select up 46 atoms, 45 bonds, 6 residues, 1 model selected > delete sel > select clear [Repeated 2 time(s)] > select #5/X:12 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 2 residues, 1 model selected > select up 15 atoms, 14 bonds, 3 residues, 1 model selected > delete sel > select add #5 26835 atoms, 23694 bonds, 8 pseudobonds, 6464 residues, 2 models selected > show #!1 models > hide #!1 models > surface (#!5 & sel) > select clear > select #5/s:700@C1 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > select up 26835 atoms, 23694 bonds, 6464 residues, 2 models selected > select clear Drag select of 3mt6_Y SES surface, 3mt6_v SES surface, 1962 of 2742 triangles, 3mt6_y SES surface, 52 of 2758 triangles, 3mt6_z SES surface, 1186 of 2720 triangles, 2 residues > select clear Drag select of 3mt6_3 SES surface, 3mt6_4 SES surface, 3mt6_v SES surface, 3mt6_w SES surface, 1558 of 2800 triangles, 3mt6_x SES surface, 186 of 2778 triangles, 3mt6_y SES surface, 2277 of 2758 triangles, 3mt6_z SES surface Drag select of 3mt6_3 SES surface, 3mt6_4 SES surface, 3mt6_Y SES surface, 3mt6_v SES surface, 3mt6_w SES surface, 3mt6_x SES surface, 3mt6_y SES surface, 3mt6_z SES surface, 2 residues > select clear Drag select of 3mt6_3 SES surface, 3mt6_4 SES surface, 3mt6_Y SES surface, 3mt6_v SES surface, 3mt6_w SES surface, 2690 of 2800 triangles, 3mt6_x SES surface, 3mt6_y SES surface, 3mt6_z SES surface, 2143 of 2720 triangles, 2 residues > select clear Drag select of 3mt6_3 SES surface, 3mt6_4 SES surface, 3mt6_O SES surface, 8882 of 178018 triangles, 3mt6_Y SES surface, 3mt6_v SES surface, 3mt6_w SES surface, 3mt6_x SES surface, 3mt6_y SES surface, 3mt6_z SES surface, 2 residues > delete sel > select #5/z:700@C6 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > delete sel > select #5/3:700@C6 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > delete sel > select #5/4:700@C6 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > delete sel > select #5/v:700@C8 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > delete sel > select #5/w:700@C7 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > delete sel > select #5/y:700@C1 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > delete sel > select #5/x:700@C2 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > delete sel > select #5/s:700@C1 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > delete sel > select #5/r:700@C6 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > delete sel > select #5/q:700@C6 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > delete sel > select #5/t:700@O11 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > delete sel > select #5/u:700@O11 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > delete sel > select #5/p:700@C1 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > delete sel > select #5/O:12@NH1 1 atom, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 2 models selected > select up 46 atoms, 45 bonds, 6 residues, 2 models selected > select up 1474 atoms, 1497 bonds, 189 residues, 2 models selected > delete sel > select #5/o:700@C2 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > delete sel > show #!1 models > hide #!1 models > select #4/A-G 11014 atoms, 10728 bonds, 1798 residues, 1 model selected > select #5/A-G 11386 atoms, 10602 bonds, 4 pseudobonds, 2272 residues, 2 models selected > color sel indigo > select #5/H-N 11312 atoms, 10523 bonds, 4 pseudobonds, 2271 residues, 2 models selected > color sel #7A7297 > select ::name=""GOL"" 84 atoms, 70 bonds, 14 residues, 1 model selected > select ::name=""MP8"" 112 atoms, 112 bonds, 14 residues, 1 model selected > select ::name=""MPD"" 536 atoms, 469 bonds, 67 residues, 2 models selected > select ::name=""MP8"" 112 atoms, 112 bonds, 14 residues, 1 model selected > select add ::name=""OTT"" 238 atoms, 224 bonds, 28 residues, 15 models selected > select add ::name=""MAA"" 322 atoms, 294 bonds, 42 residues, 15 models selected > select add ::name=""MPD"" 858 atoms, 763 bonds, 109 residues, 16 models selected > select add ::name=""GOL"" 942 atoms, 833 bonds, 123 residues, 17 models selected > select add ::name=""PRO"" 7935 atoms, 7826 bonds, 828 residues, 22 models selected > select clear > select #5/l:703@CG 1 atom, 1 residue, 1 model selected > select up 7 atoms, 7 bonds, 1 residue, 2 models selected > select up 52 atoms, 55 bonds, 7 residues, 2 models selected > select #5/A-N:703@CG Nothing selected > select #5/A-N:703@CG Nothing selected > select #5/A-N:703 Nothing selected > select #5/l:703@CG 1 atom, 1 residue, 1 model selected > select #5/a-n:703@CG 12 atoms, 12 residues, 1 model selected > select up 84 atoms, 84 bonds, 12 residues, 13 models selected > select up 624 atoms, 660 bonds, 84 residues, 13 models selected > color (#!5 & sel) red > color sel crimson > color sel fire brick > color sel tomato > color sel brown > color sel tomato > color sel indian red > style sel sphere Changed 624 atom styles > style sel sphere Changed 624 atom styles > show sel atoms > hide sel atoms > select clear > save 3MT6_1.png width 2000 supersample 4 > show #!2 models > hide #!5 models > select #2/A-G 10891 atoms, 10586 bonds, 6 pseudobonds, 1782 residues, 2 models selected > show #!1 models > hide #!1 models > color sel indigo > select #2/H-N 10551 atoms, 10253 bonds, 6 pseudobonds, 1730 residues, 2 models selected > color sel #7A7297 > select clear > select add #2 21442 atoms, 20839 bonds, 12 pseudobonds, 3512 residues, 2 models selected > surface (#!2 & sel) > select ::name=""KHS"" 2380 atoms, 2436 bonds, 56 residues, 4 models selected > style sel & #!2 sphere Changed 406 atom styles > color (#!2 & sel) forest green > select clear > show #!5 models > hide #!2 models > show #!2 models > hide #!5 models > select #2/H-N 10551 atoms, 10253 bonds, 6 pseudobonds, 1730 residues, 2 models selected > color sel indigo > select #2/A-G 10891 atoms, 10586 bonds, 6 pseudobonds, 1782 residues, 2 models selected > color sel #7A7297 > select clear > select ::name=""KHS"" 2380 atoms, 2436 bonds, 56 residues, 4 models selected > color (#!2 & sel) forest green > select clear > save 6NB1_1.png width 2000 supersample 4 > save ""/Users/ayomidefasemire/Documents/Doctoral/Main > Project/ClpP/Probac1_Figures/figures_prep.cxs"" includeMaps true ——— End of log from Thu Apr 9 16:14:06 2026 ——— opened ChimeraX session > hide #!2 models > show #!1 models > select #1/A-N:16-35 3556 atoms, 3570 bonds, 14 pseudobonds, 224 residues, 2 models selected > transparency (#!1 & sel) 80 > select #1/A-N:16-50 7280 atoms, 7308 bonds, 14 pseudobonds, 434 residues, 2 models selected > transparency (#!1 & sel) 80 > ui tool show ""Color Actions"" > color sel maroon > select clear > hide #1.1 models > select #1/A-N:16-50 7280 atoms, 7308 bonds, 14 pseudobonds, 434 residues, 2 models selected > color sel brown > select clear > select #1/A-N:16-50 7280 atoms, 7308 bonds, 14 pseudobonds, 434 residues, 2 models selected > transparency (#!1 & sel) 90 > select clear > cd ""/Users/ayomidefasemire/Documents/Doctoral/Main > Project/ClpP/Probac1_Figures"" Current working directory is: /Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Probac1_Figures > save probac_loop.png width 2000 supersample 4 > show #!4 models > hide #!1 models > show #!1 models > hide #!1 models > select #4/A-N:1-50 5033 atoms, 5095 bonds, 616 residues, 1 model selected > select #4/A-N:1-35 3353 atoms, 3387 bonds, 406 residues, 1 model selected > transparency (#!4 & sel) 90 > color sel brown > select clear > select #4/A-N:1-35 3353 atoms, 3387 bonds, 406 residues, 1 model selected > transparency (#!4 & sel) 100 > select clear > select #4/A-N:1-35 3353 atoms, 3387 bonds, 406 residues, 1 model selected > transparency (#!4 & sel) 95 > select clear > save 1YG6_loop.png width 2000 supersample 4 > show #!1 models > hide #!4 models > save probac_loop2.png width 2000 supersample 4 > hide #!1 models > show #!2 models > select #2/A-N:1-35 1241 atoms, 1253 bonds, 12 pseudobonds, 153 residues, 2 models selected > transparency (#!2 & sel) 95 > hide #2.1 models > select subtract #2.1 1241 atoms, 1253 bonds, 153 residues, 15 models selected > ui tool show ""Color Actions"" > color sel brown > select clear Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic models, 0 maps. > ui tool show ""Surface Color"" > select #2/A-N:1-35 1241 atoms, 1253 bonds, 12 pseudobonds, 153 residues, 2 models selected > color surface sel brown Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel surface brown Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color surface brown Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color surfaces brown Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color surfaces fromatoms Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color fromatoms surfaces > transparency (#!2 & sel) 95 > transparency (#!2 & sel) 80 > select clear > transparency (#!2 & sel) 90 > select #2/A-N:1-35 1241 atoms, 1253 bonds, 12 pseudobonds, 153 residues, 2 models selected > transparency (#!2 & sel) 80 > transparency (#!2 & sel) 95 > transparency (#!2 & sel) 80 > select clear > transparency (#!2 & sel) 95 > select #2/A-N:1-35 1241 atoms, 1253 bonds, 12 pseudobonds, 153 residues, 2 models selected > transparency (#!2 & sel) 95 > select clear > save 6NB1_loop.png width 2000 supersample 4 > hide #!2 models > show #!5 models > select #5/A-N:1-35 3712 atoms, 3746 bonds, 8 pseudobonds, 456 residues, 2 models selected > transparency (#!5 & sel) 95 > color sel brown > select clear > hide #4.1 models > show #4.1 models > hide #!4 models > hide #5.1 models > save 3MT6_loop.png width 2000 supersample 4 > hide #!5 models > show #!1 models > show #!2 models > surface hidePatches #1.2-15#2.2-15#!1-2 > hide #!1 models > show #!1 models > select ::name=""KHS"" 2380 atoms, 2436 bonds, 56 residues, 4 models selected > hide sel & #!1-2 atoms > style sel & #!1-2 stick Changed 1064 atom styles > hide sel & #!1-2 atoms > show sel & #!1-2 atoms > select clear > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > select clear > hide #!2 models > show #!2 models > select #1 & KHS Expected a keyword > select #1:KHS 658 atoms, 672 bonds, 14 residues, 1 model selected > color sel byhetero > select clear > select #2:KHS 406 atoms, 420 bonds, 14 residues, 1 model selected > color sel byhetero > select clear > select #2:KHS 406 atoms, 420 bonds, 14 residues, 1 model selected > color sel gold > color sel goldenrod > select clear > select #2:KHS 406 atoms, 420 bonds, 14 residues, 1 model selected > color sel byhetero > select clear > select add #1 41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 2 models selected > select add #2 63414 atoms, 63147 bonds, 26 pseudobonds, 6158 residues, 18 models selected > ui tool show ""Color Actions"" > color sel bychain > hide #!2 models > show #!2 models > ui tool show Matchmaker > matchmaker #2/A to #1/A pairing ss Parameters --- Chain pairing | ss 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 