id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18107 Crash at exit in Qt cleanup routines chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-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 0x0000000400c47000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 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 0x0000000312697000 (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 0x000000031168b000 (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 0x000000031067f000 (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 0x000000030f673000 (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 0x000000030e667000 (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 0x000000030d65b000 (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 0x000000030c64f000 (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 0x000000030b643000 (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 0x000000030a637000 (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 0x000000030962b000 (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 0x000000030861f000 (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 0x0000000307613000 (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 0x0000000306607000 (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 0x00000001f6185f00 (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, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, 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""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""64c17a9925d75a7281053d4c"", ""factorPackIds"" : { ""SIRI_AUDIO_DISABLE_MEDIA_ENTITY_SYNC"" : ""64d29746ad29a465b3bbeace"" }, ""deploymentId"" : 240000002 }, { ""rolloutId"" : ""65a8173205d942272410674b"", ""factorPackIds"" : { ""SIRI_HOME_AUTOMATION_SERVER_FLOW_DEPRECATION"" : ""65d39fa4cb0e2417d11ce5f6"" }, ""deploymentId"" : 240000001 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6wek format mmcif fromDatabase pdb 6wek title: Structure of cGMP-bound WT TAX-4 reconstituted in lipid nanodiscs [more info...] Chain information for 6wek #1 --- Chain | Description | UniProt A B C D | Cyclic nucleotide-gated cation channel | CNG_CAEEL 1-733 Non-standard residues in 6wek #1 --- CPL — 1-palmitoyl-2-linoleoyl-Sn-glycero-3-phosphocholine (palmitoyl-linoleoyl phosphatidylcholine) PCG — cyclic guanosine monophosphate PX2 — 1,2-dilauroyl-Sn-glycero-3-phosphate 36 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open /Users/daisy/Documents/TAX4/Groop-2-open/14-2-3-open-coot-0.pdb > /Users/daisy/Documents/TAX4/Groop-2-open/15-3-3-open-spicel-coot-0.pdb > /Users/daisy/Documents/TAX4/Groop-2-open/16-4-3-open-spicel-coot-0.pdb > /Users/daisy/Documents/TAX4/Groop-2-open/17-5-3-open-f-coot-0.pdb > /Users/daisy/Documents/TAX4/Groop-2-open/18-6-4-open-good-3wt-1EA-coot-0.pdb Chain information for 14-2-3-open-coot-0.pdb #2 --- Chain | Description A B C | No description available D | No description available 36 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Chain information for 15-3-3-open-spicel-coot-0.pdb #3 --- Chain | Description A B C | No description available D | No description available 36 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Chain information for 16-4-3-open-spicel-coot-0.pdb #4 --- Chain | Description A B C | No description available D | No description available 36 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Chain information for 17-5-3-open-f-coot-0.pdb #5 --- Chain | Description A B C | No description available D | No description available 36 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Chain information for 18-6-4-open-good-3wt-1EA-coot-0.pdb #6 --- Chain | Description A B C D | No description available 36 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > ui tool show Matchmaker > matchmaker #!2-6 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 6wek, chain A (#1) with 14-2-3-open-coot-0.pdb, chain B (#2), sequence alignment score = 2536 RMSD between 507 pruned atom pairs is 0.672 angstroms; (across all 512 pairs: 0.729) Matchmaker 6wek, chain A (#1) with 15-3-3-open-spicel-coot-0.pdb, chain A (#3), sequence alignment score = 2516.8 RMSD between 510 pruned atom pairs is 0.555 angstroms; (across all 512 pairs: 0.584) Matchmaker 6wek, chain A (#1) with 16-4-3-open-spicel-coot-0.pdb, chain D (#4), sequence alignment score = 2520.5 RMSD between 443 pruned atom pairs is 0.785 angstroms; (across all 512 pairs: 1.594) Matchmaker 6wek, chain A (#1) with 17-5-3-open-f-coot-0.pdb, chain D (#5), sequence alignment score = 2491.7 RMSD between 487 pruned atom pairs is 0.707 angstroms; (across all 512 pairs: 0.952) Matchmaker 6wek, chain A (#1) with 18-6-4-open-good-3wt-1EA-coot-0.pdb, chain A (#6), sequence alignment score = 2564.8 RMSD between 505 pruned atom pairs is 0.680 angstroms; (across all 512 pairs: 0.744) > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/B #1/C #1/D Alignment identifier is 1 > hide cartoons Drag select of 1194 atoms, 1156 bonds > delete sel > show cartoons > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!3 models > show #!3 models > ui tool show Matchmaker > matchmaker #!2-6 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 6wek, chain A (#1) with 14-2-3-open-coot-0.pdb, chain B (#2), sequence alignment score = 2478.4 RMSD between 491 pruned atom pairs is 0.677 angstroms; (across all 496 pairs: 0.736) Matchmaker 6wek, chain A (#1) with 15-3-3-open-spicel-coot-0.pdb, chain A (#3), sequence alignment score = 2459.2 RMSD between 494 pruned atom pairs is 0.560 angstroms; (across all 496 pairs: 0.590) Matchmaker 6wek, chain A (#1) with 16-4-3-open-spicel-coot-0.pdb, chain D (#4), sequence alignment score = 2456.9 RMSD between 428 pruned atom pairs is 0.798 angstroms; (across all 496 pairs: 1.616) Matchmaker 6wek, chain A (#1) with 17-5-3-open-f-coot-0.pdb, chain D (#5), sequence alignment score = 2434.1 RMSD between 471 pruned atom pairs is 0.714 angstroms; (across all 496 pairs: 0.964) Matchmaker 6wek, chain A (#1) with 18-6-4-open-good-3wt-1EA-coot-0.pdb, chain D (#6), sequence alignment score = 2502.4 RMSD between 493 pruned atom pairs is 0.559 angstroms; (across all 496 pairs: 0.605) > matchmaker #!2-6 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 6wek, chain A (#1) with 14-2-3-open-coot-0.pdb, chain B (#2), sequence alignment score = 2478.4 RMSD between 491 pruned atom pairs is 0.677 angstroms; (across all 496 pairs: 0.736) Matchmaker 6wek, chain A (#1) with 15-3-3-open-spicel-coot-0.pdb, chain A (#3), sequence alignment score = 2459.2 RMSD between 494 pruned atom pairs is 0.560 angstroms; (across all 496 pairs: 0.590) Matchmaker 6wek, chain A (#1) with 16-4-3-open-spicel-coot-0.pdb, chain D (#4), sequence alignment score = 2456.9 RMSD between 428 pruned atom pairs is 0.798 angstroms; (across all 496 pairs: 1.616) Matchmaker 6wek, chain A (#1) with 17-5-3-open-f-coot-0.pdb, chain D (#5), sequence alignment score = 2434.1 RMSD between 471 pruned atom pairs is 0.714 angstroms; (across all 496 pairs: 0.964) Matchmaker 6wek, chain A (#1) with 18-6-4-open-good-3wt-1EA-coot-0.pdb, chain D (#6), sequence alignment score = 2502.4 RMSD between 493 pruned atom pairs is 0.559 angstroms; (across all 496 pairs: 