Opened 2 months ago

Closed 2 months ago

#18437 closed defect (duplicate)

Crash in python_instances_of_class after "build join" command

Reported by: herrera.alfa@… Owned by: pett
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Tom Goddard) 

The following bug report has been submitted:
Platform:        macOS-14.7.5-arm64-arm-64bit
ChimeraX Version: 1.8.dev202403210048 (2024-03-21 00:48:29 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error

Thread 0x000000031e9db000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031d9cf000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031c9c3000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031b9b7000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031a9ab000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031999f000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000318993000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000317987000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031697b000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031596f000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000314963000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000001fcc9cf80 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 44 in python_instances_of_class
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 176 in _copy_custom_attrs
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 149 in combine
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/mod.py", line 522 in bind
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/mod.py", line 376 in cn_peptide_bond
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/cmd.py", line 205 in cmd_join_peptide
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/tool.py", line 774 in _jm_apply_cb
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/tool.py", line 1193 in 
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 62)


{"app_name":"ChimeraX","timestamp":"2025-08-13 11:57:03.00 -0500","app_version":"1.8.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.7.5 (23H527)","roots_installed":0,"name":"ChimeraX","incident_id":"768FAD03-8C28-4584-9D53-0453ECA121A0"}
{
  "uptime" : 540000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 1729093738,
  "deployVersion" : 210,
  "modelCode" : "Mac14,2",
  "coalitionID" : 43753,
  "osVersion" : {
    "train" : "macOS 14.7.5",
    "build" : "23H527",
    "releaseType" : "User"
  },
  "captureTime" : "2025-08-13 11:56:47.4985 -0500",
  "codeSigningMonitor" : 1,
  "incident" : "768FAD03-8C28-4584-9D53-0453ECA121A0",
  "pid" : 88829,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-07-25 16:34:15.0603 -0500",
  "procStartAbsTime" : 3739027603256,
  "procExitAbsTime" : 13034171129605,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"84939D93-11DF-572A-B9E1-4AFEBE55A994","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "D838229F-FA46-F28D-A6DE-DAAA28E4700D",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "wakeTime" : 5467,
  "sleepWakeUUID" : "50C948D9-D3CF-4221-BBCA-C38458D40500",
  "sip" : "enabled",
  "vmRegionInfo" : "0x1000000205 is in 0x1000000000-0x7000000000;  bytes after start: 517  bytes before end: 412316859898\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)         fc0000000-1000000000   [  1.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GPU Carveout (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":"0x0000000000000002, 0x0000001000000205","rawCodes":[2,68719477253],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000001000000205"},
  "termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":88829},
  "ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
  "vmregioninfo" : "0x1000000205 is in 0x1000000000-0x7000000000;  bytes after start: 517  bytes before end: 412316859898\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)         fc0000000-1000000000   [  1.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GPU Carveout (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":6156107048},{"value":99},{"value":95},{"value":0},{"value":0},{"value":11263280794378408253},{"value":11263280794315939517},{"value":14757395258967641293},{"value":4294967286},{"value":6156106978},{"value":0},{"value":54},{"value":4294967280},{"value":328},{"value":8711154688},{"value":0},{"value":10},{"value":8536051584,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8536051808,"symbolLocation":224,"symbol":"_main_thread"},{"value":1},{"value":4333848112,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":0},{"value":1},{"value":1},{"value":6156108880}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6792916000},"cpsr":{"value":1073745920},"fp":{"value":6156107120},"sp":{"value":6156107088},"esr":{"value":1442840704,"description":" Address size 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===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.8.dev202403210048 (2024-03-21)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/aho2840/Desktop/Satchell
> Lab/MCFHomologs/MCF:Homolog.paper/workingon.closed0716.cxs" format session

opened ChimeraX session  

> close session

> open "/Users/aho2840/Desktop/Satchell
> Lab/MCFHomologs/MCF:Homolog.paper/aDmX.sequence" format fasta

No such database '/users/aho2840/desktop/satchell lab/mcfhomologs/mcf'  

> open "/Users/aho2840/Desktop/Satchell
> Lab/MCFHomologs/MCF:Homolog.paper/aDmX.sequence" format fasta

No such database '/users/aho2840/desktop/satchell lab/mcfhomologs/mcf'  

> open "/Users/aho2840/Desktop/Satchell
> Lab/MCFHomologs/workingon.07.02.25.cxs" format session

opened ChimeraX session  

> hide #!1 models

> hide #!3 models

> show #9 models

> log metadata #9

The model has no metadata

> log chains #9

Chain information for cDmX.best_model.pdb #9  
---  
Chain | Description  
A | No description available  
  

> sequence chain #9/A

Alignment identifier is 9/A  

> save /Users/aho2840/Desktop/dmxinchimera format fasta alignment 9/A

> close session

> open "/Users/aho2840/Desktop/Satchell
> Lab/MCFHomologs/workingon.07.02.25.cxs" format session

opened ChimeraX session  

> close session

> open "/Users/aho2840/Desktop/Satchell
> Lab/MCFHomologs/MCF:Homolog.paper/workingon.closed0716.cxs" format session

opened ChimeraX session  

> hide #!9 models

> hide #90 models

> show #109 models

> log metadata #109

The model has no metadata

> log chains #109

Chain information for C7BKP9.ranked_0.pdb #109  
---  
Chain | Description  
A | No description available  
  

> sequence chain #109/A

Alignment identifier is 109/A  

> select
> #109/A:1731-1734,1737-1740,1848-1851,1946-1952,1955-1963,1969-1975,1979-1983,2008-2012,2055-2057,2071-2075,2078-2085,2090-2093,2106-2110,2116-2118,2159-2161,2165-2169,2195-2200,2223-2227,2272-2274,2289-2290,2294-2296,2315-2317,2529-2536,2545-2554,2557-2562,2580-2583,2599-2605,2631-2634,2762-2770,2782-2790,2798-2803,2808-2814,2852-2855,2879-2882,2918-2925,2929-2935

3318 atoms, 3331 bonds, 196 residues, 1 model selected  

> select
> #109/A:93-114,123-132,143-161,166-196,200-227,237-256,258-260,264-318,324-327,330-349,358-360,362-368,376-405,428-437,444-447,451-463,472-517,527-566,568-582,590-657,667-688,700-712,714-716,726-740,750-756,760-782,794-818,828-849,852-864,876-882,887-931,1006-1009,1018-1036,1047-1063,1069-1085,1089-1107,1119-1137,1139-1152,1163-1173,1219-1225,1229-1235,1334-1337,1341-1343,1379-1385,1391-1404,1521-1526,1568-1579,1585-1592,1596-1602,1612-1626,1634-1648,1652-1665,1669-1681,1693-1705,1718-1720,1722-1724,1746-1758,1767-1781,1786-1791,1796-1804,1810-1819,1821-1842,1854-1857,1865-1877,1881-1893,1903-1913,1915-1918,1933-1935,1937-1940,1986-1999,2027-2031,2130-2154,2178-2190,2207-2218,2228-2230,2234-2239,2241-2251,2255-2270,2291-2293,2303-2305,2322-2337,2342-2344,2348-2358,2360-2362,2364-2382,2392-2394,2399-2409,2412-2415,2485-2494,2496-2503,2510-2522,2565-2571,2584-2594,2608-2616,2625-2627,2637-2646,2727-2742,2744-2748,2755-2761,2824-2826,2832-2843,2847-2849,2861-2870,2888-2895,2898-2909

22522 atoms, 22610 bonds, 1369 residues, 1 model selected  

> show #!9 models

> show #1 models

> show #26 models

> hide #26 models

> show #38 models

> hide #38 models

> hide #!9 models

> select add #109

47153 atoms, 47629 bonds, 2957 residues, 1 model selected  

> select subtract #109

Nothing selected  

> matchmaker #109 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with C7BKP9.ranked_0.pdb,
chain A (#109), sequence alignment score = 175.4  
RMSD between 67 pruned atom pairs is 1.137 angstroms; (across all 172 pairs:
7.039)  
  

> show #!87 models

> matchmaker #87 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with 6ii6, chain A (#87),
sequence alignment score = 1498.3  
RMSD between 212 pruned atom pairs is 0.553 angstroms; (across all 223 pairs:
1.561)  
  