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A (#2), sequence alignment score = 958.6 RMSD between 183 pruned atom pairs is 0.392 angstroms; (across all 187 pairs: 0.581) > matchmaker #2/A,B,C,D,E,F,G to #1/A,B,C,D,E,F,G alg bb pairing ss Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_maker/match.py"", line 767, in cmd_match ret_vals = match(session, pairing, match_items, matrix, alg, gap_open, gap_extend, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_maker/match.py"", line 269, in match raise ValueError(""Unknown sequence alignment algorithm: %s"" % alg) ValueError: Unknown sequence alignment algorithm: bb ValueError: Unknown sequence alignment algorithm: bb File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/match_maker/match.py"", line 269, in match raise ValueError(""Unknown sequence alignment algorithm: %s"" % alg) See log for complete Python traceback. > matchmaker #2/A,B,C,D,E,F,G to #1/A,B,C,D,E,F,G 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 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A (#2), sequence alignment score = 958.6 RMSD between 183 pruned atom pairs is 0.392 angstroms; (across all 187 pairs: 0.581) > ui tool show Matchmaker > matchmaker #2/A#2/B#2/C#2/D#2/E#2/F#2/G to #1/A#1/B#1/C#1/D#1/E#1/F#1/G > pairing ss Parameters --- Chain pairing | ss 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 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A (#2), sequence alignment score = 958.6 Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain B (#1) with 6nb1, chain B (#2), sequence alignment score = 953.2 Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain C (#1) with 6nb1, chain C (#2), sequence alignment score = 925 Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain D (#1) with 6nb1, chain D (#2), sequence alignment score = 929.2 Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain E (#1) with 6nb1, chain E (#2), sequence alignment score = 928.6 Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain F (#1) with 6nb1, chain F (#2), sequence alignment score = 927.4 Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain G (#1) with 6nb1, chain G (#2), sequence alignment score = 932.8 RMSD between 9 pruned atom pairs is 1.182 angstroms; (across all 1293 pairs: 30.045) > matchmaker #2/A#2/B#2/C#2/D#2/E#2/F#2/G#2/H#2/I#2/J#2/K#2/L#2/M#2/N to > #1/A#1/B#1/C#1/D#1/E#1/F#1/G#1/H#1/I#1/J#1/K#1/L#1/M#1/N pairing ss Parameters --- Chain pairing | ss 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 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A (#2), sequence alignment score = 958.6 Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain B (#1) with 6nb1, chain B (#2), sequence alignment score = 953.2 Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain C (#1) with 6nb1, chain C (#2), sequence alignment score = 925 Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain D (#1) with 6nb1, chain D (#2), sequence alignment score = 929.2 Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain E (#1) with 6nb1, chain E (#2), sequence alignment score = 928.6 Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain F (#1) with 6nb1, chain F (#2), sequence alignment score = 927.4 Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain G (#1) with 6nb1, chain G (#2), sequence alignment score = 932.8 Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain H (#1) with 6nb1, chain H (#2), sequence alignment score = 931.6 Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain I (#1) with 6nb1, chain I (#2), sequence alignment score = 937.6 Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain J (#1) with 6nb1, chain J (#2), sequence alignment score = 933.4 Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain K (#1) with 6nb1, chain K (#2), sequence alignment score = 934.6 Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain L (#1) with 6nb1, chain L (#2), sequence alignment score = 935.8 Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain M (#1) with 6nb1, chain M (#2), sequence alignment score = 936.4 Matchmaker 16Mar26_flip_KHS_QMR_refined.pdb, chain N (#1) with 6nb1, chain N (#2), sequence alignment score = 936.4 RMSD between 57 pruned atom pairs is 1.477 angstroms; (across all 2553 pairs: 47.524) > matchmaker #!2 to #1 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 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A (#2), sequence alignment score = 958.6 RMSD between 183 pruned atom pairs is 0.392 angstroms; (across all 187 pairs: 0.581) > matchmaker #!2 to #1 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 16Mar26_flip_KHS_QMR_refined.pdb, chain A (#1) with 6nb1, chain A (#2), sequence alignment score = 958.6 RMSD between 183 pruned atom pairs is 0.392 angstroms; (across all 187 pairs: 0.581) > select #2:KHS 406 atoms, 420 bonds, 14 residues, 1 model selected > color sel byelement > color sel sandy brown > color sel byelement > color #1:KHS cornflower blue atoms > select #2:KHS 406 atoms, 420 bonds, 14 residues, 1 model selected > select #1:KHS 658 atoms, 672 bonds, 14 residues, 1 model selected > color sel byelement > color #1:KHS cornflower blue atoms > color sel byhetero > select clear > hide #!2 models > show #!2 models > show #1/A,B cartoons > hide #!1 models > hide #!2 models > show #1/A,B cartoons > show #!1 models > show #!2 models > select #1/A,B 5996 atoms, 6044 bonds, 2 pseudobonds, 378 residues, 2 models selected > hide ~select cartoons Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide ~sel cartoons > select ::name=""KHS"" 2380 atoms, 2436 bonds, 56 residues, 4 models selected > select clear > select #1/A:KHS 47 atoms, 48 bonds, 1 residue, 1 model selected > select #1-#2/A:KHS Expected an objects specifier or a keyword > select #1-2/A:KHS 76 atoms, 78 bonds, 2 residues, 2 models selected > hide ~sel atoms > select clear > color #1:KHS cornflower blue atoms > select #2/A:KHS coral atoms Expected a keyword > color #2/A:KHS coral atoms > select #1/A:KHS 47 atoms, 48 bonds, 1 residue, 1 model selected > color sel magenta > color sel dark violet > color sel blue violet > color sel dodger blue > color sel dark cyan > color sel teal > color sel slate blue > color sel dark turquoise > color sel steel blue > color sel dark cyan > color sel medium aquamarine > color sel cadet blue > color sel steel blue > color sel green > color sel lime > color sel olive > select #2/A:KHS 29 atoms, 30 bonds, 1 residue, 1 model selected > color sel dark salmon > color sel light salmon > color sel sea green > select #1/A:KHS 47 atoms, 48 bonds, 1 residue, 1 model selected > surface sel > surface hidePatches (#!1 & sel) > select clear > show #!9 models Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 2 atomic models, 1 maps. > hide #!2 models > fitmap #1 inMap #9 Fit molecule 16Mar26_flip_KHS_QMR_refined.pdb (#1) to map ClpP_volume_map_1_95A_bfactor_77_flip.mrc (#9) using 41972 atoms average map value = 0.05287, steps = 148 shifted from previous position = 1.69 rotated from previous position = 17.7 degrees atoms outside contour = 17973, contour level = 0.041998 Position of 16Mar26_flip_KHS_QMR_refined.pdb (#1) relative to ClpP_volume_map_1_95A_bfactor_77_flip.mrc (#9) coordinates: Matrix rotation and translation 1.00000000 0.00001079 -0.00007158 0.01250729 -0.00001078 0.99999999 0.00010843 -0.00778132 0.00007158 -0.00010843 0.99999999 -0.00077511 Axis -0.83170304 -0.54902092 -0.08274110 Axis point 0.00000000 -11.78504258 102.47368213 Rotation angle (degrees) 0.00746999 Shift along axis -0.00606611 > hide #!1 models > show #!2 models > fitmap #2 inMap #9 Fit molecule 6nb1 (#2) to map ClpP_volume_map_1_95A_bfactor_77_flip.mrc (#9) using 21442 atoms average map value = 0.05636, steps = 148 shifted from previous position = 2.24 rotated from previous position = 18.1 degrees atoms outside contour = 7504, contour level = 0.041998 Position of 6nb1 (#2) relative to ClpP_volume_map_1_95A_bfactor_77_flip.mrc (#9) coordinates: Matrix rotation and translation 0.07384522 0.30681292 0.94890079 45.01290705 0.03233871 -0.95173497 0.30521265 140.06556919 0.99674525 0.00814774 -0.08020301 -27.34946097 Axis -0.72939678 -0.11747463 -0.67392881 Axis point 0.00000000 63.01213740 -44.09357674 Rotation angle (degrees) 168.25025544 Shift along axis -30.85483139 > show #!1 models > select add #9 2 models selected > color #9.1 light gray > transparency sel 50 > transparency sel 70 > select #9 2 models selected > select clear > hide #!2 models > color zone #9 near #1 distance 5.04 > transparency #1.2-16#9.1 50 > undo > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > select #1/A:KHS 47 atoms, 48 bonds, 1 residue, 1 model selected > color zone #9 near sel distance 4 color blue Expected a keyword > ui tool show ""Color Zone"" > color zone #9 near #1 distance 5.04 > undo > color zone #9 near sel distance 2 farColor blue > color zone #9 near sel distance 4 farColor blue > color zone #9 near sel distance 4 Color blue Expected a keyword > color zone #9 near sel distance 4 > color zone #9 near sel distance 2 > color zone #9 near sel distance 2 blue Expected a keyword > color zone #9 near sel distance 2 > transparency sel 0 > select add #9 47 atoms, 48 bonds, 1 residue, 4 models selected > transparency sel 0 > transparency sel 50 > select clear > show #!2 models > transparency sel 60 > select add #9 2 models selected > transparency sel 60 > transparency sel 40 > select #9 2 models selected > select #9 2 models selected > select #9 2 models selected > select subtract #9 Nothing selected > lighting simple > lighting soft > lighting full > lighting simple > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > graphics silhouettes false > graphics silhouettes true > save ACP_position.png width 2000 supersample 4 > select #1/A:KHS 47 atoms, 48 bonds, 1 residue, 1 model selected > color (#!1 & sel) byhetero > select #9 2 models selected > select #2/A:KHS 29 atoms, 30 bonds, 1 residue, 1 model selected > color sel byhetero > select add #2 21442 atoms, 20839 bonds, 12 pseudobonds, 3512 residues, 2 models selected > select subtract #2 14 models selected > save ACP_position2.png width 2000 supersample 4 > graphics silhouettes false > graphics silhouettes true > lighting intensity 0.6 > lighting intensity 0.9 > lighting intensity 1.2 > lighting intensity 1.4 > save ACP_position3.png width 2000 supersample 4 > ui tool show ""Color Actions"" > hide #!9 models > select #1/A:KHS 47 atoms, 48 bonds, 1 residue, 1 model selected > select add zone #1/A,B 4.0 Expected an objects specifier or a keyword > select sel @ select sel @ undo > show sel atoms > select add #3 21792 atoms, 20779 bonds, 3899 residues, 20 models selected > select subtract #3 484 atoms, 395 bonds, 91 residues, 31 models selected > select add #4 21978 atoms, 21260 bonds, 3662 residues, 17 models selected > select subtract #4 438 atoms, 359 bonds, 77 residues, 28 models selected > select add #5 25588 atoms, 22371 bonds, 8 pseudobonds, 6318 residues, 15 models selected > select