0.605) > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > show #!5 models > show #!4 models > show #!3 models > hide #!4 models > hide #!5 models > hide #!6 models > show #!4 models > ui tool show ""Side View"" > hide #!3 models > hide #!4 models > show #!4 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > show #!1 models > hide #!1 models > show #!1 models > open 6wej format mmcif fromDatabase pdb 6wej title: Structure of cGMP-unbound WT TAX-4 reconstituted in lipid nanodiscs [more info...] Chain information for 6wej #7 --- Chain | Description | UniProt A B C D | Cyclic nucleotide-gated cation channel | CNG_CAEEL 1-733 Non-standard residues in 6wej #7 --- CPL — 1-palmitoyl-2-linoleoyl-Sn-glycero-3-phosphocholine (palmitoyl-linoleoyl phosphatidylcholine) NA — sodium ion PX2 — 1,2-dilauroyl-Sn-glycero-3-phosphate > select #1/A-D:403 44 atoms, 44 bonds, 4 residues, 1 model selected > select #1/A-D:403 44 atoms, 44 bonds, 4 residues, 1 model selected > hide sel cartoons > select add #1 16386 atoms, 16712 bonds, 56 pseudobonds, 1988 residues, 3 models selected > select subtract #1 Nothing selected > show #!3 models > hide #!3 models > show #!6 models > show #!3 models > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!7 models > show #!6 models > show #!5 models > show #!2 models > hide #!5 models > show #!4 models > show #!3 models > hide #!4 models > show #!4 models > show #!5 models > show #!7 models > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!1 models > show #!3 models > hide #!1 models > open ""/Users/daisy/Documents/TAX4/cGMP-bound/WT-cGMP/Wt-cGMP-no ligand.pdb"" > format pdb No such file/path: /Users/daisy/Documents/TAX4/cGMP-bound/WT-cGMP/Wt-cGMP-no ligand.pdb > open /Users/daisy/Documents/TAX4/cGMP-bound/WT-cGMP/Wt-cGMP.pdb format pdb No such file/path: /Users/daisy/Documents/TAX4/cGMP-bound/WT-cGMP/Wt-cGMP.pdb > open /Users/daisy/Documents/TAX4/cGMP-bound/WT- > cGMP/RealSpaceRefine_37/20250623-WT-cGMP-bound-3_real_space_refined_037.pdb Chain information for 20250623-WT-cGMP-bound-3_real_space_refined_037.pdb #8 --- Chain | Description A B C D | No description available 36 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > ui tool show Matchmaker > matchmaker #!8 to #2 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 14-2-3-open-coot-0.pdb, chain B (#2) with 20250623-WT-cGMP- bound-3_real_space_refined_037.pdb, chain A (#8), sequence alignment score = 2580.4 RMSD between 503 pruned atom pairs is 0.679 angstroms; (across all 512 pairs: 0.765) > open /Users/daisy/Documents/TAX4/apo/WT/apo-WT- > unligand-0_real_space_refined_014-coot-2.pdb Chain information for apo-WT-unligand-0_real_space_refined_014-coot-2.pdb #9 --- Chain | Description A B C D | No description available > ui tool show Matchmaker > matchmaker #!9 to #8 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 20250623-WT-cGMP-bound-3_real_space_refined_037.pdb, chain B (#8) with apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain A (#9), sequence alignment score = 2588.4 RMSD between 275 pruned atom pairs is 0.563 angstroms; (across all 510 pairs: 3.428) > hide #!3 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > show #!3 models > hide #!8 models > show #!8 models > hide #!8 models > hide #!3 models > show #!3 models > hide #!9 models > select #3/D 4230 atoms, 4332 bonds, 1 pseudobond, 512 residues, 2 models selected > color (#!3 & sel) orange red > show #!9 models > select clear > ui tool show Matchmaker > matchmaker #!3 to #9 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 apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain A (#9) with 15-3-3-open-spicel-coot-0.pdb, chain A (#3), sequence alignment score = 2529 RMSD between 287 pruned atom pairs is 0.530 angstroms; (across all 510 pairs: 3.849) > select #1/A-D:403 44 atoms, 44 bonds, 4 residues, 1 model selected > select #1/A-D:290 28 atoms, 24 bonds, 4 residues, 1 model selected > select #1/A-D:246-290 1556 atoms, 1600 bonds, 180 residues, 1 model selected > select #1/A-D:250 48 atoms, 48 bonds, 4 residues, 1 model selected > select #1/A-D:250-253 156 atoms, 156 bonds, 16 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #8/A Alignment identifier is 8/A > sequence chain #8/B Alignment identifier is 8/B > sequence chain #8/C Alignment identifier is 8/C > sequence chain #8/D Alignment identifier is 8/D > ui tool show ""Show Sequence Viewer"" > sequence chain #9/A #9/B #9/C #9/D Alignment identifier is 2 > select #9/A-D:403 44 atoms, 44 bonds, 4 residues, 1 model selected > select #9/A-D:403 44 atoms, 44 bonds, 4 residues, 1 model selected > show sel atoms > ui tool show ""Show Sequence Viewer"" > ui tool show Missing or invalid ""toolName"" argument: Expected a text string > ui tool show ""show sequence viewer"" > sequence chain #2/A #2/B #2/C #3/A #3/B #3/C #4/A #4/B #4/C #5/A #5/B #5/C > #6/A #6/B #6/C #6/D #8/A #8/B #8/C #8/D Alignment identifier is 3 > sequence chain #2/D #3/D #4/D #5/D Alignment identifier is 4 > select #2/A-C:404 #3/A-C:404 #4/A-C:404 #5/A-C:404 #6/A-D:404 #8/A-D:404 100 atoms, 80 bonds, 20 residues, 6 models selected > select #2/A-C:403-404 #3/A-C:403-404 #4/A-C:403-404 #5/A-C:403-404 > #6/A-D:403-404 #8/A-D:403-404 320 atoms, 320 bonds, 40 residues, 6 models selected 3 [ID: 3] region 20 chains [295-296] RMSD: 1.466 > select > #2/A-C:103-111,119-145,193-224,236-246,248-256,259-265,276-301,303-335,358-375,385-438,441-458,464-489,491-496,498-507,559-564,592-620 > #3/A-C:103-111,119-145,193-224,236-246,248-256,259-265,276-301,303-335,358-375,385-438,441-458,464-489,491-496,498-507,559-564,592-620 > #4/A-C:103-111,119-145,193-224,236-246,248-256,259-265,276-301,303-335,358-375,385-438,441-458,464-489,491-496,498-507,559-564,592-620 > #5/A-C:103-111,119-145,193-224,236-246,248-256,259-265,276-301,303-335,358-375,385-438,441-458,464-489,491-496,498-507,559-564,592-620 > #6/A-D:103-111,119-145,193-224,236-246,248-256,259-265,276-301,303-335,358-375,385-438,441-458,464-489,491-496,498-507,559-564,592-620 > #8/A-D:103-111,119-145,193-224,236-246,248-256,259-265,276-301,303-335,358-375,385-438,441-458,464-489,491-496,498-507,559-564,592-620 54520 atoms, 55620 bonds, 6420 residues, 6 models selected > select #2/A-C:403 #3/A-C:403 #4/A-C:403 #5/A-C:403 #6/A-D:403 #8/A-D:403 220 atoms, 220 bonds, 20 residues, 6 models selected > select #2/A-C:403 #3/A-C:403 #4/A-C:403 #5/A-C:403 #6/A-D:403 #8/A-D:403 220 atoms, 220 bonds, 20 residues, 6 models selected 3 [ID: 3] region 20 chains [295] RMSD: 1.261 > show sel & #!3 atoms > select #9/A-D:403 44 atoms, 44 bonds, 4 residues, 1 model selected > select #9/A-D:403 44 atoms, 44 bonds, 4 residues, 1 model selected > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel atoms > show sel atoms > select #1/A-D:404 20 atoms, 16 bonds, 4 residues, 1 model selected > select #1/A-D:403-404 64 atoms, 64 bonds, 8 residues, 1 model selected > select > #1/A-D:103-111,119-145,193-224,236-246,248-256,259-265,276-301,303-335,359-375,386-438,441-458,464-489,491-496,498-507,559-564,592-620 10350 atoms, 10492 bonds, 36 pseudobonds, 1232 residues, 2 models selected > select #1/A-D:403 44 atoms, 44 bonds, 4 residues, 1 model selected > select #1/A-D:403 44 atoms, 44 bonds, 4 residues, 1 model selected > select #2/A-C:403 #3/A-C:403 #4/A-C:403 #5/A-C:403 #6/A-D:403 #8/A-D:403 220 atoms, 220 bonds, 20 residues, 6 models selected > select #2/A-C:403 #3/A-C:403 #4/A-C:403 #5/A-C:403 #6/A-D:403 #8/A-D:403 220 atoms, 220 bonds, 20 residues, 6 models selected 3 [ID: 3] region 20 chains [295] RMSD: 1.261 > ui tool show ""show sequence viewer"" > sequence chain #2/D #3/D #4/D #5/D Alignment identifier is 5 > select #2/D:404 #3/D:404 #4/D:404 #5/D:404 20 atoms, 16 bonds, 4 residues, 4 models selected > select #2/D:403-404 #3/D:403-404 #4/D:403-404 #5/D:403-404 64 atoms, 64 bonds, 8 residues, 4 models selected 5 [ID: 5] region 4 chains [295-296] RMSD: 12.733 > select #2/D:403 #3/D:403 #4/D:403 #5/D:403 44 atoms, 44 bonds, 4 residues, 4 models selected > select #2/D:403 #3/D:403 #4/D:403 #5/D:403 44 atoms, 44 bonds, 4 residues, 4 models selected 5 [ID: 5] region 4 chains [295] RMSD: 15.028 > show sel & #!3 atoms > show #!2 models > hide #!2 models > hide #!9 models > view #3 clip false > view > view orient > select add #9 17009 atoms, 17420 bonds, 4 pseudobonds, 2057 residues, 6 models selected > select subtract #9 44 atoms, 44 bonds, 4 residues, 4 models selected > select add #9 17009 atoms, 17420 bonds, 4 pseudobonds, 2057 residues, 6 models selected > select subtract #9 44 atoms, 44 bonds, 4 residues, 4 models selected > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > select #2/D:442 #3/D:442 #4/D:442 #5/D:442 36 atoms, 32 bonds, 4 residues, 4 models selected > select #2/D:442 #3/D:442 #4/D:442 #5/D:442 36 atoms, 32 bonds, 4 residues, 4 models selected 5 [ID: 5] region 4 chains [334] RMSD: 46.259 > select #2/D:358 #3/D:358 #4/D:358 #5/D:358 28 atoms, 24 bonds, 4 residues, 4 models selected > select #2/D:358-375 #3/D:358-375 #4/D:358-375 #5/D:358-375 652 atoms, 672 bonds, 72 residues, 4 models selected 5 [ID: 5] region 4 chains [250-267] RMSD: 26.104 > hide #!3 models > show #!6 models > select #3/D 4230 atoms, 4332 bonds, 1 pseudobond, 512 residues, 2 models selected > select #6/D 4257 atoms, 4362 bonds, 1 pseudobond, 513 residues, 2 models selected > select #2/D#3/D#4/D#5/D#6/D#8/D#9/D 29652 atoms, 30371 bonds, 7 pseudobonds, 3586 residues, 14 models selected > ui tool show ""Color Actions"" > color sel maroon > color sel dark red > color sel tomato > color sel salmon > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > view #3 clip false > turn Y 90 > ui tool show ""Show Sequence Viewer"" > sequence chain #6/A Alignment identifier is 6/A > sequence chain #6/B Alignment identifier is 6/B > sequence chain #6/C Alignment identifier is 6/C > sequence chain #6/D Alignment identifier is 6/D > view #6 clip false > save /Users/daisy/Desktop/image1.png supersample 3 > turn Y > view > view sel > view > view orient > turn z > turn z 90 > turn X > turn Y > coulombic sel & #!6 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 18-6-4-open-good-3wt-1EA-coot-0.pdb_D SES surface #6.2: minimum, -12.98, mean 0.92, maximum 16.64 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel & #!6 Coulombic values for 18-6-4-open-good-3wt-1EA-coot-0.pdb_D SES surface #6.2: minimum, -12.98, mean 0.92, maximum 16.64 To also show corresponding color key, enter the above coulombic command and add key true > select clear Cell requested for row 5 is out of bounds for table with 10 rows! Resizing table model. > undo Drag select of 18-6-4-open-good-3wt-1EA-coot-0.pdb_D SES surface, 494277 of 497658 triangles, 219 atoms, 2048 residues, 3 pseudobonds, 211 bonds > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 18-6-4-open-good-3wt-1EA-coot-0.pdb_A SES surface #6.3: minimum, -13.34, mean 0.92, maximum 20.24 Coulombic values for 18-6-4-open-good-3wt-1EA-coot-0.pdb_B SES surface #6.4: minimum, -14.43, mean 0.88, maximum 20.44 Coulombic values for 18-6-4-open-good-3wt-1EA-coot-0.pdb_C SES surface #6.5: minimum, -15.28, mean 0.91, maximum 20.13 Coulombic values for 18-6-4-open-good-3wt-1EA-coot-0.pdb_D SES surface #6.2: minimum, -12.98, mean 0.92, maximum 16.64 To also show corresponding color key, enter the above coulombic command and add key true > select clear > view orient > turn Y > turn X > turn Y > turn X > turn Y > show #!6 atoms > turn Y > view name chainA_view > hide /A show/B Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide /A show /B Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show #!1 models > hide #!6 models > rainbow #!1 > coulombic #!1 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 6wek_A SES surface #1.2: minimum, -16.04, mean 0.82, maximum 19.74 Coulombic values for 6wek_B SES surface #1.3: minimum, -28.32, mean 0.81, maximum 13.40 Coulombic values for 6wek_C SES surface #1.4: minimum, -12.69, mean 0.82, maximum 15.13 Coulombic values for 6wek_D SES surface #1.5: minimum, -14.34, mean 0.81, maximum 13.52 To also show corresponding color key, enter the above coulombic command and add key true > color #!1 bychain > hide #!1 models > show #!6 models > color #!6 byhetero > color #!6 bychain > coulombic #!6 Coulombic values for 18-6-4-open-good-3wt-1EA-coot-0.pdb_A SES surface #6.3: minimum, -13.34, mean 0.92, maximum 20.24 Coulombic values for 18-6-4-open-good-3wt-1EA-coot-0.pdb_B SES surface #6.4: minimum, -14.43, mean 0.88, maximum 20.44 Coulombic values for 18-6-4-open-good-3wt-1EA-coot-0.pdb_C SES surface #6.5: minimum, -15.28, mean 0.91, maximum 20.13 Coulombic values for 18-6-4-open-good-3wt-1EA-coot-0.pdb_D SES surface #6.2: minimum, -12.98, mean 0.92, maximum 16.64 To also show corresponding color key, enter the above coulombic command and add key true > hide #!6 models > show #!5 models > coulombic #!5 The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: 17-5-3-open-f-coot-0.pdb #5/D THR 576 OG1 17-5-3-open-f-coot-0.pdb #5/D THR 576 CG2 17-5-3-open-f-coot-0.pdb #5/B THR 576 OG1 17-5-3-open-f-coot-0.pdb #5/B THR 576 CG2 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 17-5-3-open-f-coot-0.pdb_A SES surface #5.2: minimum, -20.79, mean 0.87, maximum 19.45 Coulombic values for 17-5-3-open-f-coot-0.pdb_B SES surface #5.3: minimum, -14.83, mean 0.93, maximum 17.57 Coulombic values for 17-5-3-open-f-coot-0.pdb_C SES surface #5.4: minimum, -22.03, mean 0.87, maximum 15.48 Coulombic values for 17-5-3-open-f-coot-0.pdb_D SES surface #5.5: minimum, -14.09, mean 0.63, maximum 16.11 To also show corresponding color key, enter the above coulombic command and add key true > mlp #!5 Map values for surface ""17-5-3-open-f-coot-0.pdb_A SES surface"": minimum -28.64, mean -1.474, maximum 23.23 Map values for surface ""17-5-3-open-f-coot-0.pdb_B SES surface"": minimum -30.43, mean -1.578, maximum 23.49 Map values for surface ""17-5-3-open-f-coot-0.pdb_C SES surface"": minimum -29.55, mean -1.324, maximum 23.64 Map values for surface ""17-5-3-open-f-coot-0.pdb_D SES surface"": minimum -29.41, mean -1.344, maximum 24.73 To also show corresponding color key, enter the above mlp command and add key true > hide #!5 models > show #!5 models > coulombic #!5 Coulombic values for 17-5-3-open-f-coot-0.pdb_A SES surface #5.2: minimum, -20.79, mean 0.87, maximum 19.45 Coulombic values for 17-5-3-open-f-coot-0.pdb_B SES surface #5.3: minimum, -14.83, mean 0.93, maximum 17.57 Coulombic values for 17-5-3-open-f-coot-0.pdb_C SES surface #5.4: minimum, -22.03, mean 0.87, maximum 15.48 Coulombic values for 17-5-3-open-f-coot-0.pdb_D SES surface #5.5: minimum, -14.09, mean 0.63, maximum 16.11 To also show corresponding color key, enter the above coulombic command and add key true > show #!5 cartoons > hide #!5 cartoons > style #!5 stick Changed 16999 atom styles > style #!5 stick Changed 16999 atom styles > nucleotides #!5 atoms > style nucleic & #!5 stick Changed 0 atom styles > nucleotides #!5 atoms > style nucleic & #!5 stick Changed 0 atom styles > nucleotides #!5 atoms > style nucleic & #!5 stick Changed 0 atom styles > nucleotides #!5 atoms > style nucleic & #!5 stick Changed 0 atom styles > hide #!5 surfaces > show #!5 cartoons > show #!5 surfaces > mlp #!5 Map values for surface ""17-5-3-open-f-coot-0.pdb_A SES surface"": minimum -28.64, mean -1.474, maximum 23.23 Map values for surface ""17-5-3-open-f-coot-0.pdb_B SES surface"": minimum -30.43, mean -1.578, maximum 23.49 Map values for surface ""17-5-3-open-f-coot-0.pdb_C SES surface"": minimum -29.55, mean -1.324, maximum 23.64 Map values for surface ""17-5-3-open-f-coot-0.pdb_D SES surface"": minimum -29.41, mean -1.344, maximum 24.73 To also show corresponding color key, enter the above mlp command and add key true > coulombic #!5 Coulombic values for 17-5-3-open-f-coot-0.pdb_A SES surface #5.2: minimum, -20.79, mean 0.87, maximum 19.45 Coulombic values for 17-5-3-open-f-coot-0.pdb_B SES surface #5.3: minimum, -14.83, mean 0.93, maximum 17.57 Coulombic values for 17-5-3-open-f-coot-0.pdb_C SES surface #5.4: minimum, -22.03, mean 0.87, maximum 15.48 Coulombic values for 17-5-3-open-f-coot-0.pdb_D SES surface #5.5: minimum, -14.09, mean 0.63, maximum 16.11 To also show corresponding color key, enter the above coulombic command and add key true > mlp #!5 Map values for surface ""17-5-3-open-f-coot-0.pdb_A SES surface"": minimum -28.64, mean -1.474, maximum 23.23 Map values for surface ""17-5-3-open-f-coot-0.pdb_B SES surface"": minimum -30.43, mean -1.578, maximum 23.49 Map values for surface ""17-5-3-open-f-coot-0.pdb_C SES surface"": minimum -29.55, mean -1.324, maximum 23.64 Map values for surface ""17-5-3-open-f-coot-0.pdb_D SES surface"": minimum -29.41, mean -1.344, maximum 24.73 To also show corresponding color key, enter the above mlp command and add key true > hide #!5 surfaces > show #!5 surfaces > hide #!5 surfaces > show #!5 atoms > show #!5 surfaces > show #!5 cartoons > hide #!5 surfaces > show #!5 surfaces > hide #!5 surfaces > show #!5 surfaces > hide #!5 surfaces > show #!5 surfaces > hide #!5 surfaces > show #!5 surfaces > hide #!5 surfaces > ui tool show ""Show Sequence Viewer"" > sequence chain #6/D Destroying pre-existing alignment with identifier 6/D Alignment identifier is 6/D > ui tool show ""Show Sequence Viewer"" > sequence chain #5/D Alignment identifier is 5/D > select #5/D:530 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/D:530 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/D:560 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/D:560 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/D:612 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5/D:612 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel cartoons > select #5/D 4230 atoms, 4332 bonds, 1 pseudobond, 512 residues, 2 models selected > color (#!5 & sel) byelement > color (#!5 & sel) byhetero > select clear > select #5/D:530 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/D:530-531 20 atoms, 20 bonds, 2 residues, 1 model selected > select #5/D:530-531 20 atoms, 20 bonds, 2 residues, 1 model selected > select #5/D:530-531 20 atoms, 20 bonds, 2 residues, 1 model selected > mlp sel Map values for surface ""17-5-3-open-f-coot-0.pdb_D SES surface"": minimum -29.41, mean -1.344, maximum 24.73 To also show corresponding color key, enter the above mlp command and add key true > select clear > mlp #!5 Map values for surface ""17-5-3-open-f-coot-0.pdb_A SES surface"": minimum -28.64, mean -1.474, maximum 23.23 Map values for surface ""17-5-3-open-f-coot-0.pdb_B SES surface"": minimum -30.43, mean -1.578, maximum 23.49 Map values for surface ""17-5-3-open-f-coot-0.pdb_C SES surface"": minimum -29.55, mean -1.324, maximum 23.64 Map values for surface ""17-5-3-open-f-coot-0.pdb_D SES surface"": minimum -29.41, mean -1.344, maximum 24.73 To also show corresponding color key, enter the above mlp command and add key true > hide #!5 surfaces > hide #!5 models > show #!6 models > hide #!6 models > show #!3 models > hide #!3 models > show #!6 models > hide #!6 models > show #!7 models > color #7 #ff7e79ff > color #7 #ffd479ff > color #7 #d783ffff > color #7 #ff8ad8ff > color #7 #941751ff > show #!7 atoms > color #7 byelement > hide #!7 models > show #!8 models > show #!8 surfaces > mlp #!8 Map values for surface ""20250623-WT-cGMP-bound-3_real_space_refined_037.pdb_A SES surface"": minimum -27.71, mean -1.509, maximum 23.29 Map values for surface ""20250623-WT-cGMP-bound-3_real_space_refined_037.pdb_B SES surface"": minimum -27.12, mean -1.445, maximum 23.8 Map values for surface ""20250623-WT-cGMP-bound-3_real_space_refined_037.pdb_C SES surface"": minimum -27.9, mean -1.5, maximum 23.76 Map values for surface ""20250623-WT-cGMP-bound-3_real_space_refined_037.pdb_D SES surface"": minimum -29.93, mean -1.535, maximum 23.97 To also show corresponding color key, enter the above mlp command and add key true > open ""/Users/daisy/Documents/TAX4/apo/EA/EA-coot-7-no ligand.pdb"" format pdb Chain information for EA-coot-7-no ligand.pdb #10 --- Chain | Description A B C D | No description available > ui tool show Matchmaker > matchmaker #!10 to #7 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 6wej, chain A (#7) with EA-coot-7-no ligand.pdb, chain A (#10), sequence alignment score = 2584.2 RMSD between 508 pruned atom pairs is 0.624 angstroms; (across all 513 pairs: 0.670) > hide #!8 models > show #!7 models > show #!7,10 cartoons > show #!7,10 surfaces > coulombic #!7,10 Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 6wej_A SES surface #7.3: minimum, -12.77, mean 0.94, maximum 21.06 Coulombic values for 6wej_B SES surface #7.4: minimum, -22.16, mean 0.93, maximum 22.05 Coulombic values for 6wej_C SES surface #7.5: minimum, -12.16, mean 0.92, maximum 22.17 Coulombic values for 6wej_D SES surface #7.6: minimum, -12.18, mean 0.95, maximum 21.28 Coulombic values for EA-coot-7-no ligand.pdb_A SES surface #10.2: minimum, -14.72, mean 0.81, maximum 17.35 Coulombic values for EA-coot-7-no ligand.pdb_B SES surface #10.3: minimum, -15.22, mean 0.81, maximum 17.57 Coulombic values for EA-coot-7-no ligand.pdb_C SES surface #10.4: minimum, -13.97, mean 0.79, maximum 23.28 Coulombic values for EA-coot-7-no ligand.pdb_D SES surface #10.5: minimum, -12.29, mean 0.79, maximum 18.64 To also show corresponding color key, enter the above coulombic command and add key true > mlp #!7,10 Map values for surface ""EA-coot-7-no ligand.pdb_A SES surface"": minimum -29.29, mean -1.657, maximum 23.49 Map values for surface ""EA-coot-7-no ligand.pdb_B SES surface"": minimum -28.52, mean -1.613, maximum 24.59 Map values for surface ""EA-coot-7-no ligand.pdb_C SES surface"": minimum -30.94, mean -1.531, maximum 