> hide #1 models

> hide #109 models

> hide #!87 models

> show #!9 models

> show #109 models

> matchmaker #9 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with 6ii6, chain A (#9),
sequence alignment score = 1498.3  
RMSD between 212 pruned atom pairs is 0.553 angstroms; (across all 223 pairs:
1.561)  
  

> hide #109 models

> show #109 models

> select #109/A:1746

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #109/A:1746-1750

78 atoms, 78 bonds, 5 residues, 1 model selected  

> select #109/A:1746

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #109/A:1746-1758

208 atoms, 208 bonds, 13 residues, 1 model selected  

> select #109/A:1746

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #109/A:1746-1800

863 atoms, 871 bonds, 55 residues, 1 model selected  

> select #109/A:1746

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #109/A:1746-1825

1244 atoms, 1254 bonds, 80 residues, 1 model selected  

> select #109/A:1746

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #109/A:1746-1895

2333 atoms, 2353 bonds, 150 residues, 1 model selected  

> select add #109

47153 atoms, 47629 bonds, 2957 residues, 1 model selected  

> select subtract #109

Nothing selected  

> select #109/A:2031

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #109/A:1746-2031

4485 atoms, 4530 bonds, 286 residues, 1 model selected  

> color sel purple

> select add #109

47153 atoms, 47629 bonds, 2957 residues, 1 model selected  

> select subtract #109

Nothing selected  

> select #109/A:2382

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #109/A:2078-2382

4892 atoms, 4947 bonds, 305 residues, 1 model selected  

> select #109/A:2382

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #109/A:2378-2382

92 atoms, 91 bonds, 5 residues, 1 model selected  

> select #109/A:2382

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #109/A:2078-2382

4892 atoms, 4947 bonds, 305 residues, 1 model selected  

> color sel medium blue

> select
> #109/A:93-114,123-132,143-161,166-196,200-227,237-256,258-260,264-318,324-327,330-349,358-360,362-368,376-405,428-437,444-447,451-463,472-517,527-566,568-582,590-657,667-688,700-712,714-716,726-740,750-756,760-782,794-818,828-849,852-864,876-882,887-931,1006-1009,1018-1036,1047-1063,1069-1085,1089-1107,1119-1137,1139-1152,1163-1173,1219-1225,1229-1235,1334-1337,1341-1343,1379-1385,1391-1404,1521-1526,1568-1579,1585-1592,1596-1602,1612-1626,1634-1648,1652-1665,1669-1681,1693-1705,1718-1720,1722-1724,1746-1758,1767-1781,1786-1791,1796-1804,1810-1819,1821-1842,1854-1857,1865-1877,1881-1893,1903-1913,1915-1918,1933-1935,1937-1940,1986-1999,2027-2031,2130-2154,2178-2190,2207-2218,2228-2230,2234-2239,2241-2251,2255-2270,2291-2293,2303-2305,2322-2337,2342-2344,2348-2358,2360-2362,2364-2382,2392-2394,2399-2409,2412-2415,2485-2494,2496-2503,2510-2522,2565-2571,2584-2594,2608-2616,2625-2627,2637-2646,2727-2742,2744-2748,2755-2761,2824-2826,2832-2843,2847-2849,2861-2870,2888-2895,2898-2909

22522 atoms, 22610 bonds, 1369 residues, 1 model selected  

> select #109/A:2405-2406

33 atoms, 32 bonds, 2 residues, 1 model selected  

> select #109/A:2405-2409

92 atoms, 93 bonds, 5 residues, 1 model selected  

> select #109/A:2441

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #109/A:2405-2441

545 atoms, 551 bonds, 37 residues, 1 model selected  

> select #109/A:2383

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #109/A:2383-2441

890 atoms, 899 bonds, 59 residues, 1 model selected  

> select #109/A:2382

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #109/A:2377-2382

102 atoms, 101 bonds, 6 residues, 1 model selected  

> select #109/A:2469

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #109/A:2469-2474

103 atoms, 103 bonds, 6 residues, 1 model selected  

> select #109/A:2649

17 atoms, 17 bonds, 1 residue, 1 model selected  

> select #109/A:2469-2649

2900 atoms, 2935 bonds, 181 residues, 1 model selected  

> select #109/A:2521

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #109/A:2521-2572

840 atoms, 851 bonds, 52 residues, 1 model selected  

> select #109/A:2485-2486

24 atoms, 23 bonds, 2 residues, 1 model selected  

> select #109/A:2485-2646

2596 atoms, 2628 bonds, 162 residues, 1 model selected  

> color sel forest green

> select add #109

47153 atoms, 47629 bonds, 2957 residues, 1 model selected  

> select subtract #109

Nothing selected  

> select
> #109/A:93-114,123-132,143-161,166-196,200-227,237-256,258-260,264-318,324-327,330-349,358-360,362-368,376-405,428-437,444-447,451-463,472-517,527-566,568-582,590-657,667-688,700-712,714-716,726-740,750-756,760-782,794-818,828-849,852-864,876-882,887-931,1006-1009,1018-1036,1047-1063,1069-1085,1089-1107,1119-1137,1139-1152,1163-1173,1219-1225,1229-1235,1334-1337,1341-1343,1379-1385,1391-1404,1521-1526,1568-1579,1585-1592,1596-1602,1612-1626,1634-1648,1652-1665,1669-1681,1693-1705,1718-1720,1722-1724,1746-1758,1767-1781,1786-1791,1796-1804,1810-1819,1821-1842,1854-1857,1865-1877,1881-1893,1903-1913,1915-1918,1933-1935,1937-1940,1986-1999,2027-2031,2130-2154,2178-2190,2207-2218,2228-2230,2234-2239,2241-2251,2255-2270,2291-2293,2303-2305,2322-2337,2342-2344,2348-2358,2360-2362,2364-2382,2392-2394,2399-2409,2412-2415,2485-2494,2496-2503,2510-2522,2565-2571,2584-2594,2608-2616,2625-2627,2637-2646,2727-2742,2744-2748,2755-2761,2824-2826,2832-2843,2847-2849,2861-2870,2888-2895,2898-2909

22522 atoms, 22610 bonds, 1369 residues, 1 model selected  

> select #109/A:1746

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #109/A:1746-2031

4485 atoms, 4530 bonds, 286 residues, 1 model selected  

> select add #109

47153 atoms, 47629 bonds, 2957 residues, 1 model selected  

> select subtract #109

Nothing selected  

> hide #109 models

> show #90 models

> show #84 models

> hide #90 models

> log metadata #84

The model has no metadata

> log chains #84

Chain information for AF-C4ULG3-F1-model_v4.pdb #84  
---  
Chain | Description | UniProt  
A | toxin AFP18 | AFP18_YERRA 1-2123  
  

> sequence chain #84/A

Alignment identifier is 84/A  

> select #84/A:1430

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #84/A:1430-1437

68 atoms, 67 bonds, 8 residues, 1 model selected  

> select #84/A:1430

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #84/A:1430-1713

2242 atoms, 2281 bonds, 284 residues, 1 model selected  

> select #84/A:256

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #84/A:256-778

4091 atoms, 4142 bonds, 523 residues, 1 model selected  

> hide #!9 models

> select #84/A:664-665

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #84/A:664-715

389 atoms, 393 bonds, 52 residues, 1 model selected  

> select #84/A:727-778

389 atoms, 394 bonds, 52 residues, 1 model selected  

> select #84/A:256-778

4091 atoms, 4142 bonds, 523 residues, 1 model selected  

> color sel medium blue

> select add #84

16760 atoms, 17065 bonds, 2123 residues, 1 model selected  

> select subtract #84

Nothing selected  

> select #84/A:1151

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #84/A:1151

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #84/A:1404

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #84/A:1151-1404

1937 atoms, 1969 bonds, 254 residues, 1 model selected  

> select
> #84/A:55-76,78-86,98-106,112-154,162-193,202-217,230-232,256-288,294-323,346-386,397-433,435-452,458-488,491-493,495-511,516-587,596-618,623-641,643-645,652-670,679-684,689-709,723-748,757-778,781-798,800-811,818-839,927-929,938-940,943-962,969-979,1027-1029,1032-1037,1040-1043,1063-1071,1077-1080,1091-1109,1116-1127,1151-1159,1161-1177,1181-1201,1206-1208,1210-1230,1236-1246,1280-1292,1296-1305,1310-1323,1330-1333,1336-1344,1391-1404,1409-1411,1430-1442,1451-1465,1470-1475,1480-1488,1494-1503,1505-1526,1538-1541,1549-1561,1565-1577,1581-1583,1585-1594,1598-1602,1614-1617,1619-1621,1667-1680,1708-1713,1718-1720,1807-1836,1859-1871,1889-1898,1909-1911,1915-1920,1924-1932,1936-1951,1972-1974,2003-2017,2023-2025,2029-2039,2041-2043,2045-2062,2080-2093

9231 atoms, 9299 bonds, 1157 residues, 1 model selected  

> select #84/A:256

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #84/A:256-778

4091 atoms, 4142 bonds, 523 residues, 1 model selected  

> color sel #040e52ff

> select add #84

16760 atoms, 17065 bonds, 2123 residues, 1 model selected  

> select subtract #84

Nothing selected  

> select
> #84/A:55-76,78-86,98-106,112-154,162-193,202-217,230-232,256-288,294-323,346-386,397-433,435-452,458-488,491-493,495-511,516-587,596-618,623-641,643-645,652-670,679-684,689-709,723-748,757-778,781-798,800-811,818-839,927-929,938-940,943-962,969-979,1027-1029,1032-1037,1040-1043,1063-1071,1077-1080,1091-1109,1116-1127,1151-1159,1161-1177,1181-1201,1206-1208,1210-1230,1236-1246,1280-1292,1296-1305,1310-1323,1330-1333,1336-1344,1391-1404,1409-1411,1430-1442,1451-1465,1470-1475,1480-1488,1494-1503,1505-1526,1538-1541,1549-1561,1565-1577,1581-1583,1585-1594,1598-1602,1614-1617,1619-1621,1667-1680,1708-1713,1718-1720,1807-1836,1859-1871,1889-1898,1909-1911,1915-1920,1924-1932,1936-1951,1972-1974,2003-2017,2023-2025,2029-2039,2041-2043,2045-2062,2080-2093

9231 atoms, 9299 bonds, 1157 residues, 1 model selected  

> select #84/A:1428-1430

29 atoms, 29 bonds, 3 residues, 1 model selected  

> select #84/A:1430-1771

2729 atoms, 2779 bonds, 342 residues, 1 model selected  

> select #84/A:1431

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #84/A:1431-1720

2289 atoms, 2330 bonds, 290 residues, 1 model selected  

> select #84/A:1429-1430

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #84/A:1430-1763

2659 atoms, 2707 bonds, 334 residues, 1 model selected  

> select #84/A:1430

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #84/A:1430-1713

2242 atoms, 2281 bonds, 284 residues, 1 model selected  

> select #84/A:1714

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #84/A:1714-2123

3310 atoms, 3382 bonds, 410 residues, 1 model selected  

> color sel #040e52ff

> select add #84

16760 atoms, 17065 bonds, 2123 residues, 1 model selected  

> select subtract #84

Nothing selected  

> select #84/A:1181

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #84/A:1181-1372

1455 atoms, 1478 bonds, 192 residues, 1 model selected  

> color sel red

> select #84/A:1756

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #84/A:1756-2062

2499 atoms, 2556 bonds, 307 residues, 1 model selected  

> color sel blue

> select add #84

16760 atoms, 17065 bonds, 2123 residues, 1 model selected  

> select subtract #84

Nothing selected  

> select #84/A:1718

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #84/A:1718-1755

314 atoms, 318 bonds, 38 residues, 1 model selected  

> color sel blue

> select #84/A:2093

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #84/A:1718-2093

3065 atoms, 3131 bonds, 376 residues, 1 model selected  

> color sel blue

> undo

> color sel blue

> select #84/A:1181

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #84/A:1181-1372

1455 atoms, 1478 bonds, 192 residues, 1 model selected  

> select #84/A:1372-1373

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select #84/A:1372-1379

63 atoms, 63 bonds, 8 residues, 1 model selected  

> select #84/A:1181

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #84/A:1181-1379

1508 atoms, 1531 bonds, 199 residues, 1 model selected  

> select #84/A:1181

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #84/A:1181-1379

1508 atoms, 1531 bonds, 199 residues, 1 model selected  

> select #84/A:1151

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #84/A:1151-1404

1937 atoms, 1969 bonds, 254 residues, 1 model selected  

> color sel red

> select add #84

16760 atoms, 17065 bonds, 2123 residues, 1 model selected  

> select subtract #84

Nothing selected  

> hide #84 models

> show #!78 models

> log metadata #78

No models had metadata

> log chains #78

Chain information for 8adb #78  
---  
Chain | Description | UniProt  
A | Wc-VDT1 | D6YWY5_WADCW 279-493  
  

> log metadata #78

No models had metadata

> log chains #78

Chain information for 8adb #78  
---  
Chain | Description | UniProt  
A | Wc-VDT1 | D6YWY5_WADCW 279-493  
  

> sequence chain #78/A

Alignment identifier is 78/A  

> select #78/A:293

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select #78/A:293-493

3033 atoms, 3061 bonds, 1 pseudobond, 196 residues, 2 models selected  

> show #89 models

> matchmaker #89 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with
AF-D6YWY5-F1-model_v4.pdb, chain A (#89), sequence alignment score = 118.2  
RMSD between 35 pruned atom pairs is 1.066 angstroms; (across all 182 pairs:
16.490)  
  

> matchmaker #78 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6ii0.cropped.06.25.23.pdb, chain B (#1) with 8adb, chain A (#78),
sequence alignment score = 101  
RMSD between 32 pruned atom pairs is 1.292 angstroms; (across all 162 pairs:
12.300)  
  

> select add #78

3385 atoms, 3275 bonds, 1 pseudobond, 350 residues, 2 models selected  

> select subtract #78

Nothing selected  

> hide #!78 models

> hide #89 models

> show #89 models

> show #1 models

*** Deleted thousands of lines to make the description small enough for Trac. TomG

> matchmaker #72 & sel to #9

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 6ii6, chain A (#9) with AF-Q327I5-F1-model_v4.pdb, chain A (#72),
sequence alignment score = 44.7  
RMSD between 15 pruned atom pairs is 1.296 angstroms; (across all 168 pairs:
18.337)  
  

> select add #72

4592 atoms, 4687 bonds, 572 residues, 1 model selected  

> select subtract #72

Nothing selected  

> select clear

> ui mousemode right "translate selected models"

> save /Users/aho2840/Desktop/image1.png supersample 3

> hide #72 models

> show #8 models

> hide #8 models

> show #85 models

> matchmaker #85 to #9

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 6ii6, chain A (#9) with AF-Q89T99-F1-model_v4.pdb, chain A (#85),
sequence alignment score = 83.5  
RMSD between 30 pruned atom pairs is 0.963 angstroms; (across all 195 pairs:
24.092)  
  

> save /Users/aho2840/Desktop/image1.png supersample 3

> hide #85 models

> show #83 models

> matchmaker #83 to #9

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 6ii6, chain A (#9) with AF-Q93RN4-F1-model_v4.pdb, chain A (#83),
sequence alignment score = 154.3  
RMSD between 61 pruned atom pairs is 1.078 angstroms; (across all 253 pairs:
13.858)  
  

> save /Users/aho2840/Desktop/image1.png supersample 3

> hide #83 models

> show #86 models

> matchmaker #86 to #9

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 6ii6, chain A (#9) with AF-Q9AMW4-F1-model_v4.pdb, chain A (#86),
sequence alignment score = 87.8  
RMSD between 30 pruned atom pairs is 0.803 angstroms; (across all 234 pairs:
23.197)  
  

> save /Users/aho2840/Desktop/image1.png supersample 3

> hide #86 models

> show #69 models

> matchmaker #69 to #9

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 6ii6, chain A (#9) with AF-Q9F3T4-F1-model_v4.pdb, chain A (#69),
sequence alignment score = 99.5  
RMSD between 15 pruned atom pairs is 1.383 angstroms; (across all 244 pairs:
24.018)  
  

> save /Users/aho2840/Desktop/image1.png supersample 3

> hide #69 models

> show #98 models

> matchmaker #98 to #9

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 6ii6, chain A (#9) with WP_095034161.1.ranked_0.pdb, chain A (#98),
sequence alignment score = 189.7  
RMSD between 60 pruned atom pairs is 1.387 angstroms; (across all 312 pairs:
13.944)  
  

> save /Users/aho2840/Desktop/image1.png supersample 3

> hide #98 models

> show #99 models

> matchmaker #99 to #9

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 6ii6, chain A (#9) with WP_095034189.1.ranked_0.pdb, chain A (#99),
sequence alignment score = 201  
RMSD between 46 pruned atom pairs is 0.814 angstroms; (across all 293 pairs:
22.670)  
  

> save /Users/aho2840/Desktop/image1.png supersample 3

> hide #99 models

> show #100 models

> matchmaker #100 to #9

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 6ii6, chain A (#9) with WP_148121377.1.ranked_0.pdb, chain A
(#100), sequence alignment score = 196.6  
RMSD between 63 pruned atom pairs is 1.204 angstroms; (across all 298 pairs:
14.062)  
  

> save /Users/aho2840/Desktop/image1.png supersample 3

> turn y 180

> save /Users/aho2840/Desktop/image1.png supersample 3

> turn y 180

> ui mousemode right select

Drag select of 355 residues  

> ui tool show Matchmaker

> matchmaker #100 & sel to #9

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 6ii6, chain A (#9) with WP_148121377.1.ranked_0.pdb, chain A
(#100), sequence alignment score = 177.3  
RMSD between 56 pruned atom pairs is 0.910 angstroms; (across all 272 pairs:
24.833)  
  

> select add #100

31107 atoms, 31455 bonds, 1953 residues, 1 model selected  

> select subtract #100

Nothing selected  

> select clear

> ui mousemode right "translate selected models"

> save /Users/aho2840/Desktop/image1.png supersample 3

> hide #100 models

> show #101 models

> matchmaker #101 to #9

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 6ii6, chain A (#9) with WP_231937687.1.ranked_0.pdb, chain A
(#101), sequence alignment score = 205.8  
RMSD between 73 pruned atom pairs is 0.941 angstroms; (across all 296 pairs:
20.392)  
  

> save /Users/aho2840/Desktop/image1.png supersample 3

> hide #101 models

> show #82 models

> matchmaker #82 to #9

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 6ii6, chain A (#9) with AF-O68703-F1-model_v4.pdb, chain A (#82),
sequence alignment score = 155.7  
RMSD between 60 pruned atom pairs is 1.095 angstroms; (across all 245 pairs:
14.853)  
  

> save /Users/aho2840/Desktop/image1.png supersample 3

> hide #82 models

> show #60 models

> save /Users/aho2840/Desktop/image1.png supersample 3

> hide #60 models

> show #61 models

> save /Users/aho2840/Desktop/image1.png supersample 3

> hide #61 models

> show #104 models

> hide #!9 models

> hide #104 models

> show #105 models

> show #104 models

> hide #105 models

> log metadata #104

The model has no metadata

> log chains #104

Chain information for GMGC10.011_528_202.ranked_0.1.2000.ranked_0.pdb #104  
---  
Chain | Description  
A | No description available  
  

> sequence chain #104/A

Alignment identifier is 104/A  

> ui mousemode right select

Drag select of 1999 residues  

> select add #104

30364 atoms, 30638 bonds, 1999 residues, 1 model selected  

> select subtract #104

Nothing selected  

> hide #104 models

> show #105 models

Drag select of 1401 residues  

> log metadata #105

The model has no metadata

> log chains #105

Chain information for GMGC10.011_528_202.ranked_0.1800.3500.pdb #105  
---  
Chain | Description  
A | No description available  
  

> sequence chain #105/A

Alignment identifier is 105/A  

> select add #105

24144 atoms, 24336 bonds, 1601 residues, 1 model selected  

> select subtract #105

Nothing selected  

> hide #105 models

> show #110 models

> log metadata #110

The model has no metadata

> log chains #110

Chain information for GMGC10.011_528_202.ranked_0.3247.4160.pdb #110  
---  
Chain | Description  
A | No description available  
  

> sequence chain #110/A

Alignment identifier is 110/A  
Drag select of 658 residues  

> select add #110

13993 atoms, 14133 bonds, 913 residues, 1 model selected  

> select subtract #110

Nothing selected  
Drag select of 660 residues  

> select add #110

13993 atoms, 14133 bonds, 913 residues, 1 model selected  

> select subtract #110

Nothing selected  

> hide #110 models

> show #111 models

> log metadata #111

The model has no metadata

> log chains #111

Chain information for GMGC10.011_528_202.ranked_0.4000.5243.pdb #111  
---  
Chain | Description  
A | No description available  
  

> sequence chain #111/A

Alignment identifier is 111/A  
Drag select of 1084 residues  

> select add #111

18385 atoms, 18537 bonds, 1244 residues, 1 model selected  

> select subtract #111

Nothing selected  

> hide #111 models

> show #105 models

> log metadata #105

The model has no metadata

> log chains #105

Chain information for GMGC10.011_528_202.ranked_0.1800.3500.pdb #105  
---  
Chain | Description  
A | No description available  
  

> sequence chain #105/A

Alignment identifier is 105/A  
Drag select of 1401 residues  

> select #105/A:1999

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #105/A:1800-1999

3067 atoms, 3094 bonds, 200 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select
> #105/A:2000-2009,2020-2028,2030-2044,2058-2088,2100-2102,2115-2127,2133-2153,2160-2178,2182-2184,2193-2202,2246-2257,2268-2271,2286-2291,2293-2304,2310-2317,2329-2334,2346-2354,2360-2362,2367-2375,2380-2396,2402-2404,2423-2434,2445-2469,2473-2488,2494-2503,2509-2525,2531-2539,2542-2551,2565-2574,2577-2589,2592-2603,2608-2620,2627-2632,2635-2654,2658-2668,2678-2695,2714-2726,2734-2757,2774-2776,2783-2790,2794-2817,2819-2821,2825-2837,2842-2881,3130-3132,3193-3195,3233-3241,3345-3347

8794 atoms, 8805 bonds, 571 residues, 1 model selected  

> select #105/A:2159-2215

853 atoms, 856 bonds, 57 residues, 1 model selected  

> select #105/A:2159-2215

853 atoms, 856 bonds, 57 residues, 1 model selected  

> select
> #105/A:2000-2009,2020-2028,2030-2044,2058-2088,2100-2102,2115-2127,2133-2153,2160-2178,2182-2184,2193-2202,2246-2257,2268-2271,2286-2291,2293-2304,2310-2317,2329-2334,2346-2354,2360-2362,2367-2375,2380-2396,2402-2404,2423-2434,2445-2469,2473-2488,2494-2503,2509-2525,2531-2539,2542-2551,2565-2574,2577-2589,2592-2603,2608-2620,2627-2632,2635-2654,2658-2668,2678-2695,2714-2726,2734-2757,2774-2776,2783-2790,2794-2817,2819-2821,2825-2837,2842-2881,3130-3132,3193-3195,3233-3241,3345-3347

8794 atoms, 8805 bonds, 571 residues, 1 model selected  

> select add #105

21077 atoms, 21241 bonds, 1401 residues, 1 model selected  

> select subtract #105

Nothing selected  

> hide #105 models

> show #110 models

> log metadata #110

The model has no metadata

> log chains #110

Chain information for GMGC10.011_528_202.ranked_0.3247.4160.pdb #110  
---  
Chain | Description  
A | No description available  
  

> sequence chain #110/A

Alignment identifier is 110/A  
Drag select of 660 residues  

> select #110/A:3499

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #110/A:3247-3499

3894 atoms, 3931 bonds, 253 residues, 1 model selected  

> select #110/A:3596-3597

33 atoms, 32 bonds, 2 residues, 1 model selected  

> select #110/A:3596-3767

2572 atoms, 2590 bonds, 172 residues, 1 model selected  

> select #110/A:3498-3499

33 atoms, 32 bonds, 2 residues, 1 model selected  

> select #110/A:3247-3499

3894 atoms, 3931 bonds, 253 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide #110 models

> show #111 models

> log metadata #111

The model has no metadata

> log chains #111

Chain information for GMGC10.011_528_202.ranked_0.4000.5243.pdb #111  
---  
Chain | Description  
A | No description available  
  

> sequence chain #111/A

Alignment identifier is 111/A  
Drag select of 1084 residues  

> select #111/A:4159

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select #111/A:4000-4159

2425 atoms, 2448 bonds, 160 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide #111 models

> select #111/A:4583

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select #111/A:4583-4640

794 atoms, 797 bonds, 58 residues, 1 model selected  

> select add #111

15960 atoms, 16088 bonds, 1084 residues, 1 model selected  

> select subtract #111

Nothing selected  

> show #111 models

> show #110 models

> select clear

> ui mousemode right "translate selected models"

> hide #111 models

> show #105 models

> hide #105 models

> show #105 models

> show #104 models

> hide #110 models

> hide #105 models

> hide #104 models

> show #104 models

> show #105 models

> toolshed show

QGestureManager::deliverEvent: could not find the target for gesture  

> combine #104,#105 name "GMGC10.011_528_202.1.3500"

Expected a keyword  

> combine #104, #105 name "GMGC10.011_528_202.1.3500"

Expected a keyword  

> combine #104, #105 close false name "GMGC10.011_528_202.1.3500"

Expected a keyword  

> combine #104, #105 close false name GMGC10.011_528_202.1.3500

Expected a keyword  

> select
> #111/A:4160-4171,4176-4187,4194-4196,4200-4202,4205-4213,4218-4226,4231-4239,4247-4254,4263-4273,4277-4290,4295-4303,4309-4318,4322-4337,4411-4413,4820-4822,4839-4841,4855-4865,4884-4891,5150-5156,5170-5176

2584 atoms, 2582 bonds, 167 residues, 1 model selected  

> combine #104, #105, close false name "GMGC10.011_528_202.1.3500"

Expected a keyword  

> combine #104, #105 close false name "GMGC10.011_528_202.1.3500"

Expected a keyword  

> combine #104, #105, close false name GMGC10.011_528_202.1.3500

Expected a keyword  

> combine #104, #105 close false name "GMGC10.011_528_202.1.3500"

Expected a keyword  

> select add #111

15960 atoms, 16088 bonds, 1084 residues, 1 model selected  

> select subtract #111

Nothing selected  

> combine #104, #105 close false name "GMGC10.011_528_202.1.3500"

Expected a keyword  

> combine #104, #105 close false name "GMGC10.011_528_202.1.3500"

Expected a keyword  

> combine # 104, # 105 close false name "GMGC10.011_528_202.1.3500"

Expected a keyword  

> ui tool show "Build Structure"

No atoms selected  

> toolshed show

> combine # 104, # 105, close false name "GMGC10.011_528_202.1.3500"

Expected a keyword  

> combine # 104, # 105, close false, name "GMGC10.011_528_202.1.3500"

Expected a keyword  

> ui tool show "Build Structure"

No atoms selected  

> select add #104

30364 atoms, 30638 bonds, 1999 residues, 1 model selected  

> select add #105

51441 atoms, 51879 bonds, 3400 residues, 2 models selected  

> build join peptide sel length 1.33 omega 180 phi -120 move small

Multiple N- and C-terminii in atoms  

> combine # 104, # 105 close false retainIds false name
> "GMGC10.011_528_202.1.3500"

Expected a keyword  

> combine # 104, # 105 close false retainIds false name "Combine"

Expected a keyword  

> combine # 104, # 105 close false retainIds false name model-name "Combine"

Expected a keyword  

> combine #104, #105 name "GMGC10.011_528_202.1.3500" close false

Expected a keyword  

> combine #104, #105 name "GMGC10.011_528_202.1.3500" close false

Expected a keyword  

> select subtract #104

21077 atoms, 21241 bonds, 1401 residues, 1 model selected  

> select subtract #105

Nothing selected  

> combine #104, #105 name "GMGC10.011_528_202.1.3500" close false

Expected a keyword  

> combine #104, #105 name "Combine" close false

Expected a keyword  

> combine #104, #105 name "GMGC10.011_528_202.1.3500"

Expected a keyword  

> combine modelId close false

Invalid "modelId" argument: Expected an integer  

> combine #104, #105 name "GMGC10.011_528_202.1.3500"

Expected a keyword  

> combine #104, #105

Expected a keyword  

> combine modelId #104, #105

Invalid "modelId" argument: Expected an integer  

> combine #104, #105 name "GMGC10.011_528_202.1.3500"

Expected a keyword  

> close false

Expected a models specifier or a keyword  

> combine #104, #105 name "GMGC10.011_528_202.1.3500"

Expected a keyword  

> close false

Expected a models specifier or a keyword  

> combine #104, #105

Expected a keyword  

> help combine

> hide #104 models

> hide #105 models

> combine #104, #105 name "GMGC10.011_528_202.1.3500"

Expected a keyword  

> close false

Expected a models specifier or a keyword  

> combine #104, #105

Expected a keyword  

> log metadata #104

The model has no metadata

> log chains #104

Chain information for GMGC10.011_528_202.ranked_0.1.2000.ranked_0.pdb #104  
---  
Chain | Description  
A | No description available  
  

> sequence chain #104/A

Alignment identifier is 104/A  

> log metadata #105

The model has no metadata

> log chains #105

Chain information for GMGC10.011_528_202.ranked_0.1800.3500.pdb #105  
---  
Chain | Description  
A | No description available  
  

> sequence chain #105/A

Alignment identifier is 105/A  

> select #104/A:1999

18 atoms, 17 bonds, 1 residue, 1 model selected  

> select #104/A:1999

18 atoms, 17 bonds, 1 residue, 1 model selected  

> select #105/A:2000

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #105/A:2000

14 atoms, 14 bonds, 1 residue, 1 model selected  

> ui tool show "Build Structure"

> build join peptide sel length 1.33 omega 180 phi -120 move small

No chain-terminal carbons in atoms  

> show #104 models

> show #105 models

> select add #105

21077 atoms, 21241 bonds, 1401 residues, 1 model selected  

> select #104/A:1999

18 atoms, 17 bonds, 1 residue, 1 model selected  

> select #104/A:1999

18 atoms, 17 bonds, 1 residue, 1 model selected  

> select #105/A:2000

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #104/A:1999

18 atoms, 17 bonds, 1 residue, 1 model selected  

> ui tool show "Build Structure"

> build join peptide sel length 1.33 omega 180 phi -120 move small

No chain-initial nitrogens in atoms  

> select #105/A:2000

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #105/A:2000

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #104/A:1999

18 atoms, 17 bonds, 1 residue, 1 model selected  

> select #104/A:1999

18 atoms, 17 bonds, 1 residue, 1 model selected  

> select #105/A:2000

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #105/A:2000

14 atoms, 14 bonds, 1 residue, 1 model selected  

> ui tool show "Build Structure"

> build join peptide sel length 1.33 omega 180 phi -120 move small

No chain-terminal carbons in atoms  

> select add #104

30378 atoms, 30652 bonds, 2000 residues, 2 models selected  

> select subtract #104

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select add #104

30378 atoms, 30652 bonds, 2000 residues, 2 models selected  

> select add #105

51441 atoms, 51879 bonds, 3400 residues, 2 models selected  

> select subtract #105

30364 atoms, 30638 bonds, 1999 residues, 1 model selected  

> select subtract #104

Nothing selected  

> select #105/A:2000

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #105/A:2000

14 atoms, 14 bonds, 1 residue, 1 model selected  

> ui tool show "Build Structure"

> build join peptide sel length 1.33 omega 180 phi -120 move small

No chain-terminal carbons in atoms  

> select add #105

21077 atoms, 21241 bonds, 1401 residues, 1 model selected  

> select subtract #105

Nothing selected  

> select #104/A:1999

18 atoms, 17 bonds, 1 residue, 1 model selected  

> select #105/A:2000

14 atoms, 14 bonds, 1 residue, 1 model selected  

> view matrix models
> #105,0.070652,0.61953,-0.78179,102.78,-0.84869,0.44916,0.27924,15.837,0.52415,0.64377,0.55752,337.8

> undo

> select add #105

21077 atoms, 21241 bonds, 1401 residues, 1 model selected  

> select subtract #105

Nothing selected  

> open /Users/aho2840/Downloads/GMGC10.011_528_202.ranked_0.1.2000.pdb

Chain information for GMGC10.011_528_202.ranked_0.1.2000.pdb #113  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/aho2840/Downloads/GMGC10.011_528_202.ranked_0.1800.3500.ranked_0.pdb

Chain information for GMGC10.011_528_202.ranked_0.1800.3500.ranked_0.pdb #114  
---  
Chain | Description  
A | No description available  
  

> hide #105 models

> hide #104 models

> select clear

> select #105/A:2000-2009

158 atoms, 160 bonds, 10 residues, 1 model selected  

> log metadata #113

The model has no metadata

> log chains #113

Chain information for GMGC10.011_528_202.ranked_0.1.2000.pdb #113  
---  
Chain | Description  
A | No description available  
  

> sequence chain #113/A

Alignment identifier is 113/A  

> log metadata #114

The model has no metadata

> log chains #114

Chain information for GMGC10.011_528_202.ranked_0.1800.3500.ranked_0.pdb #114  
---  
Chain | Description  
A | No description available  
  

> sequence chain #114/A

Alignment identifier is 114/A  

> select #114/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #114/A:1-220

3369 atoms, 3404 bonds, 220 residues, 1 model selected  

> ui tool show Matchmaker

No reference and/or match structure/chain chosen  

> matchmaker #114 & sel to #113

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 GMGC10.011_528_202.ranked_0.1.2000.pdb, chain A (#113) with
GMGC10.011_528_202.ranked_0.1800.3500.ranked_0.pdb, chain A (#114), sequence
alignment score = 104.4  
RMSD between 7 pruned atom pairs is 1.517 angstroms; (across all 188 pairs:
20.322)  
  

> undo

> select add #105

21077 atoms, 21241 bonds, 1401 residues, 1 model selected  

> select subtract #105

Nothing selected  

> ui tool show "Build Structure"

> log metadata #113

The model has no metadata

> log chains #113

Chain information for GMGC10.011_528_202.ranked_0.1.2000.pdb #113  
---  
Chain | Description  
A | No description available  
  

> sequence chain #113/A

Alignment identifier is 113/A  

> log metadata #114

The model has no metadata

> log chains #114

Chain information for GMGC10.011_528_202.ranked_0.1800.3500.ranked_0.pdb #114  
---  
Chain | Description  
A | No description available  
  

> sequence chain #114/A

Alignment identifier is 114/A  

> select sequence #113:1

Nothing selected  

> select #113/A:1

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select #113/A:1

16 atoms, 15 bonds, 1 residue, 1 model selected  

> color sel purple

> view matrix models #113,1,0,0,42.424,0,1,0,100.81,0,0,1,51.661

> select
> #113/A:10-18,30-42,46-68,70-76,109-128,144-152,159-161,182-190,196-198,201-210,221-229,231-245,259-289,301-303,316-328,334-354,361-379,383-385,394-403,447-458,469-472,487-492,494-505,511-518,530-535,547-555,561-563,568-576,581-597,603-605,624-635,646-670,674-689,695-704,710-726,732-740,743-752,766-775,778-790,793-804,809-821,828-833,836-855,859-869,879-896,915-927,935-958,975-977,984-991,995-1018,1020-1022,1026-1038,1043-1082,1331-1333,1394-1396,1434-1442,1546-1548

10303 atoms, 10318 bonds, 667 residues, 1 model selected  

> select sequence #113:1601

Nothing selected  

> color #113-114 blue

> select sequence #113:1601

Nothing selected  

> select sequence #113:1601

Nothing selected  

> select sequence #113:1601

Nothing selected  

> color #113-114 red

> select sequence #113:1601

Nothing selected  

> color #113-114 blue

> select #113/A:1601

18 atoms, 17 bonds, 1 residue, 1 model selected  

> select #113/A:1601

18 atoms, 17 bonds, 1 residue, 1 model selected  

> select add #113

24144 atoms, 24336 bonds, 1601 residues, 1 model selected  

> select subtract #113

Nothing selected  

> select sequence #113:1600

Nothing selected  

> select sequence #113:1

Nothing selected  

> select sequence #113:1

Nothing selected  

> ui tool show "Build Structure"

> select sequence #113:1

Nothing selected  

> select sequence #114:1

Nothing selected  

> select add #114

30364 atoms, 30638 bonds, 1999 residues, 1 model selected  

> color sel light sea green

> select subtract #114

Nothing selected  

> select add #114

30364 atoms, 30638 bonds, 1999 residues, 1 model selected  

> select subtract #114

Nothing selected  

> select add #113

24144 atoms, 24336 bonds, 1601 residues, 1 model selected  

> select subtract #113

Nothing selected  

> select clear

> select sequence #113:1601

Nothing selected  

> help help:user/findseq.html

> select sequence #113:1601.a

Nothing selected  

Already setting window visible!  

> select sequence #113:500

Nothing selected  

> select sequence #113/A:1

Nothing selected  

> select #113/A:1551-1601

811 atoms, 818 bonds, 51 residues, 1 model selected  

> select #113/A:1551-1601

811 atoms, 818 bonds, 51 residues, 1 model selected  

> select #113/A:1551-1601

811 atoms, 818 bonds, 51 residues, 1 model selected  

> select #113/A:1328

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #113/A:1328

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select add #113

24144 atoms, 24336 bonds, 1601 residues, 1 model selected  

> select subtract #113

Nothing selected  

> select backbone

430695 atoms, 430577 bonds, 4 pseudobonds, 89407 residues, 119 models selected  

> select add #114

448950 atoms, 449107 bonds, 4 pseudobonds, 89407 residues, 121 models selected  

> select subtract #114

418586 atoms, 418469 bonds, 4 pseudobonds, 87408 residues, 120 models selected  

> view matrix models
> #1,0.087933,-0.86706,0.49039,1.006,-0.86483,0.17784,0.4695,53.036,-0.4943,-0.46539,-0.73422,146.35,#2,-0.89897,0.39225,-0.19491,63.905,-0.10755,0.23369,0.96634,-53.218,0.4246,0.88968,-0.16789,47.925,#3,0.99749,0.064305,0.029603,-5.2612,-0.065447,0.99708,0.03939,-1.2343,-0.026983,-0.041229,0.99879,11.051,#4.1,0.99749,0.064305,0.029603,-5.2612,-0.065447,0.99708,0.03939,-1.2343,-0.026983,-0.041229,0.99879,11.051,#4.2,0.99758,0.051631,0.046527,-6.0417,-0.056688,0.99176,0.1149,-5.4915,-0.040211,-0.11726,0.99229,14.197,#5,0.57409,0.66965,0.47116,-6.3931,0.64527,-0.015795,-0.76379,44.265,-0.50403,0.74251,-0.44117,63.42,#6,0.27579,-0.2359,-0.93182,15.69,0.21074,-0.93099,0.29806,93.81,-0.93783,-0.27858,-0.20705,132.23,#7.2,0.9977,0.050561,0.045126,-5.5269,-0.051034,0.99865,0.0093772,0.25557,-0.044591,-0.011659,0.99894,10.103,#8,0.97723,0.10994,0.18147,1.3897,-0.19053,0.078401,0.97855,89.443,0.093351,-0.99084,0.097562,96.294,#10,0.11463,-0.3217,-0.93988,5.3259,0.030004,-0.94456,0.32696,40.351,-0.99296,-0.065679,-0.098622,62.78,#11,-0.2331,0.032389,-0.97191,2.1901,-0.20023,-0.97963,0.015376,39.12,-0.95162,0.19819,0.23483,61.761,#12,0.85337,0.39166,-0.34405,6.346,-0.22223,0.87031,0.43952,37.852,0.47157,-0.29861,0.82973,65.706,#13,0.41258,0.75582,-0.50845,4.3415,-0.74726,-0.03839,-0.66342,31.8,-0.52095,0.65366,0.54895,64.505,#15,0.35313,0.44633,0.82224,-6.2361,0.81687,0.28136,-0.50355,66.733,-0.45609,0.84949,-0.26524,61.735,#14.1,1,-1.2846e-06,-6.2151e-06,-0.67295,1.2846e-06,1,-2.3385e-06,0.67241,6.2151e-06,2.3385e-06,1,9.4751,#14.2,0.95879,0.014013,-0.28376,18.907,-0.28299,-0.041547,-0.95822,89.834,-0.025217,0.99904,-0.035869,22.354,#16,0.83991,0.53959,-0.05829,7.9682,-0.36606,0.48393,-0.79487,31.87,-0.40069,0.68896,0.60398,63.592,#17,-0.84748,-0.5294,0.038979,2.7278,0.52772,-0.84818,-0.045853,76.536,0.057336,-0.018289,0.99819,93.945,#18,-0.30534,0.40056,-0.8639,18.008,-0.66358,-0.74017,-0.10866,71.39,-0.68296,0.54009,0.4918,77.538,#20,-0.83713,0.23992,0.49158,3.8168,-0.52546,-0.60244,-0.60079,76.409,0.15201,-0.76125,0.63039,92.209,#21,-0.83174,-0.086289,0.54841,17.43,-0.083165,-0.95733,-0.27676,73.562,0.54889,-0.2758,0.78908,97.779,#22,0.092029,0.77872,-0.62058,-2.7618,0.77893,-0.44455,-0.44232,32.265,-0.62033,-0.44268,-0.64748,67.724,#23,-0.65444,-0.15282,0.74051,49.396,0.69832,-0.49769,0.51444,70.74,0.28993,0.85378,0.43243,98.775,#24,-0.85369,0.081819,0.51432,58.321,0.45281,-0.37123,0.81065,96.651,0.25725,0.92493,0.27986,100.57,#25,-0.54328,-0.72097,0.43018,6.2198,0.83602,-0.41763,0.35589,76.603,-0.07693,0.55299,0.82963,95.916,#26,-0.04848,-0.75452,-0.65448,0.68405,-0.1903,-0.63627,0.74762,50.425,-0.98053,0.16079,-0.11274,57.978,#27,-0.2312,-0.97003,-0.074728,55.046,0.96915,-0.22288,-0.10521,47.584,0.085402,-0.096747,0.99164,56.559,#28,-0.78826,0.57458,0.22024,-9.7602,0.58249,0.81213,-0.033949,0.17477,-0.19837,0.10152,-0.97486,57.251,#29,-0.17783,-0.56814,-0.80349,1.528,-0.96315,-0.06694,0.2605,-7.7462,-0.20179,0.82021,-0.5353,55.288,#30,-0.94944,-0.094865,-0.29927,24.199,0.31384,-0.31133,-0.89698,16.86,-0.0080808,-0.94555,0.32537,25.059,#31,0.29011,0.90143,-0.32133,8.6584,-0.76381,0.015807,-0.64525,25.138,-0.57657,0.43263,0.69311,70.069,#32,0.21892,-0.1697,-0.96087,5.2658,-0.58693,-0.80958,0.0092521,37.912,-0.77948,0.56194,-0.27684,61.873,#33,0.55912,-0.82856,0.029672,2.4374,0.38431,0.22729,-0.89479,16.02,0.73464,0.5117,0.4455,66.582,#34,0.10824,-0.41674,-0.90256,7.7073,0.95036,-0.22304,0.21695,46.278,-0.29172,-0.88124,0.37191,75.003,#35,-0.64903,-0.42808,-0.62889,39.17,-0.60028,0.79601,0.077671,53.867,0.46735,0.42793,-0.7736,106.89,#36,-0.0049215,-0.99879,0.048959,25.183,0.4139,-0.046604,-0.90913,33.499,0.91031,0.01579,0.41363,0.97237,#37,0.52715,-0.7629,0.3743,4.724,0.72072,0.63474,0.27869,37.28,-0.4502,0.12285,0.88444,57.718,#38,0.84732,0.1896,0.49608,1.3571,0.49773,0.042271,-0.8663,71.685,-0.18522,0.98095,-0.058554,86.275,#39,0.50824,0.56983,-0.64575,22.934,-0.011138,0.7541,0.65667,59.812,0.86115,-0.32655,0.38961,88.719,#40,-0.11307,0.50125,-0.85788,25.317,-0.40072,0.76708,0.50101,51.026,0.9092,0.40042,0.11413,103.41,#41,-0.25773,0.30444,0.917,33.098,0.23234,0.94074,-0.24702,61.843,-0.93787,0.1494,-0.31319,90.781,#42,-0.086963,-0.38639,0.91823,21.93,0.72242,-0.65913,-0.20894,20.511,0.68596,0.64518,0.33645,69.822,#43,-0.2917,-0.95611,-0.027749,-5.0221,-0.54266,0.14153,0.82794,66.218,-0.78767,0.25657,-0.56013,80.175,#44,0.22053,-0.96205,0.16069,-0.15813,-0.7065,-0.043973,0.70634,72.015,-0.67247,-0.2693,-0.68939,84.824,#45.2,0.99967,0.0066633,0.024669,-2.3563,-0.0048116,0.99722,-0.074375,5.0077,-0.025096,0.074232,0.99693,6.9686,#46,0.093944,-0.18137,0.97892,-10.788,-0.082168,0.9785,0.18918,45.599,-0.99218,-0.098208,0.077021,93.768,#47,-0.74537,0.41033,-0.52541,119.36,-0.45766,0.25812,0.85084,-17.586,0.48474,0.87464,-0.0046032,-41.354,#48,0.17057,-0.96514,0.19851,-1.2679,-0.90401,-0.073135,0.42121,79.069,-0.39201,-0.2513,-0.88497,85.059,#49,0.049236,-0.99871,0.01255,0.3041,-0.97362,-0.045189,0.22364,77.973,-0.22278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> ui mousemode right select

> select clear

> select sequence #113/A:1601

Nothing selected  

> select sequence #113:1601

Nothing selected  

> select sequence #113/M:1601

Nothing selected  

> select sequence #113:1601

Nothing selected  

> select sequence "#113: 1601"

Nothing selected  

> select sequence "#113: 1"

Nothing selected  

> select sequence #113:1

Nothing selected  

> select sequence #114:1

Nothing selected  
Drag select of 6 residues  

> select clear

> ui mousemode right select

> ui mousemode right "translate selected models"

> select #113/A:1328-1389

953 atoms, 961 bonds, 62 residues, 1 model selected  

> select #113/A:1328-1453

1904 atoms, 1921 bonds, 126 residues, 1 model selected  

> view matrix models #113,1,0,0,22.022,0,1,0,112.04,0,0,1,61.437

> view matrix models #113,1,0,0,24.063,0,1,0,110.97,0,0,1,61.129

> select add #113

24144 atoms, 24336 bonds, 1601 residues, 1 model selected  

> select subtract #113

Nothing selected  

> select #114/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #114/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> color sel red

> view matrix models
> #114,0.46432,0.27628,0.84147,47.474,0.84179,0.15767,-0.51627,1.4006,-0.27531,0.94806,-0.15936,-37.274

> view matrix models
> #114,0.46432,0.27628,0.84147,58.356,0.84179,0.15767,-0.51627,23.459,-0.27531,0.94806,-0.15936,-40.269

> select add #114

30364 atoms, 30638 bonds, 1999 residues, 1 model selected  

> view matrix models
> #114,0.46432,0.27628,0.84147,93.568,0.84179,0.15767,-0.51627,-5.0543,-0.27531,0.94806,-0.15936,-49.126

> view matrix models
> #114,0.46432,0.27628,0.84147,104.47,0.84179,0.15767,-0.51627,20.736,-0.27531,0.94806,-0.15936,-52.157

> select subtract #114

Nothing selected  

> select add #113

24144 atoms, 24336 bonds, 1601 residues, 1 model selected  

> view matrix models #113,1,0,0,12.507,0,1,0,55.885,0,0,1,64.573

> select #113/A:1601

18 atoms, 17 bonds, 1 residue, 1 model selected  

> select #113/A:1601

18 atoms, 17 bonds, 1 residue, 1 model selected  

> color sel lime

> view matrix models #113,1,0,0,8.1859,0,1,0,37.47,0,0,1,57.072

> ui mousemode right "rotate selected models"

> view matrix models
> #113,0.98482,-0.048637,-0.16663,8.0868,0.16349,-0.062719,0.98455,42.791,-0.058336,-0.99685,-0.053815,58.863

> view matrix models
> #113,0.99064,0.053136,-0.1257,7.8474,0.12547,-0.71686,0.68584,44.296,-0.053665,-0.69519,-0.71682,57.407

> select add #113

24144 atoms, 24336 bonds, 1601 residues, 1 model selected  

> select subtract #113

Nothing selected  

> select add #113

24144 atoms, 24336 bonds, 1601 residues, 1 model selected  

> select subtract #113

Nothing selected  

> select add #114

30364 atoms, 30638 bonds, 1999 residues, 1 model selected  

> view matrix models
> #114,0.31496,0.52687,0.78944,100.53,0.43207,-0.82017,0.37501,21.258,0.84506,0.22298,-0.48596,-30.471

> view matrix models
> #114,0.33794,0.48758,0.80502,101,-0.0026174,-0.85485,0.51886,18.665,0.94116,-0.17745,-0.28761,-26.645

> ui mousemode right "translate selected models"

> view matrix models
> #114,0.33794,0.48758,0.80502,108.85,-0.0026174,-0.85485,0.51886,35.154,0.94116,-0.17745,-0.28761,-18.01

> ui mousemode right "rotate selected models"

> view matrix models
> #114,0.28427,0.57713,0.76558,107.87,0.017549,-0.80152,0.59771,32.511,0.95858,-0.15648,-0.23797,-19.425

> view matrix models
> #114,0.13603,0.53223,0.8356,107.2,0.20108,-0.84072,0.50275,35.359,0.97009,0.099631,-0.22138,-24.759

> select subtract #114

Nothing selected  

> select add #114

30364 atoms, 30638 bonds, 1999 residues, 1 model selected  

> select subtract #114

Nothing selected  

> select add #113

24144 atoms, 24336 bonds, 1601 residues, 1 model selected  

> view matrix models
> #113,0.38071,0.92446,0.020559,0.79506,-0.39119,0.14087,0.90947,38.033,0.83787,-0.35429,0.41527,63.822

> view matrix models
> #113,0.091164,0.83199,0.54725,-0.59859,-0.99583,0.077897,0.047464,33.082,-0.0031402,-0.5493,0.83562,58.619

> ui mousemode right "translate selected models"

> view matrix models
> #113,0.091164,0.83199,0.54725,28.726,-0.99583,0.077897,0.047464,35.39,-0.0031402,-0.5493,0.83562,56.768

> view matrix models
> #113,0.091164,0.83199,0.54725,33.333,-0.99583,0.077897,0.047464,30.744,-0.0031402,-0.5493,0.83562,53.596

> select subtract #113

Nothing selected  

> ui mousemode right select

Drag select of 2 residues  

> ui tool show "Build Structure"

> build join peptide sel length 1.33 omega 180 phi -120 move small

> select add #114

54505 atoms, 54972 bonds, 3600 residues, 1 model selected  

> select subtract #114

Nothing selected  

> select add #114

54505 atoms, 54972 bonds, 3600 residues, 1 model selected  

> select subtract #114

Nothing selected  

> select #114/A:1602

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #114/A:1602-1610

152 atoms, 152 bonds, 9 residues, 1 model selected  

> log metadata #104

The model has no metadata

> log chains #104

Chain information for GMGC10.011_528_202.ranked_0.1.2000.ranked_0.pdb #104  
---  
Chain | Description  
A | No description available  
  

> sequence chain #104/A

Alignment identifier is 104/A  

> select add #114

54505 atoms, 54972 bonds, 3600 residues, 1 model selected  

> select subtract #114

Nothing selected  

> log metadata #114

The model has no metadata

> log chains #114

Chain information for GMGC10.011_528_202.ranked_0.1800.3500.ranked_0.pdb #114  
---  
Chain | Description  
A | No description available  
  

> sequence chain #114/A

Alignment identifier is 114/A  
Drag select of 259 residues  

> undo

Undo failed, probably because structures have been modified.  

> select add #114

54505 atoms, 54972 bonds, 3600 residues, 1 model selected  

> select subtract #114

Nothing selected  

> close #114

> open /Users/aho2840/Downloads/GMGC10.011_528_202.ranked_0.1.2000.pdb

Chain information for GMGC10.011_528_202.ranked_0.1.2000.pdb #113  
---  
Chain | Description  
A | No description available  
  

> open
> /Users/aho2840/Downloads/GMGC10.011_528_202.ranked_0.1800.3500.ranked_0.pdb

Chain information for GMGC10.011_528_202.ranked_0.1800.3500.ranked_0.pdb #114  
---  
Chain | Description  
A | No description available  
  

> select add #114

30364 atoms, 30638 bonds, 1999 residues, 1 model selected  
Drag select of 187 residues  

> ui mousemode right "translate selected models"

> select add #113

26356 atoms, 24336 bonds, 1742 residues, 2 models selected  

> select subtract #113

2212 atoms, 141 residues, 1 model selected  

> view matrix models #114,1,0,0,-78.219,0,1,0,37.594,0,0,1,-98.102

> select add #114

30364 atoms, 30638 bonds, 1999 residues, 1 model selected  

> select subtract #114

Nothing selected  

> log metadata #113

The model has no metadata

> log chains #113

Chain information for GMGC10.011_528_202.ranked_0.1.2000.pdb #113  
---  
Chain | Description  
A | No description available  
  

> sequence chain #113/A

Alignment identifier is 113/A  

> select #113/A:1601

18 atoms, 17 bonds, 1 residue, 1 model selected  

> select #113/A:1601

18 atoms, 17 bonds, 1 residue, 1 model selected  

> color sel lime

> log metadata #113

The model has no metadata

> log chains #113

Chain information for GMGC10.011_528_202.ranked_0.1.2000.pdb #113  
---  
Chain | Description  
A | No description available  
  

> log metadata #114

The model has no metadata

> log chains #114

Chain information for GMGC10.011_528_202.ranked_0.1800.3500.ranked_0.pdb #114  
---  
Chain | Description  
A | No description available  
  

> sequence chain #114/A

Alignment identifier is 114/A  

> select #114/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #114/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #114/A:113-170

872 atoms, 877 bonds, 58 residues, 1 model selected  

> select #114/A:113-170

872 atoms, 877 bonds, 58 residues, 1 model selected  

> select #114/A:115-116

28 atoms, 28 bonds, 2 residues, 1 model selected  

> select #114/A:115-357

3627 atoms, 3657 bonds, 243 residues, 1 model selected  

> select #114/A:340-396

827 atoms, 830 bonds, 57 residues, 1 model selected  

> select #114/A:340-584

3675 atoms, 3701 bonds, 245 residues, 1 model selected  

> select #114/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #114/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #114/A:3

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #114/A:3-302

4580 atoms, 4624 bonds, 300 residues, 1 model selected  

> select #114/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #114/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> view matrix models #114,1,0,0,-56.047,0,1,0,65.157,0,0,1,-25.546

> view matrix models #114,1,0,0,-34.375,0,1,0,59.469,0,0,1,-7.3837

> color sel red

> ui mousemode right "rotate selected models"

> view matrix models
> #114,-0.27005,0.020461,-0.96263,-15.976,-0.72402,0.65474,0.21703,61.228,0.63472,0.75557,-0.162,2.1519

> ui mousemode right "translate selected models"

> view matrix models
> #114,-0.27005,0.020461,-0.96263,-1.4491,-0.72402,0.65474,0.21703,36.958,0.63472,0.75557,-0.162,-2.3183

> ui mousemode right select

> select add #114

30364 atoms, 30638 bonds, 1999 residues, 1 model selected  

> select subtract #114

Nothing selected  
Drag select of 2 residues  

> ui tool show "Build Structure"

> build join peptide sel length 1.33 omega 180 phi -120 move small


===== Log before crash end =====

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.8.dev202403210048 (2024-03-21)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Compositor returned null texture  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac14,2
      Model Number: Z160000B1LL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.101.1
      OS Loader Version: 10151.140.19.700.2

Software:

    System Software Overview:

      System Version: macOS 14.7.5 (23H527)
      Kernel Version: Darwin 23.6.0
      Time since boot: 28 days, 14 hours, 57 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.1.1
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.16
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.56
    ChimeraX-AtomicLibrary: 14.0.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    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: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8.dev202403210048
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.9
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.3
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2
    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: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.37.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.9
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.1
    fonttools: 4.50.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2024.2.26
    idna: 3.6
    ihm: 0.43
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    Jinja2: 3.1.3
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.1.0
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.8
    ndindex: 1.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.2.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.9.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.3
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.2.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.3.0
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3302
    pyparsing: 3.1.2
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.2
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.2
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 25.1.2
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.12.0
    setuptools: 69.2.0
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.0
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.1
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.1
    typing-extensions: 4.10.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10

Change History (2)

comment:1 by Tom Goddard, 2 months ago

Component: Unassigned → Structure Editing
Description: modified (diff)
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash in python_instances_of_class after "build join" command

This ChimeraX bug may be fixed in the current ChimeraX 1.10 release. You are using a version prior to the ChimeraX 1.8 release.

comment:2 by pett, 2 months ago

Resolution: → duplicate
Status: assigned → closed

This problem is indeed fixed in current versions of ChimeraX.

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