![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#16857 closed defect (duplicate)
Crash moving window between screens
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.3-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001f4d70840 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.pdb_lib._load_libs, chimerax.surface._surface, 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree (total: 57)
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"procRole" : "Foreground",
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"modelCode" : "Mac15,6",
"coalitionID" : 1758,
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"build" : "24D60",
"releaseType" : "User"
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"captureTime" : "2025-02-14 16:22:03.2393 +0900",
"codeSigningMonitor" : 1,
"incident" : "7B11C8A1-B35C-46E6-9D88-B20DB5640D66",
"pid" : 12330,
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"cpuType" : "ARM-64",
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"procLaunch" : "2025-02-14 11:35:28.0013 +0900",
"procStartAbsTime" : 2088267234635,
"procExitAbsTime" : 2397819184434,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"storeInfo" : {"deviceIdentifierForVendor":"0D9DF10A-200C-5378-80BD-FAFC22B09513","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "7BBC0ECE-6E8A-EF23-8FB1-C7951B8AEE77",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"wakeTime" : 15,
"sleepWakeUUID" : "7D48BB10-45F4-4198-B977-E4329A093F82",
"sip" : "enabled",
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"exception" : {"codes":"0x0000000000000001, 0x0000e4fce94afe98","rawCodes":[1,251774896897688],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000e4fce94afe98 -> 0x000064fce94afe98 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":12330},
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/imageformats\/libqsvg.dylib",
"name" : "libqsvg.dylib"
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"name" : "libqmacjp2.dylib"
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/iconengines\/libqsvgicon.dylib",
"name" : "libqsvgicon.dylib"
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"size" : 81920,
"uuid" : "703104dc-b212-3b8d-9c78-4f57b3c9cb18",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/numpy_formathandler.cpython-311-darwin.so",
"name" : "numpy_formathandler.cpython-311-darwin.so"
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"uuid" : "12c53516-421d-3f7a-a81e-95bcfdb8a3ff",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/nones_formathandler.cpython-311-darwin.so",
"name" : "nones_formathandler.cpython-311-darwin.so"
},
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"uuid" : "d7bd530c-3353-37a6-b81f-ee3179d65811",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/_version.cpython-311-darwin.so",
"name" : "_version.cpython-311-darwin.so"
},
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"arch" : "arm64",
"base" : 14003093504,
"size" : 180224,
"uuid" : "87eed069-25fc-30f6-aa30-1e54859d92e2",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/frame\/_frame.cpython-311-darwin.so",
"name" : "_frame.cpython-311-darwin.so"
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"uuid" : "c1a3c2d3-b21b-3231-839d-fcbc83ca2028",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/core\/_serialize.cpython-311-darwin.so",
"name" : "_serialize.cpython-311-darwin.so"
},
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/msgpack\/_cmsgpack.cpython-311-darwin.so",
"name" : "_cmsgpack.cpython-311-darwin.so"
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"base" : 14007320576,
"size" : 737280,
"uuid" : "cc06500d-d418-3365-b197-36b1304a819e",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGL.abi3.so",
"name" : "QtOpenGL.abi3.so"
},
{
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"arch" : "arm64",
"base" : 14003830784,
"size" : 49152,
"uuid" : "b32a8c32-a5e0-3a8b-9a0d-00a26b160215",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGLWidgets.abi3.so",
"name" : "QtOpenGLWidgets.abi3.so"
},
{
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"arch" : "arm64",
"base" : 14004551680,
"size" : 49152,
"uuid" : "cd4f396b-89fe-36fd-a488-6f5b3d4b0282",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtOpenGLWidgets.framework\/Versions\/A\/QtOpenGLWidgets",
"name" : "QtOpenGLWidgets"
},
{
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"base" : 6098550784,
"size" : 81920,
"uuid" : "3133c77c-8bf7-32a3-b5db-cbfe2e50ce9d",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
"name" : "_ribbons.cpython-311-darwin.so"
},
{
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"arch" : "arm64",
"base" : 6098386944,
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"uuid" : "de871a78-14f2-3e72-9bde-e4f2c7493f1b",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
"name" : "_graphics.cpython-311-darwin.so"
},
{
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"arch" : "arm64",
"base" : 6101204992,
"size" : 475136,