23.77 Map values for surface ""EA-coot-7-no ligand.pdb_D SES surface"": minimum -28.26, mean -1.579, maximum 23.87 Map values for surface ""6wej_A SES surface"": minimum -27.68, mean -1.543, maximum 24.29 Map values for surface ""6wej_B SES surface"": minimum -28.63, mean -1.505, maximum 24.98 Map values for surface ""6wej_C SES surface"": minimum -27.66, mean -1.49, maximum 25.02 Map values for surface ""6wej_D SES surface"": minimum -28.06, mean -1.528, maximum 23.83 To also show corresponding color key, enter the above mlp command and add key true > show #!8 models > hide #!7 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > hide #!10 models > show #!10 models > show #!8 models > hide #!10 models > show #!10 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > hide #!8 models > show #!8 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > hide #!8 models > show #!8 models > open /Users/daisy/Documents/TAX4/WT-EA/Wt-cGMP.pdb Chain information for Wt-cGMP.pdb #11 --- Chain | Description A B C D | No description available 36 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > ui tool show ""Show Sequence Viewer"" > ui tool show Matchmaker > matchmaker #!11 to #8 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 20250623-WT-cGMP-bound-3_real_space_refined_037.pdb, chain B (#8) with Wt-cGMP.pdb, chain C (#11), sequence alignment score = 2623 RMSD between 507 pruned atom pairs is 0.556 angstroms; (across all 512 pairs: 0.608) > hide #!8 models > mlp #!11 Map values for surface ""Wt-cGMP.pdb_A SES surface"": minimum -28.78, mean -1.452, maximum 24.37 Map values for surface ""Wt-cGMP.pdb_B SES surface"": minimum -30.14, mean -1.399, maximum 23.95 Map values for surface ""Wt-cGMP.pdb_C SES surface"": minimum -29.01, mean -1.356, maximum 23.63 Map values for surface ""Wt-cGMP.pdb_D SES surface"": minimum -30.24, mean -1.443, maximum 23.41 To also show corresponding color key, enter the above mlp command and add key true > hide #!11 models > show #!5 models > mlp #!5 Map values for surface ""17-5-3-open-f-coot-0.pdb_A SES surface"": minimum -28.64, mean -1.474, maximum 23.23 Map values for surface ""17-5-3-open-f-coot-0.pdb_B SES surface"": minimum -30.43, mean -1.578, maximum 23.49 Map values for surface ""17-5-3-open-f-coot-0.pdb_C SES surface"": minimum -29.55, mean -1.324, maximum 23.64 Map values for surface ""17-5-3-open-f-coot-0.pdb_D SES surface"": minimum -29.41, mean -1.344, maximum 24.73 To also show corresponding color key, enter the above mlp command and add key true > hide #!5 models > show #!4 models > mlp #!4 Map values for surface ""16-4-3-open-spicel-coot-0.pdb_A SES surface"": minimum -29.02, mean -1.418, maximum 24.3 Map values for surface ""16-4-3-open-spicel-coot-0.pdb_B SES surface"": minimum -28.72, mean -1.579, maximum 23.72 Map values for surface ""16-4-3-open-spicel-coot-0.pdb_C SES surface"": minimum -28.14, mean -1.422, maximum 23.59 Map values for surface ""16-4-3-open-spicel-coot-0.pdb_D SES surface"": minimum -31.25, mean -1.456, maximum 23.89 To also show corresponding color key, enter the above mlp command and add key true > hide #!4 models > show #!3 models > mlp #!3 Map values for surface ""15-3-3-open-spicel-coot-0.pdb_A SES surface"": minimum -28.3, mean -1.478, maximum 22.89 Map values for surface ""15-3-3-open-spicel-coot-0.pdb_B SES surface"": minimum -30.67, mean -1.51, maximum 22.83 Map values for surface ""15-3-3-open-spicel-coot-0.pdb_C SES surface"": minimum -30.48, mean -1.375, maximum 24.03 Map values for surface ""15-3-3-open-spicel-coot-0.pdb_D SES surface"": minimum -29.26, mean -1.612, maximum 23.75 To also show corresponding color key, enter the above mlp command and add key true > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > show #!6 models > hide #!3,6,11 surfaces > select #6/D 4257 atoms, 4362 bonds, 1 pseudobond, 513 residues, 2 models selected > select ~sel & ##selected 12771 atoms, 13086 bonds, 3 pseudobonds, 1539 residues, 2 models selected > hide sel cartoons > hide sel atoms > hide #!11 models > hide #!3 models > show #!11 models > hide #!6 models > select #11/B 4395 atoms, 4493 bonds, 1 pseudobond, 520 residues, 2 models selected > select ~sel & ##selected 13185 atoms, 13479 bonds, 3 pseudobonds, 1560 residues, 2 models selected > hide sel cartoons > select clear > hide #!11 cartoons Drag select of 1084 atoms, 1045 bonds > delete sel > show #!6 models > show #!10 models > hide #!10 models > hide #!6 models > show #!6 models > hide #!11 models > show #!11 models > show #!6,11 cartoons > undo Undo failed, probably because structures have been modified. > undo Undo failed, probably because structures have been modified. > redo > hide #!6,10-11 surfaces > hide #!6 models > hide #!10 models > hide #!11 models > show #!11 models > show #!11 cartoons > undo > hide #!10 models > hide #!11 models > show #!11 models > hide #!6 models > show #!11 cartoons > show #!8 models > hide #!8,11 surfaces > select #6/B 4257 atoms, 4362 bonds, 1 pseudobond, 513 residues, 2 models selected > select ~sel & ##selected 12771 atoms, 13086 bonds, 3 pseudobonds, 1539 residues, 2 models selected > hide #!8,11 cartoons > undo > select #6/B 4257 atoms, 4362 bonds, 1 pseudobond, 513 residues, 2 models selected > hide #!11 models > select add #6 17028 atoms, 17448 bonds, 4 pseudobonds, 2052 residues, 3 models selected > select subtract #6 4 models selected > show #!6 models > hide #!6 models > select #8/B 4234 atoms, 4337 bonds, 1 pseudobond, 512 residues, 2 models selected > select #8/A 4234 atoms, 4337 bonds, 1 pseudobond, 512 residues, 2 models selected > select ~sel & ##selected 12702 atoms, 13011 bonds, 3 pseudobonds, 1536 residues, 2 models selected > hide sel cartoons > show #!6 models > hide #!6 models > hide sel atoms > show sel atoms > hide sel atoms Drag select of 512 residues, 1 pseudobonds > show sel atoms > show #!6 models > select clear > hide #!8 models > show #!8 models > select 492 Expected an objects specifier or a keyword > select ：492 Expected an objects specifier or a keyword > select :492 484 atoms, 440 bonds, 44 residues, 11 models selected > save /Users/daisy/Documents/TAX4/WT-EA/WT-cGMP-18-6-4-3WT-1EA.pdb models > #8-11 displayedOnly true > show #!11 models > select #11/B 4135 atoms, 4224 bonds, 11 pseudobonds, 500 residues, 2 models selected > select ~sel & ##selected 12361 atoms, 12613 bonds, 38 pseudobonds, 1499 residues, 2 models selected > hide sel cartoons > hide #!11 models > show #!10 models > select #10/A 4238 atoms, 4339 bonds, 1 pseudobond, 514 residues, 2 models selected > select #10/B 4237 atoms, 4339 bonds, 1 pseudobond, 513 residues, 2 models selected > select ~sel & ##selected 12712 atoms, 13017 bonds, 3 pseudobonds, 1540 residues, 2 models selected > hide sel cartoons > show sel atoms > hide sel atoms > select add #10 16949 atoms, 17356 bonds, 4 pseudobonds, 2053 residues, 5 models selected > show sel atoms > hide sel atoms > show sel atoms > hide sel atoms > select subtract #10 4 models selected > hide #!8 models > hide #!6 models Drag select of 513 residues, 1 pseudobonds > show sel atoms > show #!8 models > show #!6 models > select clear > hide #!10 models > hide #!8 models > hide #!6 models > show #!9 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > select #9/D 4241 atoms, 4344 bonds, 1 pseudobond, 513 residues, 2 models selected > select ~sel & ##selected 12724 atoms, 13032 bonds, 3 pseudobonds, 1540 residues, 2 models selected > hide sel cartoons > select clear Drag select of 75 atoms, 513 residues, 1 pseudobonds, 70 bonds > show sel atoms > select clear > show #!8 models > show #!7 models > hide #!7 models > show #!11 models > hide #!11 models > show #!10 models > show #!6 models > hide #!9 models > show #!9 models > hide #!10 models > show #!10 models > hide #!9 models > show #!9 models > hide #!8 models > show #!8 models > hide #!6 models > show #!5 models > hide #!8 models > hide #!9 models > hide #!10 models > hide #!5 surfaces > select #5/B 4232 atoms, 4334 bonds, 1 pseudobond, 512 residues, 2 models selected > select ~sel & ##selected 12767 atoms, 13082 bonds, 3 pseudobonds, 1539 residues, 2 models selected > hide sel cartoons > hide sel atoms > show #!9 models > show #!10 models > show #!8 models > ui tool show Matchmaker > matchmaker #!5 to #6/D pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 18-6-4-open-good-3wt-1EA-coot-0.pdb, chain D (#6) with 17-5-3-open- f-coot-0.pdb, chain B (#5), sequence alignment score = 2565.4 RMSD between 507 pruned atom pairs is 0.552 angstroms; (across all 512 pairs: 0.625) > matchmaker #!5 to #6/D pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 18-6-4-open-good-3wt-1EA-coot-0.pdb, chain D (#6) with 17-5-3-open- f-coot-0.pdb, chain B (#5), sequence alignment score = 2565.4 RMSD between 507 pruned atom pairs is 0.552 angstroms; (across all 512 pairs: 0.625) > hide #!9 models > hide #!8 models > show #!9 models > show #!8 models > hide #!9 models > show #!9 models > hide #!9 models > hide #!8 models > save /Users/daisy/Documents/TAX4/WT-EA/002.pdb > hide #!10 models > show #!4 models > show #!3 models > show #!6 models > hide #!4 models > hide #!3 models > show #!10 models > hide #!10 models > show #!7 models > hide #!6 models > hide #!5 models > hide #!7 models > show #!6 models > show #!10 models > show #!8 models > hide #!8 models > hide #!10 models > show #!5 models > show #!4 models > hide #!5 models > hide #!6 models > hide #!4 surfaces > hide #!4 models > show #!9 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!9 models > show #!9 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!9 models > show #!9 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > hide #!8 models > show #!8 models > show #!5 models > show #!4 models > hide #!4 models > hide #!5 models > show #!5 models > hide #!8 models > hide #!5 models > select add #5 16999 atoms, 17416 bonds, 4 pseudobonds, 2051 residues, 5 models selected > show #!4 models > select subtract #5 4 models selected > select #4/D 4230 atoms, 4332 bonds, 1 pseudobond, 512 residues, 2 models selected > select ~sel & ##selected 12769 atoms, 13084 bonds, 3 pseudobonds, 1539 residues, 2 models selected > hide sel cartoons > select clear > color #4 #ff9300ff > color #4 #797979ff > color #4 #5e5e5eff > color #4 #ff8ad8ff > color #4 #ff40ffff > color #4 #00fa92ff > color #4 #00fdffff > color #4 #73fdffff > show #!5 models > hide #!4 models > show #!4 models > hide #!5 models Drag select of 246 atoms, 512 residues, 251 bonds > show sel atoms > show #!5 models > select clear > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!10 models > hide #!10 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!8 models > hide #!8 models > show #!11 models > show #!9 models > hide #!11 models > hide #!5 models > hide #!4 models > show #!8 models > hide #!8 models > show #!11 models > hide #!9 models > show #!9 models > hide #!9 models > show #!8 models > show #!9 models > hide #!11 models > hide #!8 models > show #!8 models > hide #!8 models > show #!10 models > ui tool show Matchmaker > matchmaker #!9 to #10/B pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 EA-coot-7-no ligand.pdb, chain B (#10) with apo-WT- unligand-0_real_space_refined_014-coot-2.pdb, chain C (#9), sequence alignment score = 2563.2 RMSD between 513 pruned atom pairs is 0.566 angstroms; (across all 513 pairs: 0.566) > matchmaker #!9 to #10/A pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 EA-coot-7-no ligand.pdb, chain A (#10) with apo-WT- unligand-0_real_space_refined_014-coot-2.pdb, chain A (#9), sequence alignment score = 2581.2 RMSD between 508 pruned atom pairs is 0.672 angstroms; (across all 513 pairs: 0.704) > matchmaker #!9 to #10/C pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 EA-coot-7-no ligand.pdb, chain C (#10) with apo-WT- unligand-0_real_space_refined_014-coot-2.pdb, chain A (#9), sequence alignment score = 2578.2 RMSD between 508 pruned atom pairs is 0.667 angstroms; (across all 513 pairs: 0.711) > show #!4 models > show #!5 models > show #!8 models > hide #!8 models > show #!8 models > hide #!5 models > hide #!4 models > hide #!8 models > hide #!9 models > hide #!10 models > show #!10 models > show #!9 models > show #!4 models > show #!3 models > hide #!3 models > show #!5 models > show #!3 models > hide #!3 models > ui tool show Matchmaker > ui tool show ""Show Sequence Viewer"" > hide #!9 models > hide #!4 models > hide #!5 models > show #!6 models > hide #!10 models > hide #!6 models > show #!10 models > show #!9 models > show #!8 models > hide #!8 models > show #!8 models > ui tool show Matchmaker > matchmaker #!8,10 to #9/D pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain D (#9) with 20250623-WT-cGMP-bound-3_real_space_refined_037.pdb, chain B (#8), sequence alignment score = 2517.6 RMSD between 306 pruned atom pairs is 0.795 angstroms; (across all 510 pairs: 2.795) Matchmaker apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain D (#9) with EA-coot-7-no ligand.pdb, chain C (#10), sequence alignment score = 2566.8 RMSD between 511 pruned atom pairs is 0.545 angstroms; (across all 513 pairs: 0.566) > matchmaker #!8,10 to #9/C pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain C (#9) with 20250623-WT-cGMP-bound-3_real_space_refined_037.pdb, chain B (#8), sequence alignment score = 2528.4 RMSD between 307 pruned atom pairs is 0.899 angstroms; (across all 510 pairs: 2.840) Matchmaker apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain C (#9) with EA-coot-7-no ligand.pdb, chain B (#10), sequence alignment score = 2563.2 RMSD between 513 pruned atom pairs is 0.566 angstroms; (across all 513 pairs: 0.566) > matchmaker #!8,10 to #9/B pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain B (#9) with 20250623-WT-cGMP-bound-3_real_space_refined_037.pdb, chain B (#8), sequence alignment score = 2540.4 RMSD between 303 pruned atom pairs is 0.811 angstroms; (across all 510 pairs: 2.815) Matchmaker apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain B (#9) with EA-coot-7-no ligand.pdb, chain A (#10), sequence alignment score = 2566.2 RMSD between 511 pruned atom pairs is 0.617 angstroms; (across all 513 pairs: 0.632) > matchmaker #!8,10 to #9/A pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain A (#9) with 20250623-WT-cGMP-bound-3_real_space_refined_037.pdb, chain B (#8), sequence alignment score = 2588.4 RMSD between 275 pruned atom pairs is 0.563 angstroms; (across all 510 pairs: 