subtract #5 369 atoms, 301 bonds, 59 residues, 38 models selected > select add #6 42216 atoms, 42500 bonds, 14 pseudobonds, 2690 residues, 11 models selected > select subtract #6 244 atoms, 192 bonds, 44 residues, 9 models selected > select add #7 5532 atoms, 5604 bonds, 704 residues, 9 models selected > select subtract #7 230 atoms, 188 bonds, 36 residues, 8 models selected > select add #10 42106 atoms, 42417 bonds, 14 pseudobonds, 2668 residues, 9 models selected > select subtract #10 134 atoms, 109 bonds, 22 residues, 7 models selected > undo > hide sel & #!1-2 atoms > undo > show sel & #!1-2 cartoons > undo > select sel @ select clear > hide #!1-2 atoms > show #!1-2 atoms > undo > hide #!1 models > show #!1 models > hide #!1 models > hide #!2 models > show #!2 models > select #2/A:KHS 29 atoms, 30 bonds, 1 residue, 1 model selected > hide ~sel atoms > show #!1 models > select #1-2/A:KHS 76 atoms, 78 bonds, 2 residues, 2 models selected > show sel atoms > select sel : select add #2 23076 atoms, 22426 bonds, 12 pseudobonds, 3644 residues, 20 models selected > select subtract #2 1634 atoms, 1587 bonds, 132 residues, 30 models selected > select add #3 22802 atoms, 21841 bonds, 3919 residues, 16 models selected > select subtract #3 1494 atoms, 1457 bonds, 111 residues, 27 models selected > select add #4 22886 atoms, 22217 bonds, 3677 residues, 13 models selected > select subtract #4 1346 atoms, 1316 bonds, 92 residues, 24 models selected > select add #5 26394 atoms, 23218 bonds, 8 pseudobonds, 6329 residues, 11 models selected > select subtract #5 1175 atoms, 1148 bonds, 70 residues, 34 models selected > select add #6 42790 atoms, 43103 bonds, 14 pseudobonds, 2697 residues, 7 models selected > select subtract #6 818 atoms, 795 bonds, 51 residues, 5 models selected > select add #7 5993 atoms, 6090 bonds, 705 residues, 5 models selected > select subtract #7 691 atoms, 674 bonds, 37 residues, 4 models selected > select add #10 42294 atoms, 42621 bonds, 14 pseudobonds, 2664 residues, 5 models selected > select subtract #10 322 atoms, 313 bonds, 18 residues, 3 models selected > show sel atoms > select clear > style sel stick Changed 322 atom styles > select clear > undo > hide sel atoms > label (#!1 & sel) text ""{0.name} {0.number}{0.insertion_code}"" > label (#!1 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > label height 0.9 > label height 1.2 > undo > hide sel atoms > label offset 1,1,1 > label offset 1,2,1 > hide sel atoms > label offset 1,0,1 > label offset 0,0,1 > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!9 models > label delete > select clear > save ACP_position4.png width 2000 supersample 4 > hide #!9 models > hide #!2 models > show #!2 models > select #2/A:KHS 29 atoms, 30 bonds, 1 residue, 1 model selected > select #1/A:KHS 47 atoms, 48 bonds, 1 residue, 1 model selected > hide sel atoms > select #2/A:KHS 29 atoms, 30 bonds, 1 residue, 1 model selected > select sel : show sel & #!1-2 atoms > undo > select add #3 22784 atoms, 21818 bonds, 3917 residues, 20 models selected > select subtract #3 1476 atoms, 1434 bonds, 109 residues, 31 models selected > select add #4 22904 atoms, 22231 bonds, 3679 residues, 17 models selected > select subtract #4 1364 atoms, 1330 bonds, 94 residues, 28 models selected > select add #5 26421 atoms, 23240 bonds, 8 pseudobonds, 6333 residues, 15 models selected > select subtract #5 1202 atoms, 1170 bonds, 74 residues, 38 models selected > select add #6 42861 atoms, 43171 bonds, 14 pseudobonds, 2704 residues, 11 models selected > select subtract #6 889 atoms, 863 bonds, 58 residues, 9 models selected > select add #7 6085 atoms, 6177 bonds, 715 residues, 9 models selected > select subtract #7 783 atoms, 761 bonds, 47 residues, 8 models selected > select add #10 42430 atoms, 42751 bonds, 14 pseudobonds, 2677 residues, 9 models selected > select subtract #10 458 atoms, 443 bonds, 31 residues, 7 models selected > show sel atoms > select add #2 21767 atoms, 21157 bonds, 12 pseudobonds, 3528 residues, 8 models selected > select subtract #2 325 atoms, 318 bonds, 16 residues, 18 models selected > select add #1 41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 5 models selected > select subtract #1 15 models selected > undo > select add #2 21767 atoms, 21157 bonds, 12 pseudobonds, 3528 residues, 8 models selected > select subtract #2 325 atoms, 318 bonds, 16 residues, 18 models selected > show sel atoms > select #1/A:KHS 47 atoms, 48 bonds, 1 residue, 1 model selected > hide sel atoms > undo > label (#!1 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > label height 1.2 > save ACP_pos_exp.png width 2000 supersample 4 > select clear > save ACP_pos_exp.png width 2000 supersample 4 > label delete > select add #1 41972 atoms, 42308 bonds, 14 pseudobonds, 2646 residues, 2 models selected > select subtract #1 15 models selected > show #!1-2 atoms > undo > select #1/A:KHS 47 atoms, 48 bonds, 1 residue, 1 model selected > show sel atoms > select #2/A:KHS 29 atoms, 30 bonds, 1 residue, 1 model selected > hide sel atoms > select #1/A:KHS 47 atoms, 48 bonds, 1 residue, 1 model selected > select sel : label (#!1-2 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > label height 1.2 > select clear > save ACP_pos_exp2.png width 2000 supersample 4 > label delete > select #1/A:KHS 47 atoms, 48 bonds, 1 residue, 1 model selected > view sel > select clear > select add #2 21442 atoms, 20839 bonds, 12 pseudobonds, 3512 residues, 2 models selected > select subtract #2 14 models selected > select #1/A:KHS 47 atoms, 48 bonds, 1 residue, 1 model selected > select sel : select add #3 22538 atoms, 21591 bonds, 3898 residues, 19 models selected > select subtract #3 1230 atoms, 1207 bonds, 90 residues, 30 models selected > select add #2 22569 atoms, 21944 bonds, 12 pseudobonds, 3594 residues, 17 models selected > select subtract #2 1127 atoms, 1105 bonds, 82 residues, 27 models selected > select add #4 22552 atoms, 21893 bonds, 3653 residues, 13 models selected > select subtract #4 1012 atoms, 992 bonds, 68 residues, 24 models selected > select add #5 26091 atoms, 22923 bonds, 8 pseudobonds, 6309 residues, 11 models selected > select subtract #5 872 atoms, 853 bonds, 50 residues, 34 models selected > select add #6 42561 atoms, 42880 bonds, 14 pseudobonds, 2681 residues, 7 models selected > select subtract #6 589 atoms, 572 bonds, 35 residues, 5 models selected > select add #7 5817 atoms, 5918 bonds, 695 residues, 5 models selected > select subtract #7 515 atoms, 502 bonds, 27 residues, 4 models selected > select add #10 42206 atoms, 42535 bonds, 14 pseudobonds, 2659 residues, 5 models selected > select subtract #10 234 atoms, 227 bonds, 13 residues, 3 models selected > select sticks Expected an objects specifier or a keyword > style sel stick Changed 234 atom styles > style sel stick Changed 234 atom styles > show sel atoms > select clear > undo > hide ~sel cartoons > graphics silhouettes false > graphics silhouettes true > lighting shadows true > lighting shadows false > lighting full > lighting soft > lighting simple > clip off > clip on Expected a keyword > clip far Missing ""far"" keyword's argument > clip #1 far Expected a keyword > clip model #1 far Expected true or false or a keyword > clip model #1 true > hide ~sel cartoons > label (#!1 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > label delete > select clear > select #1/A:KHS 47 atoms, 48 bonds, 1 residue, 1 model selected > select sel : color (#!1-2 & sel) byhetero > select clear > undo > select clear > clip list Clipping is off > clip near on Invalid ""near"" argument: Expected 'off' or a number > clip far on #1 Invalid ""far"" argument: Expected 'off' or a number > clip model #1 true > clip model #1 false > clip front Missing ""front"" keyword's argument > clip on Expected a keyword > ui tool show ""Side View"" > hide H > label #1.2-16#2.2-15#!1-2 text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > label delete > save ACP_compare1.png width 2000 supersample 4 > select #1/A:KHS 47 atoms, 48 bonds, 1 residue, 1 model selected > select sel : label (#!1-2 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > select clear > save ACP_compare2.png width 2000 supersample 4 > label offset 1,1,1 > label offset 0.5,1,1 > label offset 0.5,0.5,1 > label offset 0.5,0.5,0.5 > label offset 0.5,0.5,1 > label offset 0.5,0.7,1 > label offset 0.5,0.5,1 > label offset 0.6,0.5,1 > label offset 0.5,0.5,1 > save ACP_compare2.png width 2000 supersample 4 > select #1/A:KHS 47 atoms, 48 bonds, 1 residue, 1 model selected > select sel : color (#!1-2 & sel) byhetero > select clear > save ACP_compare2.png width 2000 supersample 4 > label delete > save ACP_compare1.png width 2000 supersample 4 > select #1/A:KHS 47 atoms, 48 bonds, 1 residue, 1 model selected > select sel : label (#!1-2 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > label offset 0.5,0.5,1 > label offset 1,0.5,1 > label offset 0,0.5,1 > label offset 0.2,0.5,1 > label offset 0.2,0,1 > label offset 0.2,0.4,1 > label offset 0.4,0.4,1 > label offset 0.4,0.2,1 > label offset 0.5,0.2,1 > label offset 0.4,0.2,1 > select clear > label offset 0.5,0.2,1 > label offset 0.3,0.2,1 > label offset 0.4,0.2,1 > label offset 0.4,0.4,1 > label offset 0.4,0.3,1 > label offset 0.5,0.3,1 > select clear > label offset 0.6,0.3,1 > save ACP_compare2.png width 2000 supersample 4 > select #1/A:KHS 47 atoms, 48 bonds, 1 residue, 1 model selected > select sel : select clear > label delete > save ACP_compare1.png width 2000 supersample 4 > select #1/A:KHS 47 atoms, 48 bonds, 1 residue, 1 model selected > hbonds sel restrict both reveal true color yellow linewidth 3 log true > dashes 8 dashesScale 0.5 label true labelColor white labelSize 1.2 Expected a keyword > ui tool show H-Bonds > hbonds sel color #fad439 dashes 4 showDist true restrict both interModel > false intraMol false intraRes false reveal true 0 hydrogen bonds found > hbonds sel color #fad439 dashes 4 showDist true restrict both interModel > false saltOnly true intraMol false intraRes false reveal true 0 hydrogen bonds found > hbonds sel color #fad439 dashes 4 showDist true interModel false intraMol > false intraRes false reveal true 0 hydrogen bonds found > hbonds sel color #fad439 dashes 4 showDist true interModel false distSlop > 0.5 intraMol false intraRes false reveal true 0 hydrogen bonds found > hbonds sel restrict both reveal true color yellow linewidth 3 log true > dashes 8 dashesScale 0.5 label true labelColor white labelSize 1.2 Expected a keyword > hbonds sel restrict both reveal true color yellow dashes 8 0 hydrogen bonds found > hbonds #1 & sel restrict both color yellow dashes 8 0 hydrogen bonds found > hbonds #1 & sel restrict both reveal true color yellow dashes 8 interModel > false distSlop 0.4 angleSlop 30 0 hydrogen bonds found > hbonds sel color #fad439 dashes 4 showDist true interModel false distSlop > 0.5 intraMol false intraRes false reveal true 0 hydrogen bonds found > hbonds sel color #fad439 dashes 4 showDist true interModel false distSlop > 0.5 intraMol false intraRes false reveal true 0 hydrogen bonds found > hbonds sel color #fad439 dashes 4 showDist true interModel false distSlop > 0.5 intraMol false intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.5 angstroms and 20 degrees Models used: 1 16Mar26_flip_KHS_QMR_refined.pdb 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > hbonds sel color #fad439 dashes 4 showDist true intraModel false distSlop > 0.5 intraMol false intraRes false reveal true log true Finding intermodel H-bonds Constraints relaxed by 0.5 angstroms and 20 degrees Models used: 1 16Mar26_flip_KHS_QMR_refined.pdb 2 6nb1 3 1tyf 4 1yg6 5 3mt6 7 clpP_DHFR_PRBC_frank.pdb 6 28Mar_Final_shift_asym.pdb 10 28Mar_flip_KHS_QMR_refined.pdb 4 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 NAS 3mt6 #5/E ILE 188 O 16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 H9 1.920 1.022 1tyf #3/J HOH 249 O 16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAK no hydrogen 3.078 N/A 1tyf #3/J HOH 249 O 16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAR no hydrogen 2.811 N/A 1tyf #3/J HOH 266 O 16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAK no hydrogen 3.205 N/A 4 hydrogen bonds found > select add #8.1 47 atoms, 48 bonds, 1 residue, 3 models selected > select subtract #8.1 47 atoms, 48 bonds, 1 residue, 2 models selected > close #8 > hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel > false intraModel false distSlop 0.5 intraMol false intraRes false reveal > true log true Constraints relaxed by 0.5 angstroms and 20 degrees Models used: 1 16Mar26_flip_KHS_QMR_refined.pdb 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel > false intraModel false distSlop 0.5 saltOnly true intraMol false intraRes > false reveal true log true Constraints relaxed by 0.5 angstroms and 20 degrees Models used: 1 16Mar26_flip_KHS_QMR_refined.pdb 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel > false distSlop 0.5 intraMol false intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.5 angstroms and 20 degrees Models used: 1 16Mar26_flip_KHS_QMR_refined.pdb 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel > false intraModel false distSlop 0.6 angleSlop 40.0 intraMol false intraRes > false reveal true log true Constraints relaxed by 0.6 angstroms and 40 degrees Models used: 1 16Mar26_flip_KHS_QMR_refined.pdb 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel > false intraModel false distSlop 0.9 angleSlop 40.0 intraMol false intraRes > false reveal true log true Constraints relaxed by 0.9 angstroms and 40 degrees Models used: 1 16Mar26_flip_KHS_QMR_refined.pdb 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel > false angleSlop 40.0 intraMol false intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 40 degrees Models used: 1 16Mar26_flip_KHS_QMR_refined.pdb 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 NH1 16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAK 16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 HH11 3.355 2.883 1 hydrogen bonds found > ~label hbond > label delete hbond Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a keyword > label delete > ~hbonds > hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel > false intraMol false intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 16Mar26_flip_KHS_QMR_refined.pdb 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel > false saltOnly true intraMol false intraRes false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 16Mar26_flip_KHS_QMR_refined.pdb 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel > false angleSlop 30.0 saltOnly true intraMol false intraRes false reveal true > log true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 30 degrees Models used: 1 16Mar26_flip_KHS_QMR_refined.pdb 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel > false angleSlop 40.0 saltOnly true intraMol false intraRes false reveal true > log true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 40 degrees Models used: 1 16Mar26_flip_KHS_QMR_refined.pdb 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 NH1 16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAK 16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 HH11 3.355 2.883 1 hydrogen bonds found > hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel > false distSlop 0.5 angleSlop 40.0 saltOnly true intraMol false intraRes > false reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.5 angstroms and 40 degrees Models used: 1 16Mar26_flip_KHS_QMR_refined.pdb 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 NH1 16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAK 16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 HH11 3.355 2.883 1 hydrogen bonds found > hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel > false distSlop 0.5 angleSlop 40.0 saltOnly true intraRes false reveal true > log true Finding intramodel H-bonds Constraints relaxed by 0.5 angstroms and 40 degrees Models used: 1 16Mar26_flip_KHS_QMR_refined.pdb 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 NH1 16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAK 16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 HH11 3.355 2.883 1 hydrogen bonds found > hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel > false angleSlop 40.0 saltOnly true intraMol false intraRes false reveal true > log true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 40 degrees Models used: 1 16Mar26_flip_KHS_QMR_refined.pdb 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 NH1 16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAK 16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 HH11 3.355 2.883 1 hydrogen bonds found > label hbond color black Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a keyword > label pseudobonds color black height 1.2 > label pseudobonds color black height 0.5 > select clear > label pseudobonds offset 0,0.5,0 > label pseudobonds offset 0,0.4,0 > label pseudobonds offset 0,0.9,0 > label pseudobonds offset 0,0.1,0 > label pseudobonds offset 0.5,0.1,0 > label pseudobonds offset -0.5,0.1,0 > label pseudobonds offset -0.5,-0.4,0 > label pseudobonds offset -0.7,-0.4,0 > label pseudobonds offset -0.7,-0.9,0 > label pseudobonds offset -0.9,-0.9,0 > label pseudobonds offset -1.2,-0.9,0 > label pseudobonds offset -1.2,-0.9,0.5 > label pseudobonds text {dist:.2f} > undo > hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel > false angleSlop 40.0 saltOnly true intraMol false intraRes false reveal true > log true Atom specifier selects no atoms > select #1/A:KHS 47 atoms, 48 bonds, 1 residue, 1 model selected > hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel > false angleSlop 40.0 saltOnly true intraMol false intraRes false reveal true > log true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 40 degrees Models used: 1 16Mar26_flip_KHS_QMR_refined.pdb 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 NH1 16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAK 16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 HH11 3.355 2.883 1 hydrogen bonds found > label pseudobonds text @length format %.2f Expected a keyword > label pseudobonds text {0.length:.2f} > hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel > false angleSlop 40.0 saltOnly true intraMol false intraRes false reveal true > log true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 40 degrees Models used: 1 16Mar26_flip_KHS_QMR_refined.pdb 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 NH1 16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAK 16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 HH11 3.355 2.883 1 hydrogen bonds found > label pseudobonds text ""{0.length:.2f} Å"" > label pseudobonds color black height 0.5 > label pseudobonds offset -1.2,-0.9,0.5 > label pseudobonds color grey > select clear > label pseudobonds text ""{0.length:.1f} Å"" > label pseudobonds offset -1.1,-0.9,0.5 > label pseudobonds offset -1.1,-0.7,0.5 > select #1/A:206@HH12 1 atom, 1 residue, 1 model selected > select up 24 atoms, 23 bonds, 1 residue, 2 models selected > label (#!1 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > label offset 0.6,0.3,1 > label delete > hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel > false angleSlop 40.0 saltOnly true intraMol false intraRes false reveal true > log true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 40 degrees Models used: 1 16Mar26_flip_KHS_QMR_refined.pdb 0 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 0 hydrogen bonds found > select clear > select #1/A:KHS 47 atoms, 48 bonds, 1 residue, 1 model selected > hbonds sel color #fad439 dashes 4 showDist true restrict cross interModel > false angleSlop 40.0 saltOnly true intraMol false intraRes false reveal true > log true Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 40 degrees Models used: 1 16Mar26_flip_KHS_QMR_refined.pdb 1 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 NH1 16Mar26_flip_KHS_QMR_refined.pdb #1/A KHS 301 OAK 16Mar26_flip_KHS_QMR_refined.pdb #1/A ARG 206 HH11 3.355 2.883 1 hydrogen bonds found > label pseudobonds text ""{0.length:.1f} Å"" > label pseudobonds offset -1.1,-0.7,0.5 > label pseudobonds color grey height 0.5 > select #1/A:206@HH12 1 atom, 1 residue, 1 model selected > select up 24 atoms, 23 bonds, 1 residue, 2 models selected > label (#!1 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > label residues offset 0.6,0.3,1 > select clear > save ACP_hbond.png width 2000 supersample 4 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.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: Mac15,12 Model Number: MXCV3ZE/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 13822.81.10 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.7.4 (24G517) Kernel Version: Darwin 24.6.0 Time since boot: 42 days, 12 hours, 9 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal P34w-20: Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD) UI Looks like: 3440 x 1440 @ 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 autocommand: 2.2.2 babel: 2.16.0 backports.tarfile: 1.2.0 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-Clipper: 0.24.0 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-ISOLDE: 1.9 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 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 7.3.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 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 MolecularDynamicsViewer: 1.6 more-itertools: 10.3.0 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 ordered-set: 4.1.0 packaging: 23.2 packaging: 24.1 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 platformdirs: 4.2.2 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 tomli: 2.0.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 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: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect assigned normal Window Toolkit all ChimeraX