"uuid" : "0c6e9a11-e483-3d7d-a88f-8ad0507af167",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
"name" : "mmcif.cpython-311-darwin.so"
},
{
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"arch" : "arm64",
"base" : 6099779584,
"size" : 409600,
"uuid" : "1ab8e5e2-c699-3efb-8f77-d375e3793c8f",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
"name" : "_mmcif.cpython-311-darwin.so"
},
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"arch" : "arm64",
"base" : 6102532096,
"size" : 147456,
"uuid" : "1e310bc7-5f96-396b-816d-5b40a3dde12c",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
"name" : "_pdbio.cpython-311-darwin.so"
},
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"base" : 14010810368,
"size" : 3817472,
"uuid" : "579ef19c-6e85-36be-a566-c980f789fbc0",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/etree.cpython-311-darwin.so",
"name" : "etree.cpython-311-darwin.so"
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"uuid" : "c8b24269-c8a2-3244-b044-b85c3449800d",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
"name" : "_elementpath.cpython-311-darwin.so"
},
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"base" : 6630924288,
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"uuid" : "eee9d0d3-dffc-37cb-9ced-b27cd0286d8c",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
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"uuid" : "642faf7a-874e-37e6-8aba-2b0cc09a3025",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
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"base" : 6629699584,
"size" : 532476,
"uuid" : "92699527-645f-3d8d-aed8-1cfb0c034e15",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
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"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/mk16/Desktop/220250214.cxs format session
opened ChimeraX session
> select add #8
4958 atoms, 5073 bonds, 620 residues, 1 model selected
> hide sel atoms
> hide #!1 models
> show #!1 models
> select ::name="01A"
116 atoms, 122 bonds, 2 residues, 1 model selected
> select ::name="8LE"
116 atoms, 124 bonds, 4 residues, 3 models selected
> select ::name="BCO"
106 atoms, 110 bonds, 2 residues, 1 model selected
> select ::name="COA"
288 atoms, 300 bonds, 6 residues, 4 models selected
> select add #9
4252 atoms, 4200 bonds, 1 pseudobond, 649 residues, 6 models selected
> select subtract #9
240 atoms, 250 bonds, 5 residues, 3 models selected
> select add #3
10981 atoms, 10398 bonds, 14 pseudobonds, 2137 residues, 6 models selected
> select subtract #3
144 atoms, 150 bonds, 3 residues, 2 models selected
> select add #2
7549 atoms, 7464 bonds, 4 pseudobonds, 1188 residues, 4 models selected
> select subtract #2
48 atoms, 50 bonds, 1 residue, 1 model selected
> select sel : select add #2
9222 atoms, 9064 bonds, 5 pseudobonds, 1423 residues, 11 models selected
> select subtract #2
1721 atoms, 1650 bonds, 1 pseudobond, 236 residues, 8 models selected
> select add #3
12302 atoms, 11659 bonds, 15 pseudobonds, 2327 residues, 11 models selected
> select subtract #3
1465 atoms, 1411 bonds, 1 pseudobond, 193 residues, 7 models selected
> select add #4
10026 atoms, 9736 bonds, 1 pseudobond, 1679 residues, 7 models selected
> select subtract #4
1202 atoms, 1157 bonds, 1 pseudobond, 162 residues, 6 models selected
> select add #5
9517 atoms, 8838 bonds, 5 pseudobonds, 1937 residues, 6 models selected
> select subtract #5
933 atoms, 906 bonds, 121 residues, 4 models selected
> select add #6
6269 atoms, 6360 bonds, 805 residues, 4 models selected
> select subtract #6
716 atoms, 693 bonds, 94 residues, 3 models selected
> select add #7
5464 atoms, 5559 bonds, 689 residues, 3 models selected
> select subtract #7
506 atoms, 486 bonds, 69 residues, 2 models selected
> select add #1
4225 atoms, 4160 bonds, 1 pseudobond, 669 residues, 4 models selected
> select subtract #1
213 atoms, 210 bonds, 25 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 213 atom styles
> select clear
> style #8#!1,9 sphere
Changed 12982 atom styles
> undo
> select #9/A:164,208,239,273
41 atoms, 40 bonds, 4 residues, 1 model selected
> select #9/A:164,208,239,273
41 atoms, 40 bonds, 4 residues, 1 model selected
> select add #9
4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected
> select subtract #9
Nothing selected
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> select #9/A:164,208,239,273
41 atoms, 40 bonds, 4 residues, 1 model selected
> color sel byhetero
> select #8/A:311
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #8
4958 atoms, 5073 bonds, 620 residues, 1 model selected
> select subtract #8
Nothing selected
> hide #!9 models
> hide #8 models
> hide #!1 models
> open /Users/mk16/works/acyl-
> CoA_synthetase/Aquincola_tertiaricarbonis/6he0_Thioesterification_2-HIB-
> AMP_CoA.pdb
6he0_Thioesterification_2-HIB-AMP_CoA.pdb title:
Crystal structure of 2-hydroxyisobutyryl-coa ligase (HCL) In complex with
2-hib-amp and coa In the thioesterfication state [more info...]