3.428) Matchmaker apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain A (#9) with EA-coot-7-no ligand.pdb, chain D (#10), sequence alignment score = 2606.4 RMSD between 509 pruned atom pairs is 0.674 angstroms; (across all 513 pairs: 0.707) > undo > show #!9 models > hide #!9 models > hide #!6 models > show #!8 models > show #!9 models > hide #!9 models > hide #!8 models > show #!10 models > show #!9 models > ui tool show Matchmaker > matchmaker #!8,10 to #9/B pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain B (#9) with 20250623-WT-cGMP-bound-3_real_space_refined_037.pdb, chain B (#8), sequence alignment score = 2540.4 RMSD between 303 pruned atom pairs is 0.811 angstroms; (across all 510 pairs: 2.815) Matchmaker apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain B (#9) with EA-coot-7-no ligand.pdb, chain A (#10), sequence alignment score = 2566.2 RMSD between 511 pruned atom pairs is 0.617 angstroms; (across all 513 pairs: 0.632) > matchmaker #!8,10 to #9/B pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain B (#9) with 20250623-WT-cGMP-bound-3_real_space_refined_037.pdb, chain B (#8), sequence alignment score = 2540.4 RMSD between 303 pruned atom pairs is 0.811 angstroms; (across all 510 pairs: 2.815) Matchmaker apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain B (#9) with EA-coot-7-no ligand.pdb, chain A (#10), sequence alignment score = 2566.2 RMSD between 511 pruned atom pairs is 0.617 angstroms; (across all 513 pairs: 0.632) > matchmaker #!8,10 to #9/A pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain A (#9) with 20250623-WT-cGMP-bound-3_real_space_refined_037.pdb, chain B (#8), sequence alignment score = 2588.4 RMSD between 275 pruned atom pairs is 0.563 angstroms; (across all 510 pairs: 3.428) Matchmaker apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain A (#9) with EA-coot-7-no ligand.pdb, chain D (#10), sequence alignment score = 2606.4 RMSD between 509 pruned atom pairs is 0.674 angstroms; (across all 513 pairs: 0.707) > matchmaker #!8,10 to #9/C pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain C (#9) with 20250623-WT-cGMP-bound-3_real_space_refined_037.pdb, chain B (#8), sequence alignment score = 2528.4 RMSD between 307 pruned atom pairs is 0.899 angstroms; (across all 510 pairs: 2.840) Matchmaker apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain C (#9) with EA-coot-7-no ligand.pdb, chain B (#10), sequence alignment score = 2563.2 RMSD between 513 pruned atom pairs is 0.566 angstroms; (across all 513 pairs: 0.566) > matchmaker #!8,10 to #9/D pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain D (#9) with 20250623-WT-cGMP-bound-3_real_space_refined_037.pdb, chain B (#8), sequence alignment score = 2517.6 RMSD between 306 pruned atom pairs is 0.795 angstroms; (across all 510 pairs: 2.795) Matchmaker apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain D (#9) with EA-coot-7-no ligand.pdb, chain C (#10), sequence alignment score = 2566.8 RMSD between 511 pruned atom pairs is 0.545 angstroms; (across all 513 pairs: 0.566) > matchmaker #!8 to #10/A pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 EA-coot-7-no ligand.pdb, chain A (#10) with 20250623-WT-cGMP- bound-3_real_space_refined_037.pdb, chain B (#8), sequence alignment score = 2571.8 RMSD between 314 pruned atom pairs is 0.816 angstroms; (across all 510 pairs: 2.651) > matchmaker #!8 to #10/A pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 EA-coot-7-no ligand.pdb, chain A (#10) with 20250623-WT-cGMP- bound-3_real_space_refined_037.pdb, chain B (#8), sequence alignment score = 2571.8 RMSD between 314 pruned atom pairs is 0.816 angstroms; (across all 510 pairs: 2.651) > matchmaker #!9 to #10/A pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 EA-coot-7-no ligand.pdb, chain A (#10) with apo-WT- unligand-0_real_space_refined_014-coot-2.pdb, chain A (#9), sequence alignment score = 2581.2 RMSD between 508 pruned atom pairs is 0.672 angstroms; (across all 513 pairs: 0.704) > matchmaker #!9 to #10/B pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 EA-coot-7-no ligand.pdb, chain B (#10) with apo-WT- unligand-0_real_space_refined_014-coot-2.pdb, chain C (#9), sequence alignment score = 2563.2 RMSD between 513 pruned atom pairs is 0.566 angstroms; (across all 513 pairs: 0.566) > matchmaker #!9 to #10/C pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 EA-coot-7-no ligand.pdb, chain C (#10) with apo-WT- unligand-0_real_space_refined_014-coot-2.pdb, chain A (#9), sequence alignment score = 2578.2 RMSD between 508 pruned atom pairs is 0.667 angstroms; (across all 513 pairs: 0.711) > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!6 models > hide #!6 models > show #!8 models > hide #!8 models > show #!11 models > hide #!11 models > show #!8 models > select #9/A 4242 atoms, 4344 bonds, 1 pseudobond, 514 residues, 2 models selected > select ~sel & ##selected 12723 atoms, 13032 bonds, 3 pseudobonds, 1539 residues, 2 models selected > show sel cartoons > undo > ui tool show Matchmaker > matchmaker #!8 to #9/D pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain D (#9) with 20250623-WT-cGMP-bound-3_real_space_refined_037.pdb, chain B (#8), sequence alignment score = 2517.6 RMSD between 306 pruned atom pairs is 0.795 angstroms; (across all 510 pairs: 2.795) > show #!8-10 cartoons > hide #!8-10 cartoons > undo > hide #!10 models > hide #!9 models > show #!9 models > show #!8 models > hide #!9 models > show #!9 models > select add #8 16936 atoms, 17348 bonds, 4 pseudobonds, 2048 residues, 2 models selected > select ~sel & ##selected Nothing selected > show #!8-9 cartoons > undo > hide #!9 models > show #!9 models > hide #!8 models > show #!10 models > hide #!10 models > show #!10 models > hide #!9 models > show #!8 models > hide #!10 models Drag select of 2686 atoms, 512 residues, 1 pseudobonds, 2306 bonds > hide sel cartoons > hide sel atoms > select #8/A 4234 atoms, 4337 bonds, 1 pseudobond, 512 residues, 2 models selected > show sel cartoons > undo > select #8/B 4234 atoms, 4337 bonds, 1 pseudobond, 512 residues, 2 models selected > show sel cartoons > show sel atoms > show #!9 models > show #!10 models > select clear > hide #!9 models > hide #!10 models > show #!3 models > hide #!3 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!11 models > hide #!8 models > select #11/A 4122 atoms, 4207 bonds, 12 pseudobonds, 500 residues, 2 models selected > show sel cartoons > show sel atoms > select clear > select #11/A 4122 atoms, 4207 bonds, 12 pseudobonds, 500 residues, 2 models selected > select #11/B 4135 atoms, 4224 bonds, 11 pseudobonds, 500 residues, 2 models selected > hide sel cartoons > hide sel atoms > show #!10 models > show #!9 models > show #!8 models > hide #!9 models > hide #!10 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > hide #!8 models > show #!11 models > show #!8 models > show #!9 models > show #!7 models > hide #!7 models > show #!10 models > hide #!8 models > ui tool show Matchmaker > matchmaker #!11 to #9/D pairing bs Computing secondary structure Parameters --- Chain pairing | bs 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 apo-WT-unligand-0_real_space_refined_014-coot-2.pdb, chain D (#9) with Wt-cGMP.pdb, chain