id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20823 ChimeraX bug report submission a.fasemire@… "{{{ 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. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000000032337f000 (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 0x0000000322373000 (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 ""/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 0x0000000321367000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers 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 0x000000032035b000 (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 0x000000031f34f000 (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 0x000000031e343000 (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 0x000000031d337000 (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 0x000000031c32b000 (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 0x000000031b31f000 (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 0x000000031a313000 (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 0x0000000319307000 (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 Current thread 0x00000001eeb8a240 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, 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1140 \n__TEXT (graphics) 174.0M 18 \n__TPRO_CONST 128K 2 \ndyld private memory 6832K 54 \nmapped file 296.8M 62 \npage table in kernel 2554K 1 \nshared memory 3248K 29 \n=========== ======= ======= \nTOTAL 6.4G 6651 \nTOTAL, minus reserved VM space 6.3G 6651 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""7f18681fe10237c494a103e6392bb9f9d5dd251d"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""63f9578e238e7b23a1f3030a"", ""factorPackIds"" : { }, ""deploymentId"" : 240000005 }, { ""rolloutId"" : ""65a8173205d942272410674b"", ""factorPackIds"" : { ""SIRI_HOME_AUTOMATION_SERVER_FLOW_DEPRECATION"" : ""65d39fa4cb0e2417d11ce5f6"" }, ""deploymentId"" : 240000001 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 7XBZ Summary of feedback from opening 7XBZ fetched from pdb --- notes | Fetching compressed mmCIF 7xbz from http://files.rcsb.org/download/7xbz.cif Fetching CCD D4E from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/D4E/D4E.cif 7xbz title: Crystal structure of Staphylococcus aureus ClpP in complex with R-ZG197 [more info...] Chain information for 7xbz #1 --- Chain | Description | UniProt A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | A0A0D1I3W4_STAAU 1-195 Non-standard residues in 7xbz #1 --- D4E — (6S,9aS)-6-[(2S)-butan-2-yl]-8-[(1R)-1-naphthalen-1-ylethyl]-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide MG — magnesium ion MPD — (4S)-2-methyl-2,4-pentanediol 49 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > set bgColor white > open 7WGS Summary of feedback from opening 7WGS fetched from pdb --- notes | Fetching compressed mmCIF 7wgs from http://files.rcsb.org/download/7wgs.cif Fetching CCD 9A2 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/2/9A2/9A2.cif 7wgs title: Structure of ClpP from Staphylococcus aureus in complex with (S)-ZG197 [more info...] Chain information for 7wgs #2 --- Chain | Description | UniProt A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | A0A0D1I3W4_STAAU 1-195 Non-standard residues in 7wgs #2 --- 9A2 — (6S,9aS)-6-[(2R)-butan-2-yl]-8-[(1S)-1-naphthalen-1-ylethyl]-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide MPD — (4S)-2-methyl-2,4-pentanediol > open ""/Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic > Models/Pdb/D7_deposition/D7_model2.deposit_000.cif"" Summary of feedback from opening /Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic Models/Pdb/D7_deposition/D7_model2.deposit_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' on line 359 Skipping entity category: Missing column 'type' on line 42418 Missing entity information. Treating each chain as a separate entity. Invalid sheet range for struct_sheet_range ""B 5"" on line 223 Invalid sheet range for struct_sheet_range ""D 1"": invalid entity ""B"", on line 227 Invalid sheet range for struct_sheet_range ""D 2"": invalid entity ""B"", on line 228 Invalid sheet range for struct_sheet_range ""E 1"": invalid entity ""B"", on line 229 Invalid sheet range for struct_sheet_range ""E 2"": invalid entity ""B"", on line 230 72 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Skipping chem_comp category: Missing column 'type' on line 43004 Chain information for D7_model2.deposit_000.cif #3 --- Chain | Description A B C D E F G H I J K L M N | No description available > ui tool show Matchmaker > matchmaker #!1-2 to #3 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 D7_model2.deposit_000.cif, chain A (#3) with 7xbz, chain B (#1), sequence alignment score = 737.9 RMSD between 181 pruned atom pairs is 0.724 angstroms; (across all 186 pairs: 0.828) Matchmaker D7_model2.deposit_000.cif, chain A (#3) with 7wgs, chain H (#2), sequence alignment score = 739.1 RMSD between 185 pruned atom pairs is 0.726 angstroms; (across all 187 pairs: 0.875) > matchmaker #!1-2 to #3 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 D7_model2.deposit_000.cif, chain A (#3) with 7xbz, chain B (#1), sequence alignment score = 737.9 RMSD between 181 pruned atom pairs is 0.724 angstroms; (across all 186 pairs: 0.828) Matchmaker D7_model2.deposit_000.cif, chain A (#3) with 7wgs, chain H (#2), sequence alignment score = 739.1 RMSD between 185 pruned atom pairs is 0.726 angstroms; (across all 187 pairs: 0.875) > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TYR""::name=""VAL"" 80180 atoms, 81002 bonds, 41 pseudobonds, 7731 residues, 6 models selected > hide sel atoms > show sel cartoons > select ::name=""HOH"" 1230 atoms, 1230 residues, 2 models selected > delete atoms sel > delete bonds sel > select ::name=""KHS"" 658 atoms, 672 bonds, 14 residues, 1 model selected > hide sel > select add #3 42014 atoms, 42350 bonds, 14 pseudobonds, 2646 residues, 2 models selected > select subtract #3 Nothing selected > hide #!1 models > hide #!2 models > show #!2 models > show #!1 models > hide #!2 models > show #!2 models > ui tool show Matchmaker > matchmaker #!1-2 to #3 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 D7_model2.deposit_000.cif, chain A (#3) with 7xbz, chain B (#1), sequence alignment score = 737.9 RMSD between 181 pruned atom pairs is 0.724 angstroms; (across all 186 pairs: 0.828) Matchmaker D7_model2.deposit_000.cif, chain A (#3) with 7wgs, chain H (#2), sequence alignment score = 739.1 RMSD between 185 pruned atom pairs is 0.726 angstroms; (across all 187 pairs: 0.875) > matchmaker #!1-2 to #3 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 D7_model2.deposit_000.cif, chain A (#3) with 7xbz, chain B (#1), sequence alignment score = 737.9 RMSD between 181 pruned atom pairs is 0.724 angstroms; (across all 186 pairs: 0.828) Matchmaker D7_model2.deposit_000.cif, chain A (#3) with 7wgs, chain H (#2), sequence alignment score = 739.1 RMSD between 185 pruned atom pairs is 0.726 angstroms; (across all 187 pairs: 0.875) > select add #1 19894 atoms, 20150 bonds, 38 pseudobonds, 2581 residues, 3 models selected > ui tool show ""Color Actions"" > color sel deep sky blue > color sel byhetero > select subtract #1 Nothing selected > select add #2 20170 atoms, 20450 bonds, 13 pseudobonds, 2586 residues, 2 models selected > ui tool show ""Color Actions"" > color sel thistle > color sel byhetero > select add #1 40064 atoms, 40600 bonds, 51 pseudobonds, 5167 residues, 5 models selected > select subtract #1 20170 atoms, 20450 bonds, 13 pseudobonds, 2586 residues, 2 models selected > select subtract #2 Nothing selected > select add #3 42014 atoms, 