Chain information for 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #10
---
Chain | Description | UniProt
A | 2-hydroxyisobutyryl-coa synthetase | I3VE75_9BURK 1-477
Non-standard residues in 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #10
---
8LE —
[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-
oxidanyl-phosphoryl]2-methyl-2-oxidanyl-propanoate
AMP — adenosine monophosphate
COA — coenzyme A
116 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> rainbow #!10
> style #!10 ball
Changed 4012 atom styles
> close #10
> show #!1 models
> show #!9 models
> show #8 models
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
55620 atoms, 56947 bonds, 8 pseudobonds, 7139 residues, 13 models selected
> hide sel & #8#!1,9 atoms
> select clear
> hide #8 models
> show #8 models
> select add #8
4958 atoms, 5073 bonds, 620 residues, 1 model selected
> ui tool show "Color Actions"
> color sel wheat
> select #8/A:482-900
1119 atoms, 1144 bonds, 139 residues, 1 model selected
> rainbow sel
> select add #8
4958 atoms, 5073 bonds, 620 residues, 1 model selected
> select subtract #8
Nothing selected
> select add #9
4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected
> color sel wheat
> select #9/A:360-999
902 atoms, 911 bonds, 1 pseudobond, 116 residues, 2 models selected
> rainbow sel
> select
> ::name="01A"::name="8LE"::name="AMP"::name="BCO"::name="CL"::name="COA"::name="EDO"::name="HOH"::name="MG"::name="NO3"::name="PRX"
3619 atoms, 939 bonds, 11 pseudobonds, 2754 residues, 8 models selected
> color (#!1,9 & sel) byelement
> select clear
> select #9/A:438
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select add #9
4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected
> select subtract #9
Nothing selected
> select #9/A:438,3366
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #9/A:438,366
22 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> style sel ball
Changed 22 atom styles
> undo
> label sel text "{0.name} {0.number}{0.insertion_code}"
> undo
> show sel atoms
> color sel byhetero
> ~label sel residues
> select add #9
4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected
> select subtract #9
Nothing selected
> ui mousemode right distance
> distance #9/A:438@NH2 #9/A:1003@O1A
Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A ARG 438 NH2
and COA 1003 O1A (alt loc A): 2.807Å
> distance #9/A:366@NH2 #9/A:1003@O5A
Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A ARG 366 NH2
and COA 1003 O5A (alt loc A): 2.875Å
> hide #10.1 models
> ui mousemode right "translate selected models"
> ui mousemode right translate
> select #8/A:
Expected an objects specifier or a keyword
> select #8/A:555,557,488
31 atoms, 28 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 31 atom styles
> color sel byhetero
> select add #8
4958 atoms, 5073 bonds, 620 residues, 1 model selected
> select subtract #8
Nothing selected
> ui mousemode right distance
> distance #9/A:1003@OAP #8/A:488@NZ
Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A COA 1003 OAP
(alt loc A) and AF-O14975-F1-model_v4_FATP2.pdb #8/A LYS 488 NZ: 70.464Å
> undo
> select subtract #8
Nothing selected
> ~distance #9/A:1003@OAP #8/A:488@NZ
> distance #8/A:488@NZ #1/A:1003@O1A
Distance between AF-O14975-F1-model_v4_FATP2.pdb #8/A LYS 488 NZ and
6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 O1A (alt loc A):
3.679Å
> distance #8/A:555@NH1 #1/A:1003@O4A
Distance between AF-O14975-F1-model_v4_FATP2.pdb #8/A ARG 555 NH1 and
6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 O4A (alt loc A):
7.704Å
> ui mousemode right translate
> ui mousemode right distance
> distance #1/A:1003@O4A #8/A:557@NH2
Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 O4A
(alt loc A) and AF-O14975-F1-model_v4_FATP2.pdb #8/A ARG 557 NH2: 10.556Å
> ui mousemode right translate
> close #10
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
55620 atoms, 56947 bonds, 8 pseudobonds, 7139 residues, 13 models selected
> hide sel & #8#!1,9 atoms
> select clear
> select #9/A:190,192,193,216
25 atoms, 23 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select add #9
4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected
> select subtract #9
Nothing selected
> select #9/A:190,192,193,216
25 atoms, 23 bonds, 4 residues, 1 model selected
> color sel byhetero
> select add #9
4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected
> select subtract #9
Nothing selected
> ui mousemode right distance
> distance #9/A:192@OG #9/A:1003@O8A
Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A SER 192 OG and
COA 1003 O8A (alt loc A): 2.856Å
> distance #9/A:216@NE2 #9/A:1003@O8A
Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A HIS 216 NE2
and COA 1003 O8A (alt loc A): 2.666Å
> distance #9/A:1003@O7A #9/A:193@CB
Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A COA 1003 O7A
(alt loc A) and ALA 193 CB: 6.160Å
> select #9/A:190
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> distance #9/A:1003@O7A #9/A:190@CA
Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A COA 1003 O7A
(alt loc A) and GLY 190 CA (alt loc B): 4.060Å
> show sel cartoons
> select add #9
4012 atoms, 3950 bonds, 5 pseudobonds, 644 residues, 4 models selected
> select subtract #9
Nothing selected
> hide #10.1 models
> ui mousemode right translate
> select #8/A:291,293,318
27 atoms, 25 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 27 atom styles
> color sel byhetero
> select add #8
4958 atoms, 5073 bonds, 620 residues, 1 model selected
> select subtract #8
Nothing selected
> ui mousemode right distance
> distance #1/A:1003@O7A #8/A:291@NZ
Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 O7A
(alt loc A) and AF-O14975-F1-model_v4_FATP2.pdb #8/A LYS 291 NZ: 5.283Å
> distance #1/A:1003@O8A #8/A:318@OH
Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 O8A
(alt loc A) and AF-O14975-F1-model_v4_FATP2.pdb #8/A TYR 318 OH: 7.996Å
> distance #1/A:1003@O8A #8/A:293@OG
Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 O8A
(alt loc A) and AF-O14975-F1-model_v4_FATP2.pdb #8/A SER 293 OG: 4.461Å
> ui mousemode right translate
> close #10
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
55620 atoms, 56947 bonds, 8 pseudobonds, 7139 residues, 13 models selected
> hide sel & #8#!1,9 atoms
> select clear
> select #9/A:159,160,210
19 atoms, 17 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel byhetero
> show sel atoms
> ui mousemode right distance
> distance #9/A:1003@N1A #9/A:160@CG1
Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A COA 1003 N1A
(alt loc A) and VAL 160 CG1: 6.394Å
> distance #9/A:1003@N1A #9/A:159@CB
Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A COA 1003 N1A
(alt loc A) and ALA 159 CB: 5.492Å
> hide #10.1 models
> distance #9/A:210@OG1 #9/A:1003@N1A
Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A THR 210 OG1
and COA 1003 N1A (alt loc A): 4.292Å
> ui mousemode right translate
> select add #9
4012 atoms, 3950 bonds, 4 pseudobonds, 644 residues, 4 models selected
> select subtract #9
Nothing selected
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> ui tool show "Side View"
> select #8/A:264,263,314,292
35 atoms, 33 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 35 atom styles
> color sel byhetero
> ui mousemode right distance
> distance #1/A:1003@N1A #8/A:264@CD2
Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 N1A