B (#11), sequence alignment score = 2420.4 RMSD between 293 pruned atom pairs is 0.802 angstroms; (across all 497 pairs: 2.878) > hide #!9 models > show #!8 models > hide #!8 models > hide #!10 models > ui tool show Matchmaker > select #11/A 4122 atoms, 4207 bonds, 12 pseudobonds, 500 residues, 2 models selected > hide sel cartoons > hide sel atoms > select #11/B 4135 atoms, 4224 bonds, 11 pseudobonds, 500 residues, 2 models selected > show sel cartoons > show #!10 models > hide #!10 models > show sel atoms > show #!10 models > show #!9 models > show #!8 models > hide #!8 models > hide #!10 models > show #!10 models > hide #!10 models > show #!8 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!8 models > show #!8 models > hide #!9 models > show #!9 models > hide #!8 models > show #!8 models > hide #!8 models > hide #!9 models > hide #!11 models > show #!11 models > hide sel cartoons > hide sel atoms > show sel atoms > undo > select clear > select #11/B:801@C5 1 atom, 1 residue, 1 model selected Drag select of 3 atoms, 2 bonds > show sel atoms > hide sel atoms > select clear > hide #!11 atoms > show #!11 cartoons > show #!11 atoms > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!9 models > show #!8 models > hide #!8 models > color #11 #858585ff > color #11 #85858585 > color #11 #85858576 > color #11 #c7c7c776 > color #11 #c7c7c761 > color #11 #c7c7c766 > undo > hide #!9 models > select #11/B 4135 atoms, 4224 bonds, 11 pseudobonds, 500 residues, 2 models selected > select ~sel & ##selected 12361 atoms, 12613 bonds, 38 pseudobonds, 1499 residues, 2 models selected > hide sel cartoons > hide sel atoms > show #!8 models > show #!9 models > hide #!9 models > show #!10 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!10 models > hide #!11 models > show #!10 models > hide #!8 models Drag select of 2686 atoms, 513 residues, 1 pseudobonds, 2304 bonds > color #10 #8000804a > color #10 #aaaaaa4a > color #10 #5c5c5c4a > color #10 #7d7d7d4a > color #10 #b5b5b54a > color #10 #7071c24a > color #10 #c15fc24a > color #10 #ff40ffff > color #10 #ff40ff5f > color #10 #ff40ff3d > show #!11 models > set bgColor white > set bgColor #ffffff00 > select clear > set bgColor black > set bgColor transparent > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > lighting simple > lighting soft > lighting full > lighting soft > show #!9 models > hide #!11 models > select add #9 16965 atoms, 17376 bonds, 4 pseudobonds, 2053 residues, 2 models selected > select subtract #9 Nothing selected > hide #!9 models > show #!11 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > ui tool show Distances > select #10/B:456@CB 1 atom, 1 residue, 1 model selected Exactly two atoms must be selected! > select #11/B:456 14 atoms, 15 bonds, 1 residue, 1 model selected Exactly two atoms must be selected! > select subtract #11/B:456 1 bond, 2 models selected > select add #11/B:456 14 atoms, 16 bonds, 1 residue, 2 models selected Exactly two atoms must be selected! > select #11/B:456@CB 1 atom, 1 residue, 1 model selected > select #11/B:456 14 atoms, 15 bonds, 1 residue, 1 model selected > select clear > select #10/B:456@CB 1 atom, 1 residue, 1 model selected > select add #11/B:456@CB 2 atoms, 2 residues, 3 models selected > distance #10/B:456@CB #11/B:456@CB Distance between EA-coot-7-no ligand.pdb #10/B TRP 456 CB and Wt-cGMP.pdb #11/B TRP 456 CB: 2.930Å > show #!8 models > select #11/B:801@O6 1 atom, 1 residue, 1 model selected > select #8/B:619@NZ 1 atom, 1 residue, 1 model selected > select #11/B:801@O6 1 atom, 1 residue, 1 model selected > select #8/B:619@NZ 1 atom, 1 residue, 1 model selected > select #8/B:616@CD1 1 atom, 1 residue, 1 model selected > select #8/B:619@NZ 1 atom, 1 residue, 1 model selected > select add #11/B:801@O6 2 atoms, 2 residues, 3 models selected > distance #8/B:619@NZ #11/B:801@O6 Distance between 20250623-WT-cGMP-bound-3_real_space_refined_037.pdb #8/B LYS 619 NZ and Wt-cGMP.pdb #11/B PCG 801 O6: 4.007Å > hide #!11 models > show #!11 models > hide #!8 models > hide #!11 models > show #!8 models > color #10 #ff40ffff > color #10 #969696ff > color #10 #ff40ffff > color #10 #b546e1ff > color #10 #cb68e0ff > turn Y > select > #1/A-D:103-111,119-145,193-224,236-246,248-256,259-265,276-301,303-335,359-375,386-438,441-458,464-489,491-496,498-507,559-564,592-620 10350 atoms, 10492 bonds, 36 pseudobonds, 1232 residues, 2 models selected > show #!6 models > hide #!6 models > show #!5 models > hide #!5 models > show #!4 models > hide #!4 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > hide #!8 models > hide #!12 models > hide #12.1 models Drag select of 2686 atoms, 513 residues, 1 pseudobonds, 2304 bonds > color (#!10 & sel) byelement > select clear > show #!11 models > hide #!11 models > show #!8 models > select #8/B:619 9 atoms, 8 bonds, 1 residue, 1 model selected > select #10/B:619@CA 1 atom, 1 residue, 1 model selected > select clear > select #10/B:619 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear Exactly two atoms must be selected! > select clear > select #8/B:619 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/B:619 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/B:619 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/B:619 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/B:619 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/B:619 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > select add #8/B:619 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #10/B:619 18 atoms, 16 bonds, 2 residues, 3 models selected > select #10/B:619 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #8/B:619 18 atoms, 16 bonds, 2 residues, 3 models selected > select subtract #8/B:619 9 atoms, 8 bonds, 1 residue, 3 models selected > select add #8/B:619 18 atoms, 16 bonds, 2 residues, 3 models selected > select clear > select #8/B:619@CB 1 atom, 1 residue, 1 model selected > select #10/B:619@CB 1 atom, 1 residue, 1 model selected > select add #8/B:619@CB 2 atoms, 2 residues, 3 models selected > distance #10/B:619@CB #8/B:619@CB Distance between EA-coot-7-no ligand.pdb #10/B LYS 619 CB and 20250623-WT- cGMP-bound-3_real_space_refined_037.pdb #8/B LYS 619 CB: 6.665Å ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M4 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: Mac mini Model Identifier: Mac16,10 Model Number: MU9D3CH/A Chip: Apple M4 Total Number of Cores: 10 (4 performance and 6 efficiency) Memory: 16 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 41天3小时10分钟 Graphics/Displays: Apple M4: Chipset Model: Apple M4 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: XSN-27Q: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 biopython: 1.83 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-QScore: 1.1 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 DiffFit: 0.7.0 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 fsspec: 2025.5.1 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 mpmath: 1.3.0 mrcfile: 1.5.0 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 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 sympy: 1.14.0 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 torch: 2.2.1 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX