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Opened 4 months ago
Closed 4 months ago
#18107 closed defect (duplicate)
Crash at exit in Qt cleanup routines
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.mlp._mlp (total: 59)
{"app_name":"ChimeraX","timestamp":"2025-06-30 14:18:17.00 +0800","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.5 (24F74)","roots_installed":0,"name":"ChimeraX","incident_id":"AF052DCE-4C2B-47E1-9638-B92C4833ED71"}
{
"uptime" : 2100000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac16,10",
"coalitionID" : 45548,
"osVersion" : {
"train" : "macOS 15.5",
"build" : "24F74",
"releaseType" : "User"
},
"captureTime" : "2025-06-30 14:17:56.6783 +0800",
"codeSigningMonitor" : 2,
"incident" : "AF052DCE-4C2B-47E1-9638-B92C4833ED71",
"pid" : 99851,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-06-26 01:57:12.3789 +0800",
"procStartAbsTime" : 41137882172146,
"procExitAbsTime" : 50498885814674,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"72E5907F-A11E-5D6B-9634-F9D2CC669F1E","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "9C2D309A-10C5-3B54-AAC7-9440E020D708",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["countryLocationIneligible","regionIneligible","countryBillingIneligible"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "D6397BE2-AC3A-43D2-8E36-32387DEADF0F",
"wakeTime" : 439495,
"sleepWakeUUID" : "BE11653B-30A0-40B2-BDA7-2C3BC791A9D6",
"sip" : "enabled",
"vmRegionInfo" : "0x5ea894210040 is not in any region. Bytes after previous region: 103597096370241 Bytes before following region: 1474983559104\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000dea894210040","rawCodes":[1,244815621062720],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000dea894210040 -> 0x00005ea894210040 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":99851},
"vmregioninfo" : "0x5ea894210040 is not in any region. Bytes after previous region: 103597096370241 Bytes before following region: 1474983559104\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6156822984},{"value":80},{"value":112},{"value":208},{"value":4031},{"value":2390696602799538572},{"value":2390696604576374412},{"value":14757395258967641293},{"value":4294967286},{"value":6156822914},{"value":0},{"value":53},{"value":244815621062704},{"value":328},{"value":8440864680},{"value":0},{"value":11},{"value":259},{"value":8423759840,"symbolLocation":224,"symbol":"_main_thread"},{"value":316},{"value":1},{"value":4333667888,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":4435996672},{"value":1},{"value":4294967295},{"value":105553140862912}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6577154188},"cpsr":{"value":1073741824},"fp":{"value":6156823056},"sp":{"value":6156823024},"esr":{"value":1442840704,"description":" Address size 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Address size 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===== 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
Change History (2)
comment:1 by , 4 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash at exit in Qt cleanup routines |
comment:2 by , 4 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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