(alt loc A) and AF-O14975-F1-model_v4_FATP2.pdb #8/A LEU 264 CD2: 3.037Å
> distance #1/A:1003@N1A #8/A:263@OG1
Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 N1A
(alt loc A) and AF-O14975-F1-model_v4_FATP2.pdb #8/A THR 263 OG1: 4.946Å
> distance #1/A:1003@N1A #8/A:314@OE1
Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 N1A
(alt loc A) and AF-O14975-F1-model_v4_FATP2.pdb #8/A GLU 314 OE1: 9.093Å
> distance #8/A:292@CD1 #8/A:292@CG
Distance between AF-O14975-F1-model_v4_FATP2.pdb #8/A PHE 292 CD1 and CG:
1.408Å
> distance #8/A:292@CG #1/A:1003@C2A
Distance between AF-O14975-F1-model_v4_FATP2.pdb #8/A PHE 292 CG and
6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 C2A (alt loc A):
3.120Å
> select add #8
4958 atoms, 5073 bonds, 1 pseudobond, 620 residues, 2 models selected
> select subtract #8
Nothing selected
> ui mousemode right translate
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
55620 atoms, 56947 bonds, 9 pseudobonds, 7139 residues, 14 models selected
> hide sel & #8#!1,9 atoms
> close #10
> select clear
> view clip false
> select #8/A:136,267,490
33 atoms, 32 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 33 atom styles
> color sel byhetero
> ui mousemode right distance
> distance #8/A:490@OE1 #1/A:1003@O9P
Distance between AF-O14975-F1-model_v4_FATP2.pdb #8/A GLU 490 OE1 and
6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 O9P (alt loc A):
2.421Å
> distance #8/A:267@OH #1/A:1003@O9P
Distance between AF-O14975-F1-model_v4_FATP2.pdb #8/A TYR 267 OH and
6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 O9P (alt loc A):
1.918Å
> distance #1/A:1003@O9P #8/A:136@OH
Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1/A COA 1003 O9P
(alt loc A) and AF-O14975-F1-model_v4_FATP2.pdb #8/A TYR 136 OH: 4.522Å
> hide #10.1 models
> ui mousemode right translate
> select #8/A:136,267,490
33 atoms, 32 bonds, 3 residues, 1 model selected
> select #9/A:164
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> ui mousemode right distance
> distance #9/A:164@OH #9/A:1003@O9P
Distance between 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9/A TYR 164 OH and
COA 1003 O9P (alt loc A): 4.322Å
> ui mousemode right translate
> ui tool show "Side View"
> select add #9
4012 atoms, 3950 bonds, 2 pseudobonds, 644 residues, 4 models selected
> select subtract #9
Nothing selected
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #!9 models
> view #8 clip false
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/mk16/Desktop/220250214.cxs
Log from Fri Feb 14 11:22:12 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/mk16/works/acyl-
> CoA_synthetase/Aquincola_tertiaricarbonis/6he0_Thioesterification_2-HIB-
> AMP_CoA.pdb
6he0_Thioesterification_2-HIB-AMP_CoA.pdb title:
Crystal structure of 2-hydroxyisobutyryl-coa ligase (HCL) In complex with
2-hib-amp and coa In the thioesterfication state [more info...]
Chain information for 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1
---
Chain | Description | UniProt
A | 2-hydroxyisobutyryl-coa synthetase | I3VE75_9BURK 1-477
Non-standard residues in 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #1
---
8LE —
[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-
oxidanyl-phosphoryl]2-methyl-2-oxidanyl-propanoate
AMP — adenosine monophosphate
COA — coenzyme A
116 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open /Users/mk16/works/acyl-
> CoA_synthetase/Aquincola_tertiaricarbonis/6he2_openConformatin_2-HIB-
> AMP_CoA.pdb
6he2_openConformatin_2-HIB-AMP_CoA.pdb title:
Crystal structure of an open conformation of 2-hydroxyisobutyryl-coa ligase
(HCL) In complex with 2-hib-amp and coa [more info...]
Chain information for 6he2_openConformatin_2-HIB-AMP_CoA.pdb #2
---
Chain | Description | UniProt
A B | 2-hydroxyisobutyryl-coa synthetase | I3VE75_9BURK 1-477
Non-standard residues in 6he2_openConformatin_2-HIB-AMP_CoA.pdb #2
---
8LE —
[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-
oxidanyl-phosphoryl]2-methyl-2-oxidanyl-propanoate
AMP — adenosine monophosphate
COA — coenzyme A
104 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open /Users/mk16/works/acyl-
> CoA_synthetase/1pg4_AcetylCoASynthetase_Salmonella.pdb
1pg4_AcetylCoASynthetase_Salmonella.pdb title:
Acetyl coa synthetase, salmonella enterica [more info...]
Chain information for 1pg4_AcetylCoASynthetase_Salmonella.pdb #3
---
Chain | Description | UniProt
A B | acetyl-coa synthetase | ACSA_SALTY 1-652
Non-standard residues in 1pg4_AcetylCoASynthetase_Salmonella.pdb #3
---
CL — chloride ion
COA — coenzyme A
EDO — 1,2-ethanediol (ethylene glycol)
MG — magnesium ion
PRX — adenosine-5'-monophosphate-propyl ester
(adenosine-5'-propylphosphate)
> open /Users/mk16/works/acyl-CoA_synthetase/3eq6_ACSM2A_bCoA_AMP.pdb
3eq6_ACSM2A_bCoA_AMP.pdb title:
Crystal structure of human acyl-coa synthetase medium-chain family member 2A
(L64P mutation) In A ternary complex with products [more info...]
Chain information for 3eq6_ACSM2A_bCoA_AMP.pdb #4
---
Chain | Description | UniProt
A B | acyl-coenzyme A synthetase ACSM2A | ACS2A_HUMAN 32-577
Non-standard residues in 3eq6_ACSM2A_bCoA_AMP.pdb #4
---
AMP — adenosine monophosphate
BCO — butyryl coenzyme A
(S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3Λ~5~,5Λ~5~-diphosphaheptadecan-17-yl}
butanethioate (non-preferred name))
28 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open /Users/mk16/works/acyl-
> CoA_synthetase/3cw9_Alcaligenes_ChlorobenzoylCoA.pdb
3cw9_Alcaligenes_ChlorobenzoylCoA.pdb title:
4-chlorobenzoyl-coa ligase/synthetase In the thioester-forming conformation,
bound to 4-chlorophenacyl-coa [more info...]
Chain information for 3cw9_Alcaligenes_ChlorobenzoylCoA.pdb #5
---
Chain | Description
A B | chlorobenzoate COA ligase/synthetase
Non-standard residues in 3cw9_Alcaligenes_ChlorobenzoylCoA.pdb #5
---
01A — 4-chlorophenacyl-coenzyme A
AMP — adenosine monophosphate
EDO — 1,2-ethanediol (ethylene glycol)
MG — magnesium ion
NO3 — nitrate ion
> open /Users/mk16/works/acyl-CoA_synthetase/AF3/acsl4/fold_acsl4_model_0.cif
Chain information for fold_acsl4_model_0.cif #6
---
Chain | Description
A | .
Computing secondary structure
> open /Users/mk16/works/acyl-CoA_synthetase/AF3/fatp2/fold_fatp2_model_0.cif
Chain information for fold_fatp2_model_0.cif #7
---
Chain | Description
A | .
Computing secondary structure
> open /Users/mk16/works/acyl-CoA_synthetase/AF-O14975-F1-model_v4_FATP2.pdb
AF-O14975-F1-model_v4_FATP2.pdb title:
Alphafold monomer V2.0 prediction for very long-chain acyl-coa synthetase
(O14975) [more info...]
Chain information for AF-O14975-F1-model_v4_FATP2.pdb #8
---
Chain | Description | UniProt
A | very long-chain acyl-coa synthetase | S27A2_HUMAN 1-620
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #4,6-7#!1-3,5 to #8
Computing secondary structure
[Repeated 7 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#4), sequence alignment score = 652.7
RMSD between 276 pruned atom pairs is 1.237 angstroms; (across all 507 pairs:
3.918)
Matchmaker AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8) with
fold_acsl4_model_0.cif, chain A (#6), sequence alignment score = 523.9
RMSD between 232 pruned atom pairs is 1.201 angstroms; (across all 551 pairs:
15.586)
Matchmaker AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8) with
fold_fatp2_model_0.cif, chain A (#7), sequence alignment score = 3219.7
RMSD between 477 pruned atom pairs is 0.494 angstroms; (across all 620 pairs:
11.781)
Matchmaker AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8) with
6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1), sequence alignment
score = 189.9
RMSD between 73 pruned atom pairs is 1.213 angstroms; (across all 410 pairs:
19.742)
Matchmaker AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8) with
6he2_openConformatin_2-HIB-AMP_CoA.pdb, chain A (#2), sequence alignment score
= 201.4
RMSD between 67 pruned atom pairs is 1.344 angstroms; (across all 395 pairs:
23.598)
Matchmaker AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8) with
1pg4_AcetylCoASynthetase_Salmonella.pdb, chain A (#3), sequence alignment
score = 619.5
RMSD between 268 pruned atom pairs is 1.196 angstroms; (across all 553 pairs:
6.864)
Matchmaker AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8) with
3cw9_Alcaligenes_ChlorobenzoylCoA.pdb, chain A (#5), sequence alignment score
= 649.4
RMSD between 270 pruned atom pairs is 1.148 angstroms; (across all 490 pairs:
4.490)
> select #3/B#4/A
9879 atoms, 9439 bonds, 7 pseudobonds, 1851 residues, 4 models selected
> hide sel atoms
> hide sel cartoons
> select #3/B#4/A#5/B
14202 atoms, 13418 bonds, 8 pseudobonds, 2777 residues, 6 models selected
> hide sel atoms
> hide sel cartoons
> select #3/B#4/A#5/B#2/B
17814 atoms, 16998 bonds, 10 pseudobonds, 3342 residues, 8 models selected
> hide sel atoms
> hide sel cartoons
> lighting soft
> graphics silhouettes true
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> ui tool show "Color Actions"
> color sel wheat
[Repeated 1 time(s)]
> select
55227 atoms, 53936 bonds, 24 pseudobonds, 9249 residues, 16 models selected
> color sel wheat
> select
> ::name="01A"::name="8LE"::name="AMP"::name="BCO"::name="CL"::name="COA"::name="EDO"::name="HOH"::name="MG"::name="NO3"::name="PRX"
3355 atoms, 833 bonds, 11 pseudobonds, 2587 residues, 7 models selected
> color (#4#!1-3,5 & sel) byelement
> show sel atoms
> undo
> style sel ball
Changed 3355 atom styles
> style sel sphere
Changed 3355 atom styles
> style sel ball
Changed 3355 atom styles
> select ::name="HOH"
2551 atoms, 2551 residues, 5 models selected
> hide sel atoms
> select clear
> select ::name="MG"
4 atoms, 4 residues, 2 models selected
> show sel atoms
> undo
> style sel sphere
Changed 4 atom styles
> select clear
> hide #!2 models
> hide #!3 models
> hide #4 models
> hide #!5 models
> hide #6 models
> hide #7 models
> hide #8 models
> select
55227 atoms, 53936 bonds, 24 pseudobonds, 9249 residues, 16 models selected
> show #4,6-8#!1-3,5 target m
> color sel byhetero
> select clear
> hide #4,6-8#!2-3,5 target m
> select #1/:367
Expected an objects specifier or a keyword
> select #1/A:367
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:367-900
841 atoms, 849 bonds, 1 pseudobond, 109 residues, 2 models selected
> color sel powder blