![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Closed 15 months ago
#15753 closed defect (fixed)
Crash in Modeller tool _update_sequence_menus in Qt call meth_QFormLayout_removeRow()
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.5-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000700014954000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000700017784000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007ff847610fc0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/modeller/tool.py", line 349 in _update_sequence_menus
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/widgets.py", line 45 in _items_change
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/manager.py", line 129 in destroy_alignment
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py", line 445 in detach_viewer
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seq_view/tool.py", line 511 in delete
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 780 in close_request
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 2430 in
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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.map._map, 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.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 65)
{"app_name":"ChimeraX","timestamp":"2024-08-09 19:27:17.00 +0100","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.5 (23F79)","roots_installed":0,"name":"ChimeraX","incident_id":"5A35E36C-8D55-4E3B-AA6F-C25AA5FF970E"}
{
"uptime" : 570000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"coalitionID" : 523,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2024-08-09 19:26:49.5755 +0100",
"codeSigningMonitor" : 0,
"incident" : "5A35E36C-8D55-4E3B-AA6F-C25AA5FF970E",
"pid" : 64361,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-08-07 11:37:36.4810 +0100",
"procStartAbsTime" : 443000157544357,
"procExitAbsTime" : 575251380740949,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"3F04E6F6-E1E4-5487-8C8D-4858BB5E3585","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "718C56F5-17B3-6A01-634B-4D2136B595AA",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 24949,
"bridgeVersion" : {"build":"21P5077","train":"8.5"},
"sleepWakeUUID" : "071C280B-4701-467D-AD6B-9DB36D5E3440",
"sip" : "enabled",
"vmRegionInfo" : "0x13b is not in any region. Bytes before following region: 4461039301\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 109e61000-109e65000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x000000000000013b","rawCodes":[1,315],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000000000013b"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":64361},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x13b is not in any region. Bytes before following region: 4461039301\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 109e61000-109e65000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"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" : 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"uuid" : "dc4ae342-b3c4-3716-a530-b1568a67f912",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/binascii.cpython-311-darwin.so",
"name" : "binascii.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4467712000,
"size" : 32768,
"uuid" : "4e6494eb-704b-3e1a-9d97-751ef9b2d06a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_sha512.cpython-311-darwin.so",
"name" : "_sha512.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4467646464,
"size" : 16384,
"uuid" : "de8dfc82-ec28-378b-b945-07e7671a35b1",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_random.cpython-311-darwin.so",
"name" : "_random.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4467580928,
"size" : 16384,
"uuid" : "cc52d89b-b174-3a9a-94ae-0c556ec7b21b",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_bisect.cpython-311-darwin.so",
"name" : "_bisect.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4468158464,
"size" : 196608,
"uuid" : "0fa75f51-66bf-3a60-a393-65ceea03012e",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_lzma.cpython-311-darwin.so",
"name" : "_lzma.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4467515392,
"size" : 16384,
"uuid" : "4921b552-b90a-39c6-b791-14028366f5a0",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_bz2.cpython-311-darwin.so",
"name" : "_bz2.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4467417088,
"size" : 32768,
"uuid" : "6c0e3849-f845-3996-a69e-e956c62499ff",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/zlib.cpython-311-darwin.so",
"name" : "zlib.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4463517696,
"size" : 16384,
"uuid" : "52112d00-a676-3fba-b4d8-69e98fe5e2c3",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_typing.cpython-311-darwin.so",
"name" : "_typing.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4463370240,
"size" : 65536,
"uuid" : "ce1cdda7-c310-3834-8656-4829f8b0fa2a",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_datetime.cpython-311-darwin.so",
"name" : "_datetime.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4463624192,
"size" : 49152,
"uuid" : "c4d4107c-7508-3d61-88f1-4f1a33945090",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/math.cpython-311-darwin.so",
"name" : "math.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4481421312,
"CFBundleShortVersionString" : "3.11.4, (c) 2001-2023 Python Software Foundation.",
"CFBundleIdentifier" : "org.python.python",
"size" : 4030464,
"uuid" : "514efc82-c424-3863-84a8-e24ffd50343d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python",
"name" : "Python",
"CFBundleVersion" : "3.11.4"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4461039616,
"CFBundleShortVersionString" : "1.8.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 16384,
"uuid" : "194a3167-3db5-3029-8d22-1d742b826bb9",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.8.0.0"
},
{
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"arch" : "x86_64",
"base" : 140703196311552,
"size" : 241656,
"uuid" : "13597eeb-2ea0-3d48-8be1-dfc4872a784b",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
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"arch" : "x86_64",
"base" : 140703196553216,
"size" : 49144,
"uuid" : "25b2f3eb-07b4-3cb9-9457-2c26210c27c8",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
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"size" : 557048,
"uuid" : "93fb3816-608b-33af-83d2-209b4bd673ad",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
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"uuid" : "acde8386-eb3f-36f2-bc5e-069cc59d079c",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
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"source" : "A",
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"base" : 140703196975104,
"CFBundleShortVersionString" : "6.9",
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"size" : 4829181,
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"size" : 592800,
"uuid" : "baa6f02e-dff3-3562-8c99-ea2820c91ad9",
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"logWritingSignature" : "80b6c9cb1fdc2b6c2fff1c052a154654587dca3b",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/grooms/Desktop/ChimeraX/All TMBIMs.cxs" format session
opened ChimeraX session
> hide #!7 models
> show #!7 models
> hide #!9 models
> show #!9 models
> show #8 models
> hide #!9 models
> show #2 models
> view orient
> hide #8 models
> show #8 models
> hide #8 models
> select add #2
3943 atoms, 3978 bonds, 256 residues, 1 model selected
> show #8 models
> select subtract #2
Nothing selected
> select add #2
3943 atoms, 3978 bonds, 256 residues, 1 model selected
Alignment identifier is 2/A
> select clear
> select #2/A:146
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:146-147
48 atoms, 47 bonds, 2 residues, 1 model selected
> select add #2
3943 atoms, 3978 bonds, 256 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #2
3943 atoms, 3978 bonds, 256 residues, 1 model selected
> show sel target ab
> hide sel target a
> select subtract #2
Nothing selected
> select #2/A:146
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:146-147
48 atoms, 47 bonds, 2 residues, 1 model selected
> select #2/A:146-147,222
60 atoms, 58 bonds, 3 residues, 1 model selected
> select #2/A:146-147,197,222
72 atoms, 69 bonds, 4 residues, 1 model selected
> show sel target ab
> style sel ball
Changed 72 atom styles
> select #2/A:146-147
48 atoms, 47 bonds, 2 residues, 1 model selected
> select #2/A:146-192
704 atoms, 711 bonds, 47 residues, 1 model selected
> select #2/A:144
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:144
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:146
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:146-176
476 atoms, 480 bonds, 31 residues, 1 model selected
> show sel target ab
> view orient
> select #2/A:2-11,21-24,32-62,67-82,90-118,120-143,150-172,178-206,212-253
3217 atoms, 3238 bonds, 208 residues, 1 model selected
> select clear
> select #2/A:146
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:146-173
438 atoms, 442 bonds, 28 residues, 1 model selected
> hide sel target a
> select clear
> select #2/A:146
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:146-148
59 atoms, 58 bonds, 3 residues, 1 model selected
> select #2/A:146-148,151
80 atoms, 79 bonds, 4 residues, 1 model selected
> select #2/A:146-148,151,157-158
102 atoms, 100 bonds, 6 residues, 1 model selected
> select #2/A:146-148,151,157-158,167
126 atoms, 123 bonds, 7 residues, 1 model selected
> show sel target ab
> select #2/A:167
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:167
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel target a
> select #2/A:197
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:197
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:197,222
24 atoms, 22 bonds, 2 residues, 1 model selected
> select #2/A:148
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:148
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel target a
> select #2/A:176
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:176
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel target a
> select #2/A:157
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:157-158
22 atoms, 21 bonds, 2 residues, 1 model selected
> hide sel target a
> select clear
> select #2/A:182
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/A:182-190
143 atoms, 144 bonds, 9 residues, 1 model selected
> select #2/A:167
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:155-167
197 atoms, 197 bonds, 13 residues, 1 model selected
> select #2/A:172
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/A:150-172
349 atoms, 352 bonds, 23 residues, 1 model selected
> select clear
> select #2/A:146
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:146-147
48 atoms, 47 bonds, 2 residues, 1 model selected
> select #2/A:146-147,151
69 atoms, 68 bonds, 3 residues, 1 model selected
> hide sel target a
> select clear
> select #2/A:197
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:197
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:197,222-223
43 atoms, 41 bonds, 3 residues, 1 model selected
> hide sel target a
> hide #!7 models
> select #2/A:62-63
32 atoms, 32 bonds, 2 residues, 1 model selected
> select #2/A:62-93
475 atoms, 480 bonds, 32 residues, 1 model selected
> select #2/A:88-89
31 atoms, 30 bonds, 2 residues, 1 model selected
> select #2/A:88-89,91-94
112 atoms, 111 bonds, 6 residues, 1 model selected
> show sel target ab
> style sel ball
Changed 112 atom styles
> select clear
> select add #2
3943 atoms, 3978 bonds, 256 residues, 1 model selected
> hide sel target a
> select clear
> hide #8 models
> hide #2 models
> show #12 models
Alignment identifier is 4/A
Alignment identifier is 1
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
Alignment identifier is 9/A
Alignment identifier is 2
Alignment identifier is 3
> select add #12
3785 atoms, 3825 bonds, 243 residues, 1 model selected
Alignment identifier is 12/A
> select clear
> select #12/A:92
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #12/A:92-93
48 atoms, 47 bonds, 2 residues, 1 model selected
> select #12/A:92
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #12/A:92
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #12/A:92,198
36 atoms, 34 bonds, 2 residues, 1 model selected
> select #12/A:92,198,225
48 atoms, 45 bonds, 3 residues, 1 model selected
> show sel target ab
> style sel ball
Changed 48 atom styles
> view orient
> select add #12
3785 atoms, 3825 bonds, 243 residues, 1 model selected
> hide sel target a
> select clear
> select #12/A:235
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/A:235
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/A:225
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/A:225
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/A:198,225
24 atoms, 22 bonds, 2 residues, 1 model selected
> show sel target ab
> select #12/A:92
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #12/A:92
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel target ab
> select #12/A:175
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #12/A:175
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel target ab
> select #12/A:206
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #12/A:206
17 atoms, 17 bonds, 1 residue, 1 model selected
> show sel target ab
> select #12/A:61
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #12/A:61
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right "tape measure"
> marker segment #14 position -6.722,3.229,-1.314 toPosition
> -9.033,1.347,-0.7423 color yellow radius 0.1 label 3.035 labelHeight 0.3035
> labelColor yellow
> view orient
> hide #12 models
> select add #12
3785 atoms, 3825 bonds, 243 residues, 1 model selected
> select subtract #12
Nothing selected
> select add #3
1626 atoms, 1667 bonds, 207 residues, 1 model selected
> select subtract #3
Nothing selected
> show #3 models
> view orient
> hide #3 models
> show #13 models
> view orient
> hide #13 models
> show #13 models
> view orient
> select #12/A:151
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #12/A:151-176
387 atoms, 388 bonds, 26 residues, 1 model selected
> view sel
> select clear
> view orient
> select add #13
3761 atoms, 3796 bonds, 248 residues, 1 model selected
> hide sel target a
> select clear
> select
> #12/A:7-10,17-56,58-66,69-87,89-93,97-119,122-145,150-174,177-203,212-240
3221 atoms, 3245 bonds, 205 residues, 1 model selected
> select clear
> select #12/A:198
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/A:198
12 atoms, 11 bonds, 1 residue, 1 model selected
> select add #12
3785 atoms, 3825 bonds, 243 residues, 1 model selected
> select subtract #12
Nothing selected
> select add #13
3761 atoms, 3796 bonds, 248 residues, 1 model selected
Alignment identifier is 13/A
> select clear
> select #13/A:230
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:230
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:202
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:202
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:202,240
36 atoms, 34 bonds, 2 residues, 1 model selected
> select #13/A:96,202,240
60 atoms, 57 bonds, 3 residues, 1 model selected
> show sel target ab
> marker delete #14
> select down
60 atoms, 57 bonds, 3 residues, 1 model selected
> select down
60 atoms, 57 bonds, 3 residues, 1 model selected
> select down
60 atoms, 57 bonds, 3 residues, 1 model selected
> select down
60 atoms, 57 bonds, 3 residues, 1 model selected
> select down
60 atoms, 57 bonds, 3 residues, 1 model selected
> select down
60 atoms, 57 bonds, 3 residues, 1 model selected
> view
> label sel text "{0.name} {0.number}{0.insertion_code}"
> label height 2
> select #13/A:96,202,230,240
72 atoms, 68 bonds, 4 residues, 1 model selected
> show sel target ab
> select clear
> select #13/A:230
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:230
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:96,230
36 atoms, 34 bonds, 2 residues, 1 model selected
> select #13/A:96,202,230
48 atoms, 45 bonds, 3 residues, 1 model selected
> view sel
> ~label sel residues
> ui mousemode right "tape measure"
> marker segment #14 position -7.175,-1.628,0.1425 toPosition
> -5.797,1.28,2.262 color yellow radius 0.1 label 3.853 labelHeight 0.3853
> labelColor yellow
> undo
> select clear
> ui mousemode right "tape measure"
> hide #!14 models
> ui mousemode right "tape measure"
> marker delete #14
> marker segment #14 position -6.815,3.342,-1.209 toPosition
> -9.177,1.616,-0.4898 color yellow radius 0.1 label 3.012 labelHeight 0.3012
> labelColor yellow
> hide #!14 models
> select #13/A:96,202,230
48 atoms, 45 bonds, 3 residues, 1 model selected
> hide sel target a
> select clear
> select #13/A:230
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:230
12 atoms, 11 bonds, 1 residue, 1 model selected
> ~label sel residues
> select #13/A:230
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:230-231
31 atoms, 30 bonds, 2 residues, 1 model selected
> select #13/A:230-231
31 atoms, 30 bonds, 2 residues, 1 model selected
> select #13/A:230-231
31 atoms, 30 bonds, 2 residues, 1 model selected
> ~label sel residues
> select #13/A:240
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #13/A:240
24 atoms, 23 bonds, 1 residue, 1 model selected
> ~label sel residues
> select clear
> hide #13 models
> show #!9 models
> show #!14 models
> hide #!14 models
> marker segment #14 position -8.559,-2.034,2.97 toPosition
> -8.218,-1.547,5.998 color yellow radius 0.1 label 3.086 labelHeight 0.3086
> labelColor yellow
> show #!14 models
> hide #!14 models
> hide #14.1 models
> show #14.1 models
> hide #14.1 models
> select add #14.1
1 model selected
> hide #!9 models
> close #14
> show #!9 models
> ui mousemode right "tape measure"
> marker segment #14 position -8.559,-2.034,2.97 toPosition
> -8.218,-1.547,5.998 color yellow radius 0.1 label 3.086 labelHeight 0.3086
> labelColor yellow
> select #13/A:240-241
43 atoms, 42 bonds, 2 residues, 1 model selected
> select #13/A:240
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide #!14 models
> select add #9
3788 atoms, 3828 bonds, 238 pseudobonds, 238 residues, 3 models selected
> select add #8
3788 atoms, 3828 bonds, 717 pseudobonds, 238 residues, 4 models selected
> select subtract #8
3788 atoms, 3828 bonds, 238 residues, 3 models selected
> select add #13
7525 atoms, 7601 bonds, 485 residues, 3 models selected
> select subtract #13
3764 atoms, 3805 bonds, 237 residues, 2 models selected
> hide (#!9 & sel) target a
> select subtract #9
1 model selected
> select add #9
3764 atoms, 3805 bonds, 238 pseudobonds, 237 residues, 2 models selected
> show #8 models
> select add #8
3764 atoms, 3805 bonds, 717 pseudobonds, 237 residues, 3 models selected
> select subtract #8
3764 atoms, 3805 bonds, 237 residues, 2 models selected
> select subtract #9
1 model selected
> hide #8 models
> hide #!9 models
> show #3 models
> show #8 models
> select add #3
1626 atoms, 1667 bonds, 207 residues, 1 model selected
> hide #8 models
> show #8 models
> view orient
> select subtract #3
Nothing selected
> hide #8 models
> hide #3 models
> show #2 models
> select add #2
3943 atoms, 3978 bonds, 256 residues, 1 model selected
Alignment identifier is 2/A
> select subtract #2
Nothing selected
> select #2/A:67
24 atoms, 25 bonds, 1 residue, 1 model selected
> select #2/A:67-93
410 atoms, 414 bonds, 27 residues, 1 model selected
> select clear
> select #2/A:222
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:222
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:155
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/A:155
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/A:155,176
45 atoms, 44 bonds, 2 residues, 1 model selected
> select #2/A:146-147,155,176
93 atoms, 91 bonds, 4 residues, 1 model selected
> select #2/A:199
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/A:199
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/A:146-147,199
65 atoms, 63 bonds, 3 residues, 1 model selected
> select #2/A:146-147,151,199
86 atoms, 84 bonds, 4 residues, 1 model selected
> select #2/A:146-147,151,155,199
107 atoms, 105 bonds, 5 residues, 1 model selected
> select #2/A:146-147,151,155,157-158,199
129 atoms, 126 bonds, 7 residues, 1 model selected
> select #2/A:93,146-147,151,155,157-158,199
153 atoms, 149 bonds, 8 residues, 1 model selected
> show sel target ab
> select #2/A:93,146-147,151,155,157-158,199
153 atoms, 149 bonds, 8 residues, 1 model selected
> select #2/A:158
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:157-158
22 atoms, 21 bonds, 2 residues, 1 model selected
> select #2/A:157-158
22 atoms, 21 bonds, 2 residues, 1 model selected
> select #2/A:155-158
62 atoms, 62 bonds, 4 residues, 1 model selected
> select #2/A:151,155-158
83 atoms, 83 bonds, 5 residues, 1 model selected
> select #2/A:151,155-158
83 atoms, 83 bonds, 5 residues, 1 model selected
> select #2/A:151,155-158
83 atoms, 83 bonds, 5 residues, 1 model selected
> select #2/A:2-11,21-24,32-62,67-82,90-118,120-143,150-172,178-206,212-253
3217 atoms, 3238 bonds, 208 residues, 1 model selected
> show sel target ab
> hide sel target a
> select clear
> select #2/A:197
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:197
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/A:197,222
24 atoms, 22 bonds, 2 residues, 1 model selected
QGestureManager::deliverEvent: could not find the target for gesture
> show sel target ab
> select clear
> select #2/A:93
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:93
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
> select #2/A:2-11,21-24,32-62,67-82,90-118,120-143,150-172,178-206,212-253
3217 atoms, 3238 bonds, 208 residues, 1 model selected
> select #2/A:233
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #2/A:233
17 atoms, 17 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
> show #!7 models
> label height 1
> ui tool show "Side View"
> view orient
> show #3 models
> hide #2 models
> hide #!7 models
> select add #3
1626 atoms, 1667 bonds, 207 residues, 1 model selected
> select clear
> select add #3
1626 atoms, 1667 bonds, 207 residues, 1 model selected
Alignment identifier is 3/A
> select clear
> select #3/A:8-42,44-59,66-91,94-116,122-146,149-178,181-211
1460 atoms, 1492 bonds, 186 residues, 1 model selected
> select #3/A:205
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:205
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> select add #3
1626 atoms, 1667 bonds, 207 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #3
1626 atoms, 1667 bonds, 207 residues, 1 model selected
> select clear
> select #3/A
1626 atoms, 1667 bonds, 207 residues, 1 model selected
> hide sel target a
> select clear
> select #3/A:205
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:205
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> select #3/A:49
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:49
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> select #3/A:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:171
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:171,195
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel target ab
> ui mousemode right "tape measure"
> marker segment #14 position 8.73,35.39,4.979 toPosition 9.198,37.87,6.027
> color yellow radius 0.1 label 2.736 labelHeight 0.2736 labelColor yellow
> label height 2
> show #!14 models
> select #3/A:205
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:205
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:49,205
20 atoms, 18 bonds, 2 residues, 1 model selected
> hbonds sel reveal true
7 hydrogen bonds found
> show #8 models
> hbonds sel reveal true
7 hydrogen bonds found
> hide #8 models
> select #3/A:88
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3/A:88
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel target a
> cofr sel
> view orient
> volume planes z style image imageMode "full region"
No volumes specified
> volume region all imageMode "full region"
No volumes specified
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> volume step 2
No volumes specified
> volume step 1
No volumes specified
> volume style surface
No volumes specified
> volume region all imageMode "full region"
No volumes specified
> label height 1.5
> select #3/A:195
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:195
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:171,195
16 atoms, 14 bonds, 2 residues, 1 model selected
> color sel blue
> color sel cornflower blue
> select #3/A:205
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:205
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:49,205
20 atoms, 18 bonds, 2 residues, 1 model selected
> color sel purple
> select clear
> ui mousemode right "tape measure"
> marker segment #14 position 7.251,20.34,11.8 toPosition 9.169,17,11.78 color
> yellow radius 0.1 label 3.852 labelHeight 0.3852 labelColor yellow
> label height 1.5
> color #14 #23230bff
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #3 models
> hide #!14 models
> show #!1 models
> hide #!1 models
> show #2 models
> select add #2
3943 atoms, 3978 bonds, 256 residues, 1 model selected
Alignment identifier is 2/A
> select clear
> select #2/A:93
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:63-93
454 atoms, 458 bonds, 31 residues, 1 model selected
> select clear
> select #2/A:84
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/A:84
11 atoms, 10 bonds, 1 residue, 1 model selected
> save "/Users/grooms/Desktop/ChimeraX/All TMBIMs.cxs"
> hide #2 models
> show #3 models
> hide #3 models
> show #2 models
> select add #2
3943 atoms, 3978 bonds, 256 residues, 1 model selected
> select subtract #2
Nothing selected
> hide #2 models
> select add #10
1850 atoms, 1885 bonds, 248 residues, 1 model selected
> select add #11
3724 atoms, 3799 bonds, 491 residues, 2 models selected
> close #2
> undo
> select add #11
3724 atoms, 3799 bonds, 491 residues, 2 models selected
> hide #10 target m
> open /Users/grooms/Desktop/ChimeraX/AlphaFold/CrBI-1-new-
> AlphaFold-4-8-24/best_model.pdb
Chain information for best_model.pdb #2
---
Chain | Description
A | No description available
> rename #2 "CrBI-1 AAlphafold"
> select subtract #10
1874 atoms, 1914 bonds, 243 residues, 1 model selected
> select subtract #11
Nothing selected
> select add #2
3943 atoms, 3978 bonds, 256 residues, 1 model selected
> ui tool show "AlphaFold Error Plot"
> alphafold pae #2 file /Users/grooms/Desktop/ChimeraX/AlphaFold/CrBI-1-new-
> AlphaFold-4-8-24/best_model_pae.json
> color bfactor #2 palette alphafold
3943 atoms, 256 residues, atom bfactor range 41.7 to 97.4
> select subtract #2
Nothing selected
> select add #2
3943 atoms, 3978 bonds, 256 residues, 1 model selected
Alignment identifier is 2/A
> select clear
> select #2/A:146
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:146-147
48 atoms, 47 bonds, 2 residues, 1 model selected
> select #2/A:146-147,222
60 atoms, 58 bonds, 3 residues, 1 model selected
> select #2/A:146-147,197,222
72 atoms, 69 bonds, 4 residues, 1 model selected
> select #2/A:146-147,197,222,233
89 atoms, 86 bonds, 5 residues, 1 model selected
> show sel target ab
> select clear
> select #2/A:178
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:173-178
65 atoms, 64 bonds, 6 residues, 1 model selected
> ui tool show Angles/Torsions
Either three or four atoms must be selected!
> ui mousemode right "tape measure"
> marker segment #14 position 2.359,-30.09,-4.306 toPosition
> 13.25,-10.28,8.002 color yellow radius 0.1 label 25.74 labelHeight 2.574
> labelColor yellow
No items chosen in table
> show #!1 models
> hide #!1 models
> show #!14 models
> ui mousemode right "bond rotation"
> show sel target ab
> hide #!14 models
> hide sel target a
> view sel
> select #2/A:196
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/A:196
19 atoms, 18 bonds, 1 residue, 1 model selected
> view sel
> view orient
> select #2/A:199
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/A:172-199
413 atoms, 416 bonds, 28 residues, 1 model selected
> view sel
> select clear
> select #2/A:178
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:173-178
65 atoms, 64 bonds, 6 residues, 1 model selected
> select #2/A:172
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #2/A:172-178
84 atoms, 83 bonds, 7 residues, 1 model selected
> select #2/A:173
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2/A:173-178
65 atoms, 64 bonds, 6 residues, 1 model selected
> select #2/A:173
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2/A:173-177
58 atoms, 57 bonds, 5 residues, 1 model selected
> label sel residues attribute pae_domain
> ui tool show "Altloc Explorer"
> select add #2
3943 atoms, 3978 bonds, 256 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #2
3943 atoms, 3978 bonds, 256 residues, 2 models selected
> hbonds sel reveal true
419 hydrogen bonds found
> view orient
> select subtract #2
Nothing selected
> show #8 models
> select #2/A:167
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:167-168
43 atoms, 42 bonds, 2 residues, 1 model selected
> select #2/A:167
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:167
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:199
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #2/A:199
17 atoms, 16 bonds, 1 residue, 1 model selected
> view orient
> select #2/A:182-183
34 atoms, 33 bonds, 2 residues, 1 model selected
> select #2/A:176
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:176
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide #8 models
> select add #2
3943 atoms, 3978 bonds, 241 pseudobonds, 256 residues, 3 models selected
> select subtract #2
Nothing selected
> select add #2
3943 atoms, 3978 bonds, 241 pseudobonds, 256 residues, 3 models selected
> hide (#!2 & sel) target a
> select subtract #2
Nothing selected
> select #2/A:176
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:176
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:176,182
39 atoms, 37 bonds, 2 residues, 1 model selected
> view sel
> show sel target ab
> select #2/A:176
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:176
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel target a
> select #2/A:167
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:167
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
> show #8 models
> hide #8 models
> hide #!2 models
> show #3 models
> view orient
> select add #3
1626 atoms, 1667 bonds, 207 residues, 1 model selected
Alignment identifier is 3/A
> select subtract #3
Nothing selected
> select #3/A:60-61
22 atoms, 21 bonds, 2 residues, 1 model selected
> select #3/A:60
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:60
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #3
1626 atoms, 1667 bonds, 207 residues, 1 model selected
> hide #3 models
> select subtract #3
Nothing selected
> show #!2 models
> view orient
> hide #!2 models
> show #12 models
> view orient
> hide #12 models
> show #!2 models
> select add #2
3943 atoms, 3978 bonds, 241 pseudobonds, 256 residues, 3 models selected
Alignment identifier is 2/A
> select clear
> select #2/A:178
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:173-178
65 atoms, 64 bonds, 1 pseudobond, 6 residues, 2 models selected
> select #2/A:173-178
65 atoms, 64 bonds, 1 pseudobond, 6 residues, 2 models selected
> select #2/A:173
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2/A:173-177
58 atoms, 57 bonds, 5 residues, 1 model selected
> label sel text "Loop TM5-6"
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select add #2
3943 atoms, 3978 bonds, 241 pseudobonds, 256 residues, 3 models selected
> hide #!2 models
> select subtract #2
Nothing selected
> show #10 models
> hide #10 models
> show #12 models
> select add #12
3785 atoms, 3825 bonds, 243 residues, 1 model selected
> hbonds sel reveal true
1270 hydrogen bonds found
> hbonds sel reveal true
1270 hydrogen bonds found
> hbonds sel reveal true
1270 hydrogen bonds found
> hbonds sel reveal true
1270 hydrogen bonds found
> hide #12 models
> select subtract #12
Nothing selected
> show #!2 models
> select #2/A:173
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2/A:173-178
65 atoms, 64 bonds, 6 residues, 1 model selected
> ~label sel residues
> view sel
> select #2/A:182
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/A:182
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/A:167,182
39 atoms, 37 bonds, 2 residues, 1 model selected
> style sel ball
Changed 39 atom styles
> select clear
> hide #2 models
> show #12 models
> show #8 models
> view orient
> hide #8 models
> select add #12
3785 atoms, 3825 bonds, 243 pseudobonds, 243 residues, 2 models selected
Alignment identifier is 12/A
> select clear
> select #12/A:214
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #12/A:214
15 atoms, 14 bonds, 1 residue, 1 model selected
> show #8 models
> hide #12 models
> show #13 models
> show #12 models
> hide #12 models
> hide #8 models
> show #8 models
> select add #12
3785 atoms, 3825 bonds, 243 pseudobonds, 243 residues, 2 models selected
> select subtract #12
Nothing selected
> select add #13
3761 atoms, 3796 bonds, 248 residues, 1 model selected
> select add #8