42350 bonds, 14 pseudobonds, 2646 residues, 2 models selected > ui tool show ""Color Actions"" > color sel tan > color sel burly wood > color sel tan > select clear > select #2/G:9A2 38 atoms, 41 bonds, 1 residue, 1 model selected > select #1/G:34 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/G:9A2, #1/M:D4E Expected an objects specifier or a keyword > select #2/G:9A2, #1/M:D4E Expected an objects specifier or a keyword > select #2/G:9A2, #1/M:D4E Expected an objects specifier or a keyword > select #2/G:9A2 38 atoms, 41 bonds, 1 residue, 1 model selected > select add #1/M:D4E 76 atoms, 82 bonds, 2 residues, 2 models selected > select sel : undo > select sel : hide ~sel cartoons, atoms > show sel atoms > style sel stick Changed 1036 atom styles > select @H* 21014 atoms, 2646 residues, 1 model selected > hide sel > select #3/M:301@FAD 1 atom, 1 residue, 1 model selected > select up 47 atoms, 48 bonds, 1 residue, 1 model selected > hide sel > select #2/G:9A2 38 atoms, 41 bonds, 1 residue, 1 model selected > select #2/G:9A2 38 atoms, 41 bonds, 1 residue, 1 model selected > hide ~sel & #1 cartoons, atoms > select add #1/M:D4E 76 atoms, 82 bonds, 2 residues, 2 models selected > hide ~sel & #1 cartoons, atoms > hide ~sel & #2 cartoons, atoms > select clear > select #3/M:106 17 atoms, 16 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select #3/M:125 24 atoms, 23 bonds, 1 residue, 1 model selected > select up 2954 atoms, 2977 bonds, 188 residues, 1 model selected > select down 24 atoms, 23 bonds, 1 residue, 1 model selected > hide sel atoms > select up 2954 atoms, 2977 bonds, 188 residues, 1 model selected > select down 24 atoms, 23 bonds, 1 residue, 1 model selected > select #3/M:124 22 atoms, 21 bonds, 1 residue, 1 model selected > hide sel atoms > select #3/M:126 20 atoms, 20 bonds, 1 residue, 1 model selected > hide sel atoms > select #3/M:37 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 2954 atoms, 2977 bonds, 188 residues, 1 model selected > select down 19 atoms, 18 bonds, 1 residue, 1 model selected > hide sel atoms > select #3/M:36 24 atoms, 23 bonds, 1 residue, 1 model selected > hide sel atoms > select #3/M:41 24 atoms, 23 bonds, 1 residue, 1 model selected > hide sel atoms > select #3/M:43 19 atoms, 18 bonds, 1 residue, 1 model selected > hide sel atoms > select #3/M:44 20 atoms, 20 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select #3/M:203 19 atoms, 18 bonds, 1 residue, 1 model selected > select clear > select #3/M:203 19 atoms, 18 bonds, 1 residue, 1 model selected > hide sel > hide sel cartoons > select #3/M:126 20 atoms, 20 bonds, 1 residue, 1 model selected > select up 2954 atoms, 2977 bonds, 188 residues, 1 model selected > select down 20 atoms, 20 bonds, 1 residue, 1 model selected > hide sel cartoons > select #3/M:125 24 atoms, 23 bonds, 1 residue, 1 model selected > hide sel cartoons > select #3/M:124 22 atoms, 21 bonds, 1 residue, 1 model selected > hide sel cartoons > select #3/L:66 10 atoms, 9 bonds, 1 residue, 1 model selected > hide sel cartoons > hide sel atoms > lighting simple > select #2/G:201@C38 1 atom, 1 residue, 1 model selected > select #2/G:201@C38 1 atom, 1 residue, 1 model selected > select #2/G:201@C38 1 atom, 1 residue, 1 model selected > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 38 atoms, 41 bonds, 1 residue, 1 model selected > hide sel atoms > select #3/M:40@CD 1 atom, 1 residue, 1 model selected > select #3/M:40 15 atoms, 14 bonds, 1 residue, 1 model selected > transparency sel 50 cartoons, atoms > select #3/M:42 16 atoms, 15 bonds, 1 residue, 1 model selected > transparency sel 50 cartoons, atoms > select #3/M:41 24 atoms, 23 bonds, 1 residue, 1 model selected > transparency sel 50 cartoons, atoms > select #3/M:73 19 atoms, 18 bonds, 1 residue, 1 model selected > transparency sel 50 cartoons, atoms > select #3/M:72 12 atoms, 11 bonds, 1 residue, 1 model selected > transparency sel 50 cartoons, atoms > select #3/M:75@CA 1 atom, 1 residue, 1 model selected > transparency sel 50 cartoons, atoms > select clear > select #3/M:206@CD 1 atom, 1 residue, 1 model selected > select #3/M:206@CA 1 atom, 1 residue, 1 model selected > select #3/M:206 24 atoms, 23 bonds, 1 residue, 1 model selected > transparency sel 50 cartoons, atoms > transparency sel 70 cartoons, atoms > select #3/M:104 19 atoms, 18 bonds, 1 residue, 1 model selected > transparency sel 70 cartoons, atoms > select #3/M:103 14 atoms, 13 bonds, 1 residue, 1 model selected > transparency sel 70 cartoons, atoms > select #3/M:102 11 atoms, 10 bonds, 1 residue, 1 model selected > transparency sel 70 cartoons, atoms > select #3/M:101 16 atoms, 15 bonds, 1 residue, 1 model selected > transparency sel 70 cartoons, atoms > select #3/M:75 19 atoms, 18 bonds, 1 residue, 1 model selected > transparency sel 70 cartoons, atoms > select #3/M:43 19 atoms, 18 bonds, 1 residue, 1 model selected > select #3/M:42 16 atoms, 15 bonds, 1 residue, 1 model selected > transparency sel 70 cartoons, atoms > select #3/M:43 19 atoms, 18 bonds, 1 residue, 1 model selected > transparency sel 70 cartoons, atoms > select #3/M:44 20 atoms, 20 bonds, 1 residue, 1 model selected > transparency sel 70 cartoons, atoms > select clear > select #3/L:62 19 atoms, 18 bonds, 1 residue, 1 model selected > transparency sel 70 cartoons, atoms > select clear > select #3/L:62 19 atoms, 18 bonds, 1 residue, 1 model selected > transparency sel 0 cartoons, atoms > select clear > cd ""/Users/ayomidefasemire/Documents/Doctoral/Main Project/ZG_ProBac"" Current working directory is: /Users/ayomidefasemire/Documents/Doctoral/Main Project/ZG_ProBac > save tyr76_Rzg197_clash1.png width 4000 supersample 4 > open spin_movie.cxc > movie record size 3840,2160 > turn y 2 180 > wait 180 > movie stop > movie encode output my_movie.mp4 quality highest Movie saved to my_movie.mp4 executed spin_movie.cxc > open spin_movie.cxc > movie record size 3840,2160 > turn y 2 180 > wait 180 > movie stop > movie encode output my_movie.mp4 quality highest Movie saved to my_movie.mp4 executed spin_movie.cxc > select #2/G:9A2 38 atoms, 41 bonds, 1 residue, 1 model selected > show sel atoms > select add #1/M:D4E 76 atoms, 82 bonds, 2 residues, 2 models selected > hide sel atoms > undo > select #1/M:D4E 38 atoms, 41 bonds, 1 residue, 1 model selected > hide sel atoms > select #3/M:104 19 atoms, 18 bonds, 1 residue, 1 model selected > transparency sel 0 cartoons, atoms > select #3/M:103 14 atoms, 13 bonds, 1 residue, 1 model selected > transparency sel 0 cartoons, atoms > select #3/M:102 11 atoms, 10 bonds, 1 residue, 1 model selected > transparency sel 0 cartoons, atoms > select #3/M:101 16 atoms, 15 bonds, 1 residue, 1 model selected > transparency sel 0 cartoons, atoms > select clear > select #3/M:73 19 atoms, 18 bonds, 1 residue, 1 model selected > hide sel atoms > select #3/M:72 12 atoms, 11 bonds, 1 residue, 1 model selected > hide sel atoms > select #3/M:73 19 atoms, 18 bonds, 1 residue, 1 model selected > transparency sel 0 cartoons, atoms > select #3/M:72 12 atoms, 11 bonds, 1 residue, 1 model selected > transparency sel 0 cartoons, atoms > select clear > select #3/M:75 19 atoms, 18 bonds, 1 residue, 1 model selected > transparency sel 0 cartoons, atoms > select clear > select #3/M:206 24 atoms, 23 bonds, 1 residue, 1 model selected > transparency sel 0 cartoons, atoms > select clear > select #3/M:40 15 atoms, 14 bonds, 1 residue, 1 model selected > transparency sel 0 cartoons, atoms > select clear > save S_zg197.png width 4000 supersample 4 > open spin_movie.cxc > movie record size 3840,2160 > turn y 2 180 > wait 180 > movie stop > movie encode output my_movie.mp4 quality highest Movie saved to my_movie.mp4 executed spin_movie.cxc > select #1/M:D4E 38 atoms, 41 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #3/M:206@CA 1 atom, 1 residue, 1 model selected > select #3/M:206@CA 1 atom, 1 residue, 1 model selected > select #3/M:206@CA 1 atom, 1 residue, 1 model selected > select #3/M:206 24 atoms, 23 bonds, 1 residue, 1 model selected > transparency sel 50 cartoons, atoms > select clear > select #3/M:104 19 atoms, 18 bonds, 1 residue, 1 model selected > transparency sel 70 cartoons, atoms > select clear > select #3/L:96 20 atoms, 20 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select #3/M:206 24 atoms, 23 bonds, 1 residue, 1 model selected > transparency sel 0 cartoons, atoms > hide sel atoms > save S_R_zg197.png width 4000 supersample 4 > open spin_movie.cxc > movie record size 3840,2160 > turn y 2 180 > wait 180 > movie stop > movie encode output my_movie.mp4 quality highest Movie saved to my_movie.mp4 executed spin_movie.cxc > save ""/Users/ayomidefasemire/Documents/Doctoral/Main > Project/ZG_ProBac/ZG197_EcClpP_compare.cxs"" > select clear > close #1-3 > open 7XBZ 7xbz title: Crystal structure of Staphylococcus aureus ClpP in complex with R-ZG197 [more info...] Chain information for 7xbz #1 --- Chain | Description | UniProt A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | A0A0D1I3W4_STAAU 1-195 Non-standard residues in 7xbz #1 --- D4E — (6S,9aS)-6-[(2S)-butan-2-yl]-8-[(1R)-1-naphthalen-1-ylethyl]-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide MG — magnesium ion MPD — (4S)-2-methyl-2,4-pentanediol 49 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 7WGS 7wgs title: Structure of ClpP from Staphylococcus aureus in complex with (S)-ZG197 [more info...] Chain information for 7wgs #2 --- Chain | Description | UniProt A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | A0A0D1I3W4_STAAU 1-195 Non-standard residues in 7wgs #2 --- 9A2 — (6S,9aS)-6-[(2R)-butan-2-yl]-8-[(1S)-1-naphthalen-1-ylethyl]-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide MPD — (4S)-2-methyl-2,4-pentanediol > hide #!1 models > show #!1 models > open 6tty Summary of feedback from opening 6tty fetched from pdb --- note | Fetching compressed mmCIF 6tty from http://files.rcsb.org/download/6tty.cif 6tty title: Structure of ClpP from Staphylococcus aureus (apo, closed state) [more info...] Chain information for 6tty #3 --- Chain | Description | UniProt A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | A0A077UUA2_STAAU 1-195 70 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > ui tool show Matchmaker > matchmaker #!1-2 to #3 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 6tty, chain E (#3) with 7xbz, chain H (#1), sequence alignment score = 980.2 RMSD between 185 pruned atom pairs is 0.407 angstroms; (across all 185 pairs: 0.407) Matchmaker 6tty, chain E (#3) with 7wgs, chain B (#2), sequence alignment score = 980.2 RMSD between 184 pruned atom pairs is 0.477 angstroms; (across all 185 pairs: 0.507) > matchmaker #!1-2 to #3 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 6tty, chain E (#3) with 7xbz, chain H (#1), sequence alignment score = 980.2 RMSD between 185 pruned atom pairs is 0.407 angstroms; (across all 185 pairs: 0.407) Matchmaker 6tty, chain E (#3) with 7wgs, chain B (#2), sequence alignment score = 980.2 RMSD between 184 pruned atom pairs is 0.477 angstroms; (across all 185 pairs: 0.507) > select ::name=""HOH"" 3203 atoms, 3203 residues, 3 models selected > delete atoms sel > delete bonds sel > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 59427 atoms, 60200 bonds, 31 pseudobonds, 7765 residues, 6 models selected > hide sel atoms > show sel cartoons > select clear > select add #3 20603 atoms, 20876 bonds, 4 pseudobonds, 2666 residues, 2 models selected > ui tool show ""Color Actions"" > color sel tan > select clear > select add #2 20170 atoms, 20450 bonds, 13 pseudobonds, 2586 residues, 2 models selected > ui tool show ""Color Actions"" > color sel thistle > select add #1 40064 atoms, 40600 bonds, 51 pseudobonds, 5167 residues, 5 models selected > select subtract #2 19894 atoms, 20150 bonds, 38 pseudobonds, 2581 residues, 3 models selected > ui tool show ""Color Actions"" > color sel light sky blue > color sel byhetero > select subtract #1 Nothing selected > select add #2 20170 atoms, 20450 bonds, 13 pseudobonds, 2586 residues, 2 models selected > color (#!2 & sel) byhetero > select clear > select #1/E:D4E 76 atoms, 82 bonds, 2 residues, 1 model selected > select add #2/K:9A2 114 atoms, 123 bonds, 3 residues, 2 models selected > select sel : select clear > select #1/E:D4E 76 atoms, 82 bonds, 2 residues, 1 model selected > select add #2/K:9A2 114 atoms, 123 bonds, 3 residues, 2 models selected > select #1/I:99 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/E:201@F41 1 atom, 1 residue, 1 model selected > select up 38 atoms, 41 bonds, 1 residue, 1 model selected > select add #2/K:9A2 76 atoms, 82 bonds, 2 residues, 2 models selected > select sel : select sel : hide ~sel cartoons, atoms > select clear Drag select of 76 atoms, 77 residues, 82 bonds > show sel atoms > style sel stick Changed 734 atom styles > select clear > undo > select clear > select #2/K:63 12 atoms, 12 bonds, 1 residue, 1 model selected > select #3/K:63 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 12 atom styles > select #2/K:63 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 12 atom styles > select #1/E:63 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 12 atom styles > select clear > open spin_movie.cxc > movie record size 3840,2160 > turn y 2 180 > wait 180 > movie stop > movie encode output my_movie.mp4 quality highest Movie saved to my_movie.mp4 executed spin_movie.cxc > lighting simple > open spin_movie.cxc > movie record size 3840,2160 > turn y 2 180 > wait 180 > movie stop > movie encode output my_movie.mp4 quality highest Movie saved to my_movie.mp4 executed spin_movie.cxc > lighting full > lighting soft > lighting simple > lighting shadows true > lighting shadows false > lighting full > lighting flat > lighting full > lighting simple > lighting shadows true > lighting shadows false > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > select #2/J:52 9 atoms, 8 bonds, 1 residue, 1 model selected Drag select of 13 residues > hide sel cartoons > select clear Drag select of 3 residues > hide sel cartoons Drag select of 4 residues > hide sel cartoons > save apo_zg197.png width 4000 supersample 4 > select #2/K:30 8 atoms, 7 bonds, 1 residue, 1 model selected > open 6tty 6tty title: Structure of ClpP from Staphylococcus aureus (apo, closed state) [more info...] Chain information for 6tty #4 --- Chain | Description | UniProt A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | A0A077UUA2_STAAU 1-195 70 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > close #4 > open 1YG6 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 Drag select of 10 residues > select clear Drag select of 8 residues > select clear Drag select of 1 residues Drag select of 5 residues Drag select of 8 residues > select clear > select #3/K:31 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/K:31 8 atoms, 7 bonds, 1 residue, 1 model selected Drag select of 9 residues > select clear Drag select of 5 residues Drag select of 9 atoms, 15 residues, 9 bonds > select clear > select #2/K:29 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/K:29 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 32 atoms, 31 bonds, 4 residues, 1 model selected > select up 1467 atoms, 1486 bonds, 190 residues, 1 model selected > select down 32 atoms, 31 bonds, 4 residues, 1 model selected > hide sel cartoons > select #2/K:30 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 32 atoms, 31 bonds, 4 residues, 1 model selected > hide sel cartoons > select #1/E:31 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel cartoons > select #1/E:29 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel cartoons Drag select of 13 residues > hide sel cartoons Drag select of 3 residues > hide sel cartoons Drag select of 3 residues > hide sel cartoons Drag select of 2 residues > hide sel cartoons Drag select of 9 residues > hide sel cartoons Drag select of 10 residues > hide sel cartoons > save apo2_zg197.png width 4000 supersample 4 > save apo3_zg197.png width 4000 supersample 4 > select #2/K:61 12 atoms, 12 bonds, 1 residue, 1 model selected > select clear > save apo4_zg197.png width 4000 supersample 4 > save ""/Users/ayomidefasemire/Documents/Doctoral/Main > Project/ZG_ProBac/apo_zg_compare.cxs"" > close #1-3 > open ""/Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic > Models/Pdb/D7_deposition/D7_model2.deposit_000.cif"" Summary of feedback from opening /Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic Models/Pdb/D7_deposition/D7_model2.deposit_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' on line 359 Skipping entity category: Missing column 'type' on line 42418 Missing entity information. Treating each chain as a separate entity. Invalid sheet range for struct_sheet_range ""B 5"" on line 223 Invalid sheet range for struct_sheet_range ""D 1"": invalid entity ""B"", on line 227 Invalid sheet range for struct_sheet_range ""D 2"": invalid entity ""B"", on line 228 Invalid sheet range for struct_sheet_range ""E 1"": invalid entity ""B"", on line 229 Invalid sheet range for struct_sheet_range ""E 2"": invalid entity ""B"", on line 230 72 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Skipping chem_comp category: Missing column 'type' on line 43004 Chain information for D7_model2.deposit_000.cif #1 --- Chain | Description A B C D E F G H I J K L M N | No description available > ui tool show Matchmaker > matchmaker #!1 to #4 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 1yg6, chain I (#4) with D7_model2.deposit_000.cif, chain A (#1), sequence alignment score = 934.6 RMSD between 176 pruned atom pairs is 0.252 angstroms; (across all 181 pairs: 2.818) > matchmaker #!1 to #4 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 1yg6, chain I (#4) with D7_model2.deposit_000.cif, chain A (#1), sequence alignment score = 934.6 RMSD between 176 pruned atom pairs is 0.252 angstroms; (across all 181 pairs: 2.818) > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TYR""::name=""VAL"" 61831 atoms, 62481 bonds, 14 pseudobonds, 5250 residues, 3 models selected > hide sel atoms > show sel cartoons > select clear > select ::name=""HOH"" 953 atoms, 953 residues, 1 model selected > delete atoms sel > delete bonds sel > select #4/C:18 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select add #4 20587 atoms, 20901 bonds, 2632 residues, 1 model selected > ui tool show ""Color Actions"" > color sel tan > select subtract #4 Nothing selected > select add #1 42014 atoms, 42350 bonds, 14 pseudobonds, 2646 residues, 2 models selected > ui tool show ""Color Actions"" > color sel sky blue > color sel byhetero > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 47 atoms, 48 bonds, 1 residue, 1 model selected > select sel : hide ~sel cartoons, atoms > show sel atoms > style sel stick Changed 427 atom styles > select @H* 21014 atoms, 2646 residues, 1 model selected > hide sel > open 7XBZ format mmcif fromDatabase pdb 7xbz title: Crystal structure of Staphylococcus aureus ClpP in complex with R-ZG197 [more info...] Chain information for 7xbz #2 --- Chain | Description | UniProt A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | A0A0D1I3W4_STAAU 1-195 Non-standard residues in 7xbz #2 --- D4E — (6S,9aS)-6-[(2S)-butan-2-yl]-8-[(1R)-1-naphthalen-1-ylethyl]-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide MG — magnesium ion MPD — (4S)-2-methyl-2,4-pentanediol 49 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select clear > select ::name=""KHS"" 658 atoms, 672 bonds, 14 residues, 1 model selected > hide sel > ui tool show Matchmaker > matchmaker #!2 to #4 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 1yg6, chain A (#4) with 7xbz, chain C (#2), sequence alignment score = 751.1 RMSD between 181 pruned atom pairs is 0.725 angstroms; (across all 185 pairs: 0.910) > matchmaker #!2 to #4 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 1yg6, chain A (#4) with 7xbz, chain C (#2), sequence alignment score = 751.1 RMSD between 181 pruned atom pairs is 0.725 angstroms; (across all 185 pairs: 0.910) > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TYR""::name=""VAL"" 81137 atoms, 82034 bonds, 28 pseudobonds, 7792 residues, 5 models selected > hide sel atoms > show sel cartoons > select ::name=""HOH"" 491 atoms, 491 residues, 1 model selected > delete atoms sel > delete bonds sel > hide #!2 models > show #!2 models > select ::name=""KHS"" 658 atoms, 672 bonds, 14 residues, 1 model selected > show sel atoms > select #1/M:301@CAC 1 atom, 1 residue, 1 model selected > select up 47 atoms, 48 bonds, 1 residue, 1 model selected > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 38 atoms, 41 bonds, 1 residue, 1 model selected > select sel : hide ~sel cartoons, atoms > select @H* 21014 atoms, 2646 residues, 1 model selected > hide sel > show sel atoms > style sel stick Changed 21014 atom styles > undo > select clear Drag select of 64 residues, 57 atoms, 61 bonds > show sel atoms > style sel stick Changed 828 atom styles > select @H* 21014 atoms, 2646 residues, 1 model selected > hide sel > ui tool show Matchmaker > ui tool show ""Show Sequence Viewer"" > select clear > select add #4 20587 atoms, 20901 bonds, 2632 residues, 1 model selected > select subtract #4 Nothing selected > select add #2 19894 atoms, 20150 bonds, 38 pseudobonds, 2581 residues, 3 models selected > ui tool show ""Color Actions"" > color sel dark sea green > color sel byhetero > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #4/B Alignment identifier is 4/B > select #4/B:74 8 atoms, 7 bonds, 1 residue, 1 model selected > select #4/B:74 8 atoms, 7 bonds, 1 residue, 1 model selected > hide #!2 models > select #4/B:62 12 atoms, 12 bonds, 1 residue, 1 model selected > select #4/B:62 12 atoms, 12 bonds, 1 residue, 1 model selected > show #!2 models > select add #4 20587 atoms, 20901 bonds, 2632 residues, 1 model selected > select subtract #4 Nothing selected > select add #2 19894 atoms, 20150 bonds, 38 pseudobonds, 2581 residues, 3 models selected > ui tool show ""Color Actions"" > color sel thistle > color sel byhetero > select clear > select #4/B:62 12 atoms, 12 bonds, 1 residue, 1 model selected > select add #1/N:76 33 atoms, 33 bonds, 2 residues, 2 models selected > select add #2/D:63 45 atoms, 45 bonds, 3 residues, 3 models selected > select add #2/C:D4E 83 atoms, 86 bonds, 4 residues, 3 models selected > select add #1/N:KHS 130 atoms, 134 bonds, 5 residues, 3 models selected > hide ~sel cartoons, atoms > select clear > select #1/N:301@FAD 1 atom, 1 residue, 1 model selected > select up 47 atoms, 48 bonds, 1 residue, 1 model selected > hide sel > lighting full > lighting soft > lighting simple > save apo_EcClpP.png width 4000 supersample 4 > select #2/C:201@F42 1 atom, 1 residue, 1 model selected > select up 38 atoms, 41 bonds, 1 residue, 1 model selected > color sel magenta > color sel byhetero > select clear > select #2/C:201@F42 1 atom, 1 residue, 1 model selected > select up 38 atoms, 41 bonds, 1 residue, 1 model selected > color sel purple > color sel byhetero > select clear > save apo_EcClpP.png width 4000 supersample 4 > select add #4 20587 atoms, 20901 bonds, 2632 residues, 1 model selected > color sel byhetero > select subtract #4 Nothing selected > save apo_EcClpP.png width 4000 supersample 4 > select #2/C:201@F42 1 atom, 1 residue, 1 model selected > select up 38 atoms, 41 bonds, 1 residue, 1 model selected > hide sel > save apo2_EcClpP.png width 4000 supersample 4 > cd ""/Users/ayomidefasemire/Documents/Doctoral/Main Project/ZG_ProBac"" Current working directory is: /Users/ayomidefasemire/Documents/Doctoral/Main Project/ZG_ProBac > save ""/Users/ayomidefasemire/Documents/Doctoral/Main > Project/ZG_ProBac/apo_EcClpP_compare.cxs"" QPainter::begin: Paint device returned engine == 0, type: 2 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/ayomidefasemire/Documents/Doctoral/Main > Project/ZG_ProBac/SaClpP_EcClpP_ZG180_compare_Ayo.cxs"" Log from Sat Aug 1 19:27:04 2026UCSF 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/ZG_ProBac/Comparison of SaClpP_7WID with our ClpP C1_model.cxs"" Log from Fri Jul 24 19:28:48 2026UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:/Users/mklimecka/Downloads/7WID.cif Summary of feedback from opening C:/Users/mklimecka/Downloads/7WID.cif --- warnings | Unable to fetch template for '9DF': might have incorrect bonds Unable to fetch template for 'MG': might have incorrect bonds Unable to fetch template for 'MPD': might have incorrect bonds 7WID.cif title: Crystal structure of Staphylococcus aureus ClpP in complex with ZG180 [more info...] Chain information for 7WID.cif #1 --- Chain | Description | UniProt A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | A0A0D1I3W4_STAAU Non-standard residues in 7WID.cif #1 --- 9DF — (6S,9aS)-6-[(2S)-butan-2-yl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide MG — magnesium ion MPD — (4S)-2-methyl-2,4-pentanediol > hide surfaces > select #1 22004 atoms, 20718 bonds, 62 pseudobonds, 4197 residues, 3 models selected > hide sel surfaces > style sel stick Changed 22004 atom styles > show sel cartoons > hide sel atoms > ~select #1 Nothing selected > open C:/Users/mklimecka/Downloads/C1_model.cif Summary of feedback from opening C:/Users/mklimecka/Downloads/C1_model.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 1376 Missing entity information. Treating each chain as a separate entity. Unable to fetch template for 'KHS': might have incorrect bonds Bad residue range for struct_conf ""7"" near line 164 Invalid residue range for struct_conf ""8"": invalid entity ""B"", near line 165 Invalid residue range for struct_conf ""9"": invalid entity ""B"", near line 166 Invalid residue range for struct_conf ""10"": invalid entity ""B"", near line 167 Invalid residue range for struct_conf ""11"": invalid entity ""B"", near line 168 Invalid residue range for struct_conf ""12"": invalid entity ""B"", near line 169 2 messages similar to the above omitted Bad residue range for struct_conf ""21"" near line 178 Invalid residue range for struct_conf ""22"": invalid entity ""D"", near line 179 Invalid residue range for struct_conf ""23"": invalid entity ""D"", near line 180 Invalid residue range for struct_conf ""24"": invalid entity ""D"", near line 181 Invalid residue range for struct_conf ""25"": invalid entity ""D"", near line 182 Invalid residue range for struct_conf ""26"": invalid entity ""D"", near line 183 2 messages similar to the above omitted Bad residue range for struct_conf ""35"" near line 192 Invalid residue range for struct_conf ""36"": invalid entity ""F"", near line 193 Invalid residue range for struct_conf ""37"": invalid entity ""F"", near line 194 Invalid residue range for struct_conf ""38"": invalid entity ""F"", near line 195 Invalid residue range for struct_conf ""39"": invalid entity ""F"", near line 196 Invalid residue range for struct_conf ""40"": invalid entity ""F"", near line 197 2 messages similar to the above omitted Bad residue range for struct_conf ""49"" near line 206 Invalid residue range for struct_conf ""50"": invalid entity ""H"", near line 207 Invalid residue range for struct_conf ""51"": invalid entity ""H"", near line 208 Invalid residue range for struct_conf ""52"": invalid entity ""H"", near line 209 Invalid residue range for struct_conf ""53"": invalid entity ""H"", near line 210 Invalid residue range for struct_conf ""54"": invalid entity ""H"", near line 211 2 messages similar to the above omitted Bad residue range for struct_conf ""63"" near line 220 Invalid residue range for struct_conf ""64"": invalid entity ""J"", near line 221 Invalid residue range for struct_conf ""65"": invalid entity ""J"", near line 222 Invalid residue range for struct_conf ""66"": invalid entity ""J"", near line 223 Invalid residue range for struct_conf ""67"": invalid entity ""J"", near line 224 Invalid residue range for struct_conf ""68"": invalid entity ""J"", near line 225 2 messages similar to the above omitted Bad residue range for struct_conf ""77"" near line 234 Invalid residue range for struct_conf ""78"": invalid entity ""L"", near line 235 Invalid residue range for struct_conf ""79"": invalid entity ""L"", near line 236 Invalid residue range for struct_conf ""80"": invalid entity ""L"", near line 237 Invalid residue range for struct_conf ""81"": invalid entity ""L"", near line 238 Invalid residue range for struct_conf ""82"": invalid entity ""L"", near line 239 2 messages similar to the above omitted Bad residue range for struct_conf ""91"" near line 248 Invalid residue range for struct_conf ""92"": invalid entity ""N"", near line 249 Invalid residue range for struct_conf ""93"": invalid entity ""N"", near line 250 Invalid residue range for struct_conf ""94"": invalid entity ""N"", near line 251 Invalid residue range for struct_conf ""95"": invalid entity ""N"", near line 252 Invalid residue range for struct_conf ""96"": invalid entity ""N"", near line 253 2 messages similar to the above omitted Invalid sheet range for struct_sheet_range ""10 1"" near line 1244 Invalid sheet range for struct_sheet_range ""11 1"": invalid entity ""B"", near line 1245 Invalid sheet range for struct_sheet_range ""12 1"": invalid entity ""B"", near line 1246 Invalid sheet range for struct_sheet_range ""13 1"": invalid entity ""B"", near line 1247 Invalid sheet range for struct_sheet_range ""14 1"": invalid entity ""B"", near line 1248 72 messages similar to the above omitted Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Skipping chem_comp category: Missing column 'type' near line 43979 Chain information for C1_model.cif #2 --- Chain | Description A B C D E F G H I J K L M N | No description available > select #2 41972 atoms, 42308 bonds, 812 pseudobonds, 2646 residues, 3 models selected > style sel stick Changed 41972 atom styles > show sel cartoons > hide sel atoms > 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 7WID.cif, chain H (#1) with C1_model.cif, chain F (#2), sequence alignment score = 740.3 RMSD between 185 pruned atom pairs is 0.785 angstroms; (across all 188 pairs: 0.931) > ~select #2 Nothing selected > show atoms > show surfaces > hide #!1 models > show #!1 models > 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 22004 atoms, 20718 bonds, 62 pseudobonds, 4197 residues, 3 models selected > color sel bychain > select #2 41972 atoms, 42308 bonds, 812 pseudobonds, 2646 residues, 3 models selected > ~select #2 14 models selected > select #1 22004 atoms, 20718 bonds, 62 pseudobonds, 4197 residues, 3 models selected > ~select #1 14 models selected > select #2 41972 atoms, 42308 bonds, 812 pseudobonds, 2646 residues, 3 models selected > color sel bychain > ~select #2 14 models selected > hide #!2 models > show #!2 models > hide #!2 models > show #!1 cartoons > select #1 22004 atoms, 20718 bonds, 62 pseudobonds, 4197 residues, 3 models selected > show sel cartoons > hide sel surfaces > hide sel atoms > select #2 41972 atoms, 42308 bonds, 812 pseudobonds, 2646 residues, 3 models selected > show #!2 models > hide sel surfaces > show sel cartoons > hide sel atoms > ui tool show Matchmaker > show sel atoms > hide sel cartoons > show sel surfaces > select #1 22004 atoms, 20718 bonds, 62 pseudobonds, 4197 residues, 3 models selected > hide sel cartoons > show sel surfaces > show sel atoms > ~select #1 14 models selected > select #2 41972 atoms, 42308 bonds, 812 pseudobonds, 2646 residues, 3 models selected > hide sel atoms > hide #!2 models > show #!2 models > transparency sel 50 > ui tool show Matchmaker > ~select #2 14 models selected > save > ""C:/Users/mklimecka/WORK/Projekty/CnBCh/Protacs/CryoEM/PROTAC2/Comparison of > our model C1_model_with ZG180_7WID_in yellow.cxs"" > save > ""C:/Users/mklimecka/WORK/Projekty/CnBCh/Protacs/CryoEM/PROTAC2/Comparison of > our model C1_model_with ZG180_7WID_in yellow.tif"" width 1325 height 818 > supersample 3 > hide #!2 models > show #!2 models > show atoms > hide atoms > undo > select #2 41972 atoms, 42308 bonds, 812 pseudobonds, 2646 residues, 3 models selected > hide sel atoms > ~select #2 14 models selected > select #1 22004 atoms, 20718 bonds, 62 pseudobonds, 4197 residues, 3 models selected > show sel cartoons > hide sel surfaces > select #2 41972 atoms, 42308 bonds, 812 pseudobonds, 2646 residues, 3 models selected > hide sel surfaces > show sel cartoons > ~select #2 14 models selected > hide #!2 models > ui mousemode right select > select #1/K:201@C6 1 atom, 1 residue, 1 model selected > select #1/K:201@O33 1 atom, 1 residue, 1 model selected > color sel byhetero > ui mousemode right translate > select ::name=""9DF"" 518 atoms, 560 bonds, 14 residues, 1 model selected > color sel byhetero > show #!2 models > show sel surfaces > hide sel surfaces > select #1 22004 atoms, 20718 bonds, 62 pseudobonds, 4197 residues, 3 models selected > ~select #1 28 models selected > select #2 41972 atoms, 42308 bonds, 812 pseudobonds, 2646 residues, 3 models selected > show sel surfaces > show sel atoms > select ::name=""KHS"" 658 atoms, 672 bonds, 14 residues, 1 model selected > color sel byhetero > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > 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/C-D,G-I,K-N:193 73 atoms, 64 bonds, 9 residues, 1 model selected > select #1/C-D,G-I,K-N:193 73 atoms, 64 bonds, 9 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #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 Alignment identifier is 2 > select #2/A-N:206 336 atoms, 322 bonds, 14 residues, 1 model selected > select #2/A-N:206 336 atoms, 322 bonds, 14 residues, 1 model selected > hide #!1 models > color (#!2 & sel) byhetero > select ::name=""KHS"" 658 atoms, 672 bonds, 14 residues, 1 model selected > hide sel atoms > select ::name=""9DF"" 518 atoms, 560 bonds, 14 residues, 1 model selected > show #!1 models > toolshed show Downloading bundle chimerax_cryozeta-0.3.6-py3-none-any.whl Errors may have occurred when running pip: pip standard error: \--- WARNING: Value for scheme.platlib does not match. Please report this to distutils: C:\Users\mklimecka\AppData\Local\UCSF\ChimeraX\1.3\site-packages sysconfig: C:\Users\mklimecka\AppData\Roaming\Python\Python39\site-packages WARNING: Value for scheme.purelib does not match. Please report this to distutils: C:\Users\mklimecka\AppData\Local\UCSF\ChimeraX\1.3\site-packages sysconfig: C:\Users\mklimecka\AppData\Roaming\Python\Python39\site-packages WARNING: Value for scheme.headers does not match. Please report this to distutils: C:\Users\mklimecka\AppData\Local\UCSF\ChimeraX\Python39\Include\chimerax- cryozeta sysconfig: C:\Users\mklimecka\AppData\Roaming\Python\Python39\Include\chimerax-cryozeta WARNING: Value for scheme.scripts does not match. Please report this to distutils: C:\Users\mklimecka\AppData\Local\UCSF\ChimeraX\Python39\Scripts sysconfig: C:\Users\mklimecka\AppData\Roaming\Python\Python39\Scripts WARNING: Value for scheme.data does not match. Please report this to distutils: C:\Users\mklimecka\AppData\Local\UCSF\ChimeraX sysconfig: C:\Users\mklimecka\AppData\Roaming\Python WARNING: Additional context: user = True home = None root = None prefix = None WARNING: Value for scheme.headers does not match. Please report this to distutils: C:\Users\mklimecka\AppData\Local\UCSF\ChimeraX\Python39\Include\UNKNOWN sysconfig: C:\Users\mklimecka\AppData\Roaming\Python\Python39\Include\UNKNOWN WARNING: You are using pip version 21.2.4; however, version 26.0.1 is available. You should consider upgrading via the 'C:\Program Files\ChimeraX 1.3\bin\ChimeraX.exe -m pip install --upgrade pip' command. \--- pip standard output: \--- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\mklimecka\downloads\chimerax_cryozeta-0.3.6-py3-none- any.whl Requirement already satisfied: ChimeraX-Core~=1.1 in c:\program files\chimerax 1.3\bin\lib\site-packages (from chimerax-cryozeta==0.3.6) (1.3) Requirement already satisfied: ChimeraX-UI~=1.0 in c:\program files\chimerax 1.3\bin\lib\site-packages (from chimerax-cryozeta==0.3.6) (1.13.7) Requirement already satisfied: ChimeraX-MouseModes~=1.0 in c:\program files\chimerax 1.3\bin\lib\site-packages (from ChimeraX-UI~=1.0->chimerax- cryozeta==0.3.6) (1.1) Requirement already satisfied: ChimeraX-SelInspector~=1.0 in c:\program files\chimerax 1.3\bin\lib\site-packages (from ChimeraX-UI~=1.0->chimerax- cryozeta==0.3.6) (1.0) Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program files\chimerax 1.3\bin\lib\site-packages (from ChimeraX-UI~=1.0->chimerax- cryozeta==0.3.6) (1.1) Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program files\chimerax 1.3\bin\lib\site-packages (from ChimeraX- Graphics~=1.0->ChimeraX-UI~=1.0->chimerax-cryozeta==0.3.6) (1.1) Requirement already satisfied: ChimeraX-Arrays~=1.0 in c:\program files\chimerax 1.3\bin\lib\site-packages (from ChimeraX- Graphics~=1.0->ChimeraX-UI~=1.0->chimerax-cryozeta==0.3.6) (1.0) Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in c:\program files\chimerax 1.3\bin\lib\site-packages (from ChimeraX- SelInspector~=1.0->ChimeraX-UI~=1.0->chimerax-cryozeta==0.3.6) (1.0) Installing collected packages: chimerax-cryozeta Successfully installed chimerax-cryozeta-0.3.6 \--- Successfully installed chimerax-cryozeta-0.3.6 No change in list of installed bundles > hide #!2 models > show #!2 models > save > ""C:/Users/mklimecka/WORK/Projekty/CnBCh/Protacs/CryoEM/PROTAC2/Comparison of > SaClpP_7WID with our ClpP C1_model.cxs"" ——— End of log from Fri Jul 24 19:28:48 2026 ——— opened ChimeraX session > set bgColor white > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > close Unsupported scale factor (0.000000) detected on Display0 [Repeated 3 time(s)] > open ""/Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic > Models/Pdb/D7_deposition/D7_model2.deposit_000.cif"" Summary of feedback from opening /Users/ayomidefasemire/Documents/Doctoral/Main Project/ClpP/Atomic Models/Pdb/D7_deposition/D7_model2.deposit_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' on line 359 Skipping entity category: Missing column 'type' on line 42418 Missing entity information. Treating each chain as a separate entity. Invalid sheet range for struct_sheet_range ""B 5"" on line 223 Invalid sheet range for struct_sheet_range ""D 1"": invalid entity ""B"", on line 227 Invalid sheet range for struct_sheet_range ""D 2"": invalid entity ""B"", on line 228 Invalid sheet range for struct_sheet_range ""E 1"": invalid entity ""B"", on line 229 Invalid sheet range for struct_sheet_range ""E 2"": invalid entity ""B"", on line 230 72 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Skipping chem_comp category: Missing column 'type' on line 43004 Chain information for D7_model2.deposit_000.cif #1 --- Chain | Description A B C D E F G H I J K L M N | No description available > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TYR""::name=""VAL"" 41356 atoms, 41678 bonds, 14 pseudobonds, 2632 residues, 2 models selected > select ::name=""KHS"" 658 atoms, 672 bonds, 14 residues, 1 model selected > select clear > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TYR""::name=""VAL"" 41356 atoms, 41678 bonds, 14 pseudobonds, 2632 residues, 2 models selected > show sel cartoons > hide sel atoms > select clear > select ::name=""KHS"" 658 atoms, 672 bonds, 14 residues, 1 model selected > hide sel > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > open 7wh5 Summary of feedback from opening 7wh5 fetched from pdb --- notes | Fetching compressed mmCIF 7wh5 from http://files.rcsb.org/download/7wh5.cif Fetching CCD 9DF from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/9DF/9DF.cif 7wh5 title: Crystal structure of human ClpP in complex with ZG180 [more info...] Chain information for 7wh5 #2 --- Chain | Description | UniProt A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit, mitochondrial | CLPP_HUMAN 57-277 Non-standard residues in 7wh5 #2 --- 9DF — (6S,9aS)-6-[(2S)-butan-2-yl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide MG — magnesium ion > open 7wid Summary of feedback from opening 7wid fetched from pdb --- note | Fetching compressed mmCIF 7wid from http://files.rcsb.org/download/7wid.cif 7wid title: Crystal structure of Staphylococcus aureus ClpP in complex with ZG180 [more info...] Chain information for 7wid #3 --- Chain | Description | UniProt A B C D E F G H I J K L M N | ATP-dependent Clp protease proteolytic subunit | A0A0D1I3W4_STAAU 1-195 Non-standard residues in 7wid #3 --- 9DF — (6S,9aS)-6-[(2S)-butan-2-yl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide MG — magnesium ion MPD — (4S)-2-methyl-2,4-pentanediol 59 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > ui tool show Matchmaker > matchmaker #!2-3 to #1 Computing secondary structure [Repeated 2 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker D7_model2.deposit_000.cif, chain A (#1) with 7wh5, chain I (#2), sequence alignment score = 636.9 RMSD between 168 pruned atom pairs is 0.766 angstroms; (across all 176 pairs: 1.243) Matchmaker D7_model2.deposit_000.cif, chain A (#1) with 7wid, chain H (#3), sequence alignment score = 740.3 RMSD between 181 pruned atom pairs is 0.720 angstroms; (across all 188 pairs: 0.949) > matchmaker #!2-3 to #1 Computing secondary structure [Repeated 2 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker D7_model2.deposit_000.cif, chain A (#1) with 7wh5, chain I (#2), sequence alignment score = 636.9 RMSD between 168 pruned atom pairs is 0.766 angstroms; (across all 176 pairs: 1.243) Matchmaker D7_model2.deposit_000.cif, chain A (#1) with 7wid, chain H (#3), sequence alignment score = 740.3 RMSD between 181 pruned atom pairs is 0.720 angstroms; (across all 188 pairs: 0.949) > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 79445 atoms, 80372 bonds, 52 pseudobonds, 7630 residues, 6 models selected > hide sel atoms > show sel cartoons > select ::name=""HOH"" 1809 atoms, 1809 residues, 2 models selected > delete atoms sel > delete bonds sel > hide #!1 models > hide #!2 models > select add #3 20449 atoms, 20718 bonds, 36 pseudobonds, 2642 residues, 3 models selected > ui tool show ""Color Actions"" > color sel light sky blue > select ::name=""9DF"" 1036 atoms, 1120 bonds, 28 residues, 2 models selected > color (#!3 & sel) byhetero > select clear > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!1 models > select add #1 42014 atoms, 42350 bonds, 14 pseudobonds, 2646 residues, 2 models selected > ui tool show ""Color Actions"" > color sel burly wood > select clear > show #!2 models > hide #!3 models > hide #!1 models > select add #2 18818 atoms, 19208 bonds, 30 pseudobonds, 2414 residues, 3 models selected > ui tool show ""Color Actions"" > color sel light slate gray > color sel thistle > select clear > select ::name=""9DF"" 1036 atoms, 1120 bonds, 28 residues, 2 models selected > select add #3 20967 atoms, 21278 bonds, 36 pseudobonds, 2656 residues, 4 models selected > select subtract #3 518 atoms, 560 bonds, 14 residues, 1 model selected > color sel byhetero > select clear > show #!3 models > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A Alignment identifier is 3/A > select #2/A:146 14 atoms, 15 bonds, 1 residue, 1 model selected > select #2/A:146 14 atoms, 15 bonds, 1 residue, 1 model selected > ui tool show Matchmaker > matchmaker #!3 to #2 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7wh5, chain B (#2) with 7wid, chain C (#3), sequence alignment score = 614.7 RMSD between 164 pruned atom pairs is 0.705 angstroms; (across all 172 pairs: 1.166) > matchmaker #!3 to #2 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7wh5, chain B (#2) with 7wid, chain C (#3), sequence alignment score = 614.7 RMSD between 164 pruned atom pairs is 0.705 angstroms; (across all 172 pairs: 1.166) > show sel atoms > hide sel atoms > style sel stick Changed 14 atom styles > style sel stick Changed 14 atom styles > show sel atoms > select #3/A:91 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/B:90 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/B:91 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > show sel atoms > hide sel atoms > show sel atoms > style sel stick Changed 8 atom styles > select clear > hide #!2 models > show #!1 models > ui tool show Matchmaker > matchmaker #!3 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker D7_model2.deposit_000.cif, chain A (#1) with 7wid, chain H (#3), sequence alignment score = 740.3 RMSD between 181 pruned atom pairs is 0.720 angstroms; (across all 188 pairs: 0.949) > matchmaker #!3 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker D7_model2.deposit_000.cif, chain A (#1) with 7wid, chain H (#3), sequence alignment score = 740.3 RMSD between 181 pruned atom pairs is 0.720 angstroms; (across all 188 pairs: 0.949) > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 37 atoms, 40 bonds, 1 residue, 1 model selected > select sel :< 5 917 atoms, 896 bonds, 69 residues, 3 models selected > select sel :< 5 3537 atoms, 3526 bonds, 3 pseudobonds, 319 residues, 6 models selected > hide ~selected cartoons, atoms Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide ~selected cartoons atoms Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide ~selected cartoons atoms Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide ~selected cartoons Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide ~selected cartoons Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide ~select cartoons atoms Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide ~select cartoons Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide ~sel cartoons atoms Expected ',' or a keyword > hide ~sel cartoons, atoms > show sel & #!1,3 atoms > style sel & #!1,3 stick Changed 2660 atom styles > select :@H* Expected an objects specifier or a keyword > select @H* 21014 atoms, 2646 residues, 1 model selected > hide sel > select #1/D:301@FAD 1 atom, 1 residue, 1 model selected > select #1/D:301@FAD 1 atom, 1 residue, 1 model selected > select down 1 atom, 1 residue, 1 model selected > select down 1 atom, 1 residue, 1 model selected > select up 47 atoms, 48 bonds, 1 residue, 1 model selected > hide sel > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 37 atoms, 40 bonds, 1 residue, 1 model selected > color sel red > color sel byhetero > color sel purple > color sel byhetero > select #3/L:60 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 62 atoms, 63 bonds, 7 residues, 1 model selected > hide ~sel & #3 cartoons > hide ~sel & #3 cartoons, atoms > select add ::name=""9DF"" 1098 atoms, 1183 bonds, 35 residues, 2 models selected > show sel atoms > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 37 atoms, 40 bonds, 1 residue, 1 model selected > select up 1457 atoms, 1476 bonds, 188 residues, 1 model selected > select down 37 atoms, 40 bonds, 1 residue, 1 model selected > select add sel :< 3 & ~sel 427 atoms, 426 bonds, 22 residues, 3 models selected > select add sel :< 3 & ~sel 1782 atoms, 1747 bonds, 144 residues, 3 models selected > hide ~sel cartoons, atoms > select clear > select #1/E:66 10 atoms, 9 bonds, 1 residue, 1 model selected > select up 388 atoms, 392 bonds, 26 residues, 1 model selected > select up 2836 atoms, 2859 bonds, 181 residues, 1 model selected > hide sel atoms > select #1/D:33 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 301 atoms, 302 bonds, 18 residues, 1 model selected > select up 2954 atoms, 2977 bonds, 188 residues, 1 model selected > select down 301 atoms, 302 bonds, 18 residues, 1 model selected > select down 19 atoms, 18 bonds, 1 residue, 1 model selected > hide sel atoms > select #1/D:105 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 307 atoms, 308 bonds, 22 residues, 1 model selected > hide sel atoms > select #1/D:33 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 301 atoms, 302 bonds, 18 residues, 1 model selected > hide sel atoms > select clear > select #1/D:128@CG 1 atom, 1 residue, 1 model selected > select up 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 44 atoms, 44 bonds, 3 residues, 1 model selected > hide sel cartoons, atoms > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 20 atoms, 20 bonds, 1 residue, 1 model selected > hide sel cartoons, atoms > select #1/D:124 22 atoms, 21 bonds, 1 residue, 1 model selected > hide sel cartoons, atoms > select #1/D:20 16 atoms, 15 bonds, 1 residue, 1 model selected > hide sel cartoons, atoms > select #1/D:33 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 301 atoms, 302 bonds, 18 residues, 1 model selected > select down 19 atoms, 18 bonds, 1 residue, 1 model selected > hide sel cartoons, atoms > select #1/D:34 21 atoms, 21 bonds, 1 residue, 1 model selected > hide sel cartoons, atoms > select #1/E:96 20 atoms, 20 bonds, 1 residue, 1 model selected > select up 99 atoms, 99 bonds, 6 residues, 1 model selected > select up 2836 atoms, 2859 bonds, 181 residues, 1 model selected > select down 99 atoms, 99 bonds, 6 residues, 1 model selected > select clear > lighting full > lighting soft > lighting simple > lighting full > lighting simple > label #1,3 text ""{0.name} {0.number}{0.insertion_code}"" > ~label #1,3 residues > select clear > select #1/D:106 17 atoms, 16 bonds, 1 residue, 1 model selected > select up 307 atoms, 308 bonds, 22 residues, 1 model selected > hide sel cartoons, atoms > select #1/D:202@CG1 1 atom, 1 residue, 1 model selected > select up 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 799 atoms, 802 bonds, 50 residues, 1 model selected > select up 2836 atoms, 2859 bonds, 181 residues, 1 model selected > select down 799 atoms, 802 bonds, 50 residues, 1 model selected > transparency sel 70 cartoons > transparency sel 70 cartoons, atoms > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 17 atoms, 17 bonds, 1 residue, 1 model selected > select up 56 atoms, 56 bonds, 3 residues, 1 model selected > transparency sel 70 cartoons, atoms > select #1/E:92 12 atoms, 11 bonds, 1 residue, 1 model selected > select up 99 atoms, 99 bonds, 6 residues, 1 model selected > select up 2836 atoms, 2859 bonds, 181 residues, 1 model selected > select down 99 atoms, 99 bonds, 6 residues, 1 model selected > transparency sel 70 cartoons, atoms > select #1/E:98 22 atoms, 21 bonds, 1 residue, 1 model selected > transparency sel 70 cartoons, atoms > select clear > select #1/D:46 14 atoms, 13 bonds, 1 residue, 1 model selected > select up 95 atoms, 95 bonds, 6 residues, 1 model selected > select up 2836 atoms, 2859 bonds, 181 residues, 1 model selected > select down 95 atoms, 95 bonds, 6 residues, 1 model selected > transparency sel 70 cartoons, atoms > select #1/E:94 17 atoms, 16 bonds, 1 residue, 1 model selected > select up 99 atoms, 99 bonds, 6 residues, 1 model selected > transparency sel 0 cartoons, atoms > select #1/E:98 22 atoms, 21 bonds, 1 residue, 1 model selected > transparency sel 0 cartoons, atoms > select #1/D:202@CB 1 atom, 1 residue, 1 model selected > select #1/D:202@CD1 1 atom, 1 residue, 1 model selected > select up 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 799 atoms, 802 bonds, 50 residues, 1 model selected > select up 2836 atoms, 2859 bonds, 181 residues, 1 model selected > select down 799 atoms, 802 bonds, 50 residues, 1 model selected > transparency sel 0 cartoons, atoms > select #1/D:205 17 atoms, 17 bonds, 1 residue, 1 model selected > select up 56 atoms, 56 bonds, 3 residues, 1 model selected > transparency sel 0 cartoons, atoms > select clear > select #1/E:94 17 atoms, 16 bonds, 1 residue, 1 model selected > select up 99 atoms, 99 bonds, 6 residues, 1 model selected > hide sel cartoons, atoms > select #1/E:98 22 atoms, 21 bonds, 1 residue, 1 model selected > hide sel cartoons, atoms > select #1/D:41 24 atoms, 23 bonds, 1 residue, 1 model selected > select up 80 atoms, 79 bonds, 4 residues, 1 model selected > transparency sel 70 cartoons, atoms > select clear [Repeated 1 time(s)] > select #1/D:74@CB 1 atom, 1 residue, 1 model selected > select up 21 atoms, 21 bonds, 1 residue, 1 model selected > select up 388 atoms, 392 bonds, 26 residues, 1 model selected > select down 21 atoms, 21 bonds, 1 residue, 1 model selected > transparency sel 70 cartoons, atoms > select #1/D:73 19 atoms, 18 bonds, 1 residue, 1 model selected > transparency sel 70 cartoons, atoms > select #3/L:61@CB 1 atom, 1 residue, 1 model selected > select up 12 atoms, 12 bonds, 1 residue, 1 model selected > transparency sel 70 cartoons, atoms > select #3/L:60 8 atoms, 7 bonds, 1 residue, 1 model selected > transparency sel 70 cartoons, atoms > select clear > select #1/D:205 17 atoms, 17 bonds, 1 residue, 1 model selected > select up 56 atoms, 56 bonds, 3 residues, 1 model selected > transparency sel 50 cartoons, atoms > select clear [Repeated 1 time(s)] > select #1/D:203@CG 1 atom, 1 residue, 1 model selected > select up 19 atoms, 18 bonds, 1 residue, 1 model selected > transparency sel 50 cartoons, atoms > select clear [Repeated 1 time(s)] > select #1/E:66 10 atoms, 9 bonds, 1 residue, 1 model selected > select up 388 atoms, 392 bonds, 26 residues, 1 model selected > select down 10 atoms, 9 bonds, 1 residue, 1 model selected > select up 388 atoms, 392 bonds, 26 residues, 1 model selected > select up 2836 atoms, 2859 bonds, 181 residues, 1 model selected > transparency sel 50 cartoons, atoms > select clear [Repeated 1 time(s)] > cd /Users/ayomidefasemire/Documents/Doctoral Current working directory is: /Users/ayomidefasemire/Documents/Doctoral > cd ""/Users/ayomidefasemire/Documents/Doctoral/Main Project/ZG_ProBac"" Current working directory is: /Users/ayomidefasemire/Documents/Doctoral/Main Project/ZG_ProBac > save tyr76_clash1.png width 4000 supersample 4 > save tyr76_clash2.png width 4000 supersample 4 > save tyr76_clash3.png width 4000 supersample 4 > save 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