3761 atoms, 3796 bonds, 1270 pseudobonds, 248 residues, 2 models selected
> select subtract #8
3761 atoms, 3796 bonds, 248 residues, 1 model selected
> hide #8 models
> show #8 models
> hbonds sel reveal true
1297 hydrogen bonds found
> hide #13 models
> select subtract #13
Nothing selected
> hide #8 models
> show #13 models
> select add #13
3761 atoms, 3796 bonds, 246 pseudobonds, 248 residues, 2 models selected
Alignment identifier is 13/A
> select clear
> hide #13 models
> show #12 models
> select add #12
3785 atoms, 3825 bonds, 243 residues, 1 model selected
Alignment identifier is 12/A
> select subtract #12
Nothing selected
> show #8 models
> select add #12
3785 atoms, 3825 bonds, 243 residues, 1 model selected
> hide #8 models
> show #8 models
> hbonds sel reveal true
1270 hydrogen bonds found
> select #12/A:235
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/A:235
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide #12 models
> show #10 models
> hide #10 models
> show #13 models
> select add #12
3785 atoms, 3825 bonds, 243 pseudobonds, 243 residues, 2 models selected
> select add #13
7546 atoms, 7621 bonds, 243 pseudobonds, 491 residues, 3 models selected
> select subtract #12
3761 atoms, 3796 bonds, 248 residues, 1 model selected
Alignment identifier is 13/A
> select #13/A:230
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:230
12 atoms, 11 bonds, 1 residue, 1 model selected
> view sel
> hide #8 models
> show #8 models
> hbonds sel reveal true
9 hydrogen bonds found
> view orient
> select add #13
3761 atoms, 3796 bonds, 2 pseudobonds, 248 residues, 2 models selected
> select add #8
3761 atoms, 3796 bonds, 9 pseudobonds, 248 residues, 2 models selected
> hide #8 models
> select subtract #8
3761 atoms, 3796 bonds, 248 residues, 1 model selected
> hide sel target a
> select clear
> hide #13 models
> show #12 models
> select add #12
3785 atoms, 3825 bonds, 243 residues, 1 model selected
> hide sel target a
> select subtract #12
Nothing selected
> select add #12
3785 atoms, 3825 bonds, 243 residues, 1 model selected
Alignment identifier is 12/A
> select subtract #12
Nothing selected
> select #12/A:171
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #12/A:171
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #12/A:171,180
25 atoms, 23 bonds, 2 residues, 1 model selected
> select #12/A:171,180,239
49 atoms, 46 bonds, 3 residues, 1 model selected
> select #12/A:171,180,198,239
61 atoms, 57 bonds, 4 residues, 1 model selected
> select #12/A:171,180,198,225,239
73 atoms, 68 bonds, 5 residues, 1 model selected
> show sel target ab
> style sel ball
Changed 73 atom styles
> select #12/A:168
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #12/A:168-199
517 atoms, 522 bonds, 32 residues, 1 model selected
> view sel
> select #12/A:92
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #12/A:92-93
48 atoms, 47 bonds, 2 residues, 1 model selected
> show sel target ab
> ui mousemode right "tape measure"
> marker segment #14 position -6.722,3.229,-1.314 toPosition
> -9.033,1.347,-0.7423 color yellow radius 0.1 label 3.035 labelHeight 0.3035
> labelColor yellow
> show #!14 models
> marker delete #14
> show #!7 models
> hide #!7 models
> hide #12 models
> show #2 models
> select add #2
3991 atoms, 4025 bonds, 258 residues, 2 models selected
> show #8 models
> select add #8
3991 atoms, 4025 bonds, 9 pseudobonds, 258 residues, 3 models selected
> hide #8 models
> select subtract #8
3991 atoms, 4025 bonds, 258 residues, 2 models selected
> show #8 models
> select add #12
7728 atoms, 7803 bonds, 499 residues, 2 models selected
> select subtract #12
3943 atoms, 3978 bonds, 256 residues, 1 model selected
> hbonds sel reveal true
419 hydrogen bonds found
> select subtract #2
Nothing selected
> select add #2
3943 atoms, 3978 bonds, 241 pseudobonds, 256 residues, 2 models selected
Alignment identifier is 2/A
> select subtract #2
Nothing selected
> select #2/A:173
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2/A:173-177
58 atoms, 57 bonds, 5 residues, 1 model selected
> select #2/A:2-11,21-24,32-62,67-82,90-118,120-143,150-172,178-206,212-253
3217 atoms, 3238 bonds, 191 pseudobonds, 208 residues, 2 models selected
> select #2/A:178
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:178
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide #8 models
> select #2/A:165
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2/A:165-185
309 atoms, 312 bonds, 15 pseudobonds, 21 residues, 2 models selected
> view sel
> select #2/A:229
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:229
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel target a
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> select #2/A:182
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/A:182-183
34 atoms, 33 bonds, 2 residues, 1 model selected
> select #2/A:181-182
34 atoms, 33 bonds, 2 residues, 1 model selected
> select #2/A:181-182
34 atoms, 33 bonds, 2 residues, 1 model selected
> select #2/A:182
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/A:182
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/A:167
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:167
24 atoms, 23 bonds, 1 residue, 1 model selected
> view sel
> select #2/A:167
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:167-169
50 atoms, 49 bonds, 3 residues, 1 model selected
> select #2/A:182
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/A:179-182
65 atoms, 65 bonds, 4 residues, 1 model selected
> select #2/A:167-169,179-182
115 atoms, 114 bonds, 2 pseudobonds, 7 residues, 2 models selected
> view sel
> select clear
> hide #2 models
> show #10 models
> hide #10 models
> show #13 models
> view orient
> show #8 models
> hbonds #13 reveal true
1297 hydrogen bonds found
> select add #13
3761 atoms, 3796 bonds, 246 pseudobonds, 248 residues, 2 models selected
> hbonds sel reveal true
1297 hydrogen bonds found
Alignment identifier is 13/A
> select add #8
3761 atoms, 3796 bonds, 1297 pseudobonds, 248 residues, 2 models selected
> select subtract #8
3761 atoms, 3796 bonds, 248 residues, 1 model selected
> select clear
> select #13/A:207
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #13/A:207-220
207 atoms, 210 bonds, 1 pseudobond, 14 residues, 2 models selected
> view sel
> select ~sel & ##selected
3554 atoms, 3586 bonds, 1296 pseudobonds, 234 residues, 2 models selected
> hide (#13 & sel) target a
> hide #8 models
> select clear
> select #13/A:217
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #13/A:217
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #13/A:216-217
25 atoms, 25 bonds, 2 residues, 1 model selected
> select #13/A:216-220
73 atoms, 74 bonds, 1 pseudobond, 5 residues, 2 models selected
> select ~sel & ##selected
3688 atoms, 3722 bonds, 1296 pseudobonds, 243 residues, 2 models selected
> hide (#13 & sel) target a
> select clear
> hide #13 models
> show #12 models
> select add #12
3785 atoms, 3825 bonds, 243 residues, 1 model selected
> show #13 models
> select add #13
7546 atoms, 7621 bonds, 246 pseudobonds, 491 residues, 3 models selected
> select add #8
7546 atoms, 7621 bonds, 1297 pseudobonds, 491 residues, 3 models selected
> select add #2
11489 atoms, 11599 bonds, 1297 pseudobonds, 747 residues, 4 models selected
Alignment identifier is 12/A
Alignment identifier is 13/A
Alignment identifier is 2/A
> hide #12 models
> select clear
> select #13/A:60
14 atoms, 13 bonds, 1 residue, 1 model selected
> select
> #12/A:7-10,17-56,58-66,69-87,89-93,97-119,122-145,150-174,177-203,212-240
3221 atoms, 3245 bonds, 205 residues, 1 model selected
> select #13/A:96
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #13/A:96
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel target ab
> select add #13
3761 atoms, 3796 bonds, 246 pseudobonds, 248 residues, 2 models selected
> select subtract #13
Nothing selected
> select add #13
3761 atoms, 3796 bonds, 246 pseudobonds, 248 residues, 2 models selected
> select add #8
3761 atoms, 3796 bonds, 1297 pseudobonds, 248 residues, 2 models selected
> select subtract #8
3761 atoms, 3796 bonds, 248 residues, 1 model selected
> ui tool show "Model Loops"
> modeller refine 12/A:1:all-missing 13/A:1:all-missing numModels 5 fast false
> adjacentFlexible 1 protocol standard
No Modeller license key provided. Get a license key by registering at the
Modeller web site.
> ui tool show AlphaFold
> alphafold match #13
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Fetching compressed AlphaFold A8HYH9 from
https://alphafold.ebi.ac.uk/files/AF-A8HYH9-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A8HYH9 (chain A)
AlphaFold prediction matching CrLfg4 AlphaFoldl.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | A8HYH9 | A8HYH9_CHLRE | 3.61 | 248 | 248 | 100
Opened 1 AlphaFold model
> alphafold match #13
1 AlphaFold model found using sequence similarity searches: A8HYH9 (chain A)
AlphaFold prediction matching CrLfg4 AlphaFoldl.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | A8HYH9 | A8HYH9_CHLRE | 3.61 | 248 | 248 | 100
Opened 1 AlphaFold model
> hide #!14 models
> hide #13 models
> select subtract #13
Nothing selected
> hide #!15 models
> hide #15.1 models
> hide #14.1 models
> show #14.1 models
> hide #14.1 models
> hide #!14 models
> select add #15
1851 atoms, 1886 bonds, 248 residues, 2 models selected
> select subtract #15.1
1 model selected
> select add #15
1851 atoms, 1886 bonds, 248 residues, 2 models selected
> select subtract #15
Nothing selected
> show #!15 models
> view orient
> hide #!15 models
> show #15.1 models
> hide #!15 models
> hide #15.1 models
> show #!9 models
> select add #9
3764 atoms, 3805 bonds, 237 residues, 1 model selected
Alignment identifier is 9/A
> select clear
> select #9/A:207
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #9/A:207
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #9/A:196,207
27 atoms, 25 bonds, 2 residues, 1 model selected
> select #9/A:196,207,219
39 atoms, 36 bonds, 3 residues, 1 model selected
> select #9/A:90,196,207,219
63 atoms, 59 bonds, 4 residues, 1 model selected
> select ~sel & ##selected
3701 atoms, 3746 bonds, 233 residues, 1 model selected
> hide (#!9 & sel) target a
> select ~sel & ##selected
63 atoms, 59 bonds, 4 residues, 1 model selected
> show (#!9 & sel) target ab
> select clear
> view orient
> hide #!9 models
> show #2 models
> view orient
> select add #2
3943 atoms, 3978 bonds, 256 residues, 1 model selected
> hide sel target a
> view orient
Alignment identifier is 2/A
> select clear
> select #2/A:210
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:210
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #2/A:233
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #2/A:233
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #2/A:182,233
32 atoms, 31 bonds, 2 residues, 1 model selected
> select #2/A:167,182,233
56 atoms, 54 bonds, 3 residues, 1 model selected
> show sel target ab
> view orient
> hide #2 models
> show #!14 models
> show #14.1 models
> hide #!14 models
> hide #14.1 models
> show #!14 models
> show #14.1 models
> show #8 models
> hbonds #14.1 reveal true
2403 hydrogen bonds found
> show #15.1 models
> hide #!14 models
> hide #14.1 models
> hide #!15 models
> hide #15.1 models
> show #!15 models
> show #15.1 models
> hide #!15 target m
> hide #15.1 models
> show #15.1 models
> open "/Users/grooms/Desktop/ChimeraX/AlphaFold/Lfg1 AlphaFold/Lfg1
> AlphaFold.pdb"
Chain information for Lfg1 AlphaFold.pdb #16
---
Chain | Description
A | No description available
> hide #!15 models
> hide #15.1 models
> select add #16
3841 atoms, 3879 bonds, 246 residues, 2 models selected
> hide #8 models
> select add #2
7728 atoms, 7803 bonds, 499 residues, 2 models selected
> select subtract #2
3785 atoms, 3825 bonds, 243 residues, 1 model selected
> ui tool show "ESMFold Error Plot"
> esmfold pae #16 file "/Users/grooms/Desktop/ChimeraX/AlphaFold/Lfg1
> AlphaFold/best_model_pae.json"
> color bfactor #16 palette esmfold
3785 atoms, 243 residues, atom bfactor range 41.8 to 98.6
> color bfactor #16 palette esmfold
3785 atoms, 243 residues, atom bfactor range 41.8 to 98.6
> color bfactor #16 palette esmfold
3785 atoms, 243 residues, atom bfactor range 41.8 to 98.6
> color bfactor #16 palette esmfold
3785 atoms, 243 residues, atom bfactor range 41.8 to 98.6
> alphafold pae #16 colorDomains true
> color bfactor #16 palette esmfold
3785 atoms, 243 residues, atom bfactor range 41.8 to 98.6
> hide #16 models
> select subtract #16
Nothing selected
> show #13 models
> view orient
> select #13/A:64
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #13/A:64-123
890 atoms, 899 bonds, 60 residues, 1 model selected
> select #13/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #13/A:1-237
3569 atoms, 3604 bonds, 237 residues, 1 model selected
> hide sel target a
> select #13/A:248
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #13/A
3761 atoms, 3796 bonds, 248 residues, 1 model selected
> hide sel target a
> select #13/A:230
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:230
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:202,230
24 atoms, 22 bonds, 2 residues, 1 model selected
> select #13/A:96,202,230
48 atoms, 45 bonds, 3 residues, 1 model selected
> select #13/A:96,202,230,240
72 atoms, 68 bonds, 4 residues, 1 model selected
> show sel target ab
> style sel ball
Changed 72 atom styles
> select #13/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #13/A
3761 atoms, 3796 bonds, 248 residues, 1 model selected
> undo
> select #13/A:1-2
29 atoms, 28 bonds, 2 residues, 1 model selected
> select #13/A
3761 atoms, 3796 bonds, 248 residues, 1 model selected
> hbonds sel reveal true
2318 hydrogen bonds found
> select #13/A:240
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #13/A:240
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #13/A:230,240
36 atoms, 34 bonds, 2 residues, 1 model selected
> select #13/A:202,230,240
48 atoms, 45 bonds, 3 residues, 1 model selected
> select #13/A:96,202,230,240
72 atoms, 68 bonds, 4 residues, 1 model selected
> hide #* target a
> show sel target ab
> hide #13 models
> show #15.1 models
> hide #!15 models
> hide #15.1 models
> show #13 models
> hbonds sel reveal true
57 hydrogen bonds found
> select #13/A:1-3
40 atoms, 39 bonds, 3 residues, 1 model selected
> select #13/A
3761 atoms, 3796 bonds, 12 pseudobonds, 248 residues, 2 models selected
> hbonds sel reveal true
2318 hydrogen bonds found
> select clear
> show #8 models
> select #13/A:230
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:230
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #13/A:202,230
24 atoms, 22 bonds, 2 residues, 1 model selected
> select #13/A:202,216-220,230
97 atoms, 96 bonds, 1 pseudobond, 7 residues, 2 models selected
> select #13/A:96,202,216-220,230
121 atoms, 119 bonds, 3 pseudobonds, 8 residues, 2 models selected
> select #13/A:96,202,216-220,230,240
145 atoms, 142 bonds, 3 pseudobonds, 9 residues, 2 models selected
> hide #* target a
> show (#13 & sel) target ab
> select #13/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #13/A
3761 atoms, 3796 bonds, 246 pseudobonds, 248 residues, 2 models selected
> hbonds sel reveal true
2318 hydrogen bonds found
> select clear
> view orient
> select #13/A:240
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #13/A:240
24 atoms, 23 bonds, 1 residue, 1 model selected
> view sel
> select #13/A:35-88
832 atoms, 840 bonds, 51 pseudobonds, 54 residues, 2 models selected
> select #13/A:35-93
906 atoms, 914 bonds, 56 pseudobonds, 59 residues, 2 models selected
> select #13/A:89
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #13/A:89-106
282 atoms, 283 bonds, 12 pseudobonds, 18 residues, 2 models selected
QGestureManager::deliverEvent: could not find the target for gesture
> view sel
> hide #* target a
> show (#13 & sel) target ab
> select #13/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #13/A
3761 atoms, 3796 bonds, 246 pseudobonds, 248 residues, 2 models selected
> show (#13 & sel) target ab
> select #13/A:240
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #13/A:240
24 atoms, 23 bonds, 1 residue, 1 model selected
> view sel
> select #13/A:247
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #13/A:247
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #13/A:219,247
39 atoms, 37 bonds, 2 residues, 1 model selected
> select #13/A:219,244,247
54 atoms, 51 bonds, 2 pseudobonds, 3 residues, 2 models selected
> select #13/A:181,219,244,247
65 atoms, 61 bonds, 3 pseudobonds, 4 residues, 2 models selected
> hide #* target a
> show (#13 & sel) target ab
> select #13/A:247-248
39 atoms, 38 bonds, 2 residues, 1 model selected
> select #13/A:211-248
628 atoms, 634 bonds, 30 pseudobonds, 38 residues, 2 models selected
> view sel
> hide #8 models
> select clear
> show #8 models
> select #13/A:247
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #13/A:247
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #13/A:244,247
39 atoms, 37 bonds, 2 pseudobonds, 2 residues, 2 models selected
> select #13/A:181,244,247
50 atoms, 47 bonds, 3 pseudobonds, 3 residues, 2 models selected
> style (#13 & sel) ball
Changed 50 atom styles
> hide #8 models
> select clear
> show #2 models
> hide #2 models
> hide #13 models
> show #2 models
> view orient
> coulombic #2
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for CrBI-1 AAlphafold_A SES surface #2.1: minimum, -13.41,
mean 1.94, maximum 22.56
To also show corresponding color key, enter the above coulombic command and
add key true
> nucleotides #!2 atoms
> style nucleic & #!2 stick
Changed 0 atom styles
> coulombic #!2
Coulombic values for CrBI-1 AAlphafold_A SES surface #2.1: minimum, -13.41,
mean 1.94, maximum 22.56
To also show corresponding color key, enter the above coulombic command and
add key true
> color #!2 bypolymer
> color #!2 bynucleotide
> color #!2 byhetero
> color #!2 bychain
> color #!2 bypolymer
> rainbow #!2
> coulombic #!2
Coulombic values for CrBI-1 AAlphafold_A SES surface #2.1: minimum, -13.41,
mean 1.94, maximum 22.56
To also show corresponding color key, enter the above coulombic command and
add key true
> style #!2 stick
Changed 3943 atom styles
> style #!2 stick
Changed 3943 atom styles
> style #!2 stick
Changed 3943 atom styles
> ui tool show "AlphaFold Error Plot"
> alphafold pae #2 file /Users/grooms/Desktop/ChimeraX/AlphaFold/CrBI-1-new-
> AlphaFold-4-8-24/best_model_pae.json
> alphafold pae #2 colorDomains true
> color bfactor #2 palette alphafold
3943 atoms, 256 residues, 1 surfaces, atom bfactor range 41.7 to 97.4
> select add #2
3943 atoms, 3978 bonds, 256 residues, 1 model selected
> coulombic sel
Coulombic values for CrBI-1 AAlphafold_A SES surface #2.1: minimum, -13.41,
mean 1.94, maximum 22.56
To also show corresponding color key, enter the above coulombic command and
add key true
> hbonds sel reveal true
502 hydrogen bonds found
> style sel ball
Changed 3943 atom styles
> style sel ball
Changed 3943 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> show sel cartoons
> hide sel cartoons
> show sel atoms
> hide sel atoms
> show sel atoms
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/grooms/Desktop/movie2.mp4
Movie saved to /Users/grooms/Desktop/movie2.mp4
> style sel ball
Changed 3943 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> hide sel surfaces
> style sel stick
Changed 3943 atom styles
> style sel ball
Changed 3943 atom styles
> style sel sphere
Changed 3943 atom styles
> show #13 models
> hide #!2 models
> select add #13
7704 atoms, 7774 bonds, 504 residues, 3 models selected
> style sel & #13 sphere
Changed 3761 atom styles
> select #13/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #13/A
3761 atoms, 3796 bonds, 248 residues, 1 model selected
> style sel sphere
Changed 3761 atom styles
> style sel sphere
Changed 3761 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 3761 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> mlp sel
Map values for surface "CrLfg4 AlphaFoldl.pdb_A SES surface": minimum -25.77,
mean -0.057, maximum 23.92
To also show corresponding color key, enter the above mlp command and add key
true
> undo
> hide sel surfaces
> show sel cartoons
> show #!2 models
> hide #!13 models
> hide #!2 surfaces
> select subtract #13
1 model selected
> select add #2
3943 atoms, 3978 bonds, 241 pseudobonds, 256 residues, 2 models selected
> hide sel surfaces
> select subtract #2
1 model selected
> hide #!2 models
> show #12 models
> style #12 sphere
Changed 3785 atom styles
> undo
> select #13/A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #13/A
3761 atoms, 3796 bonds, 248 residues, 1 model selected
> style #12 sphere
Changed 3785 atom styles
> undo
> show #12 target ab
> style #12 sphere
Changed 3785 atom styles
> show #!2 models
> hide #12 models
> select subtract #13
1 model selected
> hide #!2 models
> show #!13 models
> select add #13
3761 atoms, 3796 bonds, 248 residues, 1 model selected
> show (#!13 & sel) target ab
> style sel sphere
Changed 3761 atom styles
> select clear
> show #12 models
> hide #!13 models
> coulombic #12
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for CrLfg1 AlphaFold_A SES surface #12.1: minimum, -14.23,
mean -0.28, maximum 15.79
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic #!12
Coulombic values for CrLfg1 AlphaFold_A SES surface #12.1: minimum, -14.23,
mean -0.28, maximum 15.79
To also show corresponding color key, enter the above coulombic command and
add key true
> select add #12
3785 atoms, 3825 bonds, 243 residues, 1 model selected
> coulombic sel
Coulombic values for CrLfg1 AlphaFold_A SES surface #12.1: minimum, -14.23,
mean -0.28, maximum 15.79
To also show corresponding color key, enter the above coulombic command and
add key true
> hide (#!12 & sel) target a
> select clear
> hide #!12 surfaces
> hide #!12 models
> show #!2 models
> hide #2 target a
> hide #!2 models
> select add #2
3943 atoms, 3978 bonds, 241 pseudobonds, 256 residues, 2 models selected
> show #!2 models
> hide #* target a
> show (#!2 & sel) target ab
> style sel stick
Changed 3943 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel ball
Changed 3943 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel ball
Changed 3943 atom styles
> hide sel surfaces
> coulombic sel
Coulombic values for CrBI-1 AAlphafold_A SES surface #2.1: minimum, -13.41,
mean 1.94, maximum 22.56
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> hide #!2 models
> show #!13 models
> coulombic #!13
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for CrLfg4 AlphaFoldl.pdb_A SES surface #13.1: minimum,
-13.77, mean 0.10, maximum 10.90
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!13 surfaces
> view orient
> coulombic #!13
Coulombic values for CrLfg4 AlphaFoldl.pdb_A SES surface #13.1: minimum,
-13.77, mean 0.10, maximum 10.90
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!13 surfaces
> show #3 models
> hide #!13 models
> view orient
> coulombic #3
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
BsYetJpH7.pdb #3/A ARG 62 NE
BsYetJpH7.pdb #3/A ARG 62 CG
BsYetJpH7.pdb #3/A ARG 62 NH1
BsYetJpH7.pdb #3/A ARG 62 NH2
BsYetJpH7.pdb #3/A ARG 62 CD
BsYetJpH7.pdb #3/A ARG 62 CZ
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for BsYetJpH7.pdb_A SES surface #3.1: minimum, -11.00, mean
0.29, maximum 16.87
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp #!3
Map values for surface "BsYetJpH7.pdb_A SES surface": minimum -25.48, mean
2.065, maximum 23.46
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic #!3
Coulombic values for BsYetJpH7.pdb_A SES surface #3.1: minimum, -11.00, mean
0.29, maximum 16.87
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!3 surfaces
> show #!6 models
> hide #!3 models
> view orient
> coulombic #!6
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
BsYetJ-pH8.pdb #6/A ARG 62 NE
BsYetJ-pH8.pdb #6/A ARG 62 CG
BsYetJ-pH8.pdb #6/A ARG 62 NH1
BsYetJ-pH8.pdb #6/A ARG 62 NH2
BsYetJ-pH8.pdb #6/A ARG 62 CD
BsYetJ-pH8.pdb #6/A ARG 62 CZ
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for BsYetJ-pH8.pdb_A SES surface #6.2: minimum, -18.95, mean
0.24, maximum 14.52
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 residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
BsYetJ-pH6.pdb #5/A ARG 60
BsYetJ-pH6.pdb #5/A ARG 61
BsYetJ-pH6.pdb #5/A ARG 62
BsYetJ-pH6.pdb #5/A LYS 63
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for BsYetJ-pH6.pdb_A SES surface #5.1: minimum, -15.58, mean
-0.75, maximum 13.22
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!5 surfaces
> hide #!5 models
> show #!3 models
> view orient
> style #!3 sphere
Changed 1626 atom styles
> select add #3
1626 atoms, 1667 bonds, 207 residues, 1 model selected
> style sel sphere
Changed 1626 atom styles
> coulombic sel
Coulombic values for BsYetJpH7.pdb_A SES surface #3.1: minimum, -11.00, mean
0.29, maximum 16.87
To also show corresponding color key, enter the above coulombic command and
add key true
> style sel stick
Changed 1626 atom styles
> hide sel surfaces
> coulombic sel
Coulombic values for BsYetJpH7.pdb_A SES surface #3.1: minimum, -11.00, mean
0.29, maximum 16.87
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!3 models
> show #!5 models
> select subtract #3
1 model selected
> select add #5
1644 atoms, 1648 bonds, 244 residues, 1 model selected
> hide #!5 models
> show #!5 models
> view orient
> hide #!5 models
> show #!2 models
> hide #!2 surfaces
> style #!2 stick
Changed 3943 atom styles
> show #!2 cartoons
> hide #2 target a
> view orient
> select subtract #5
1 model selected
> hide #!2 models
> show #!13 models
> hide #!13 models
> show #!12 models
> hide #!12 models
> show #!5 models
> view orient
> hide #!5 models
> show #!6 models
> hide #!6 surfaces
> hide #!6 models
> show #!5 models
> select clear
> select #13/A:12-13
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #13/A:12-14
36 atoms, 35 bonds, 3 residues, 1 model selected
> select #13/A:18
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #13/A:18-60
668 atoms, 671 bonds, 43 residues, 1 model selected
> select #13/A:217
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #13/A:217-230
214 atoms, 216 bonds, 14 residues, 1 model selected
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-22.5.11
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0)
OS Loader Version: 580~2215
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 12 days, 7 hours, 47 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 1.0.5
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: 1.8
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: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
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: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
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: 3.0.15
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: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
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: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
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: 2.0.1
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: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 15 months ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in Modeller tool _update_sequence_menus in Qt call meth_QFormLayout_removeRow() |
comment:2 by , 15 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Thanks for reporting this problem. Should be fixed in the next daily build.
Fix: https://github.com/RBVI/ChimeraX/commit/881c007c67fff894e18884887b0d5aff256f1e1c
Note:
See TracTickets
for help on using tickets.
Looks like a crash in the Qt window toolkit related to removing a row in a QFormLayout() somehow triggered Modeller responding to closing a sequence view windows
Eric is on vacation and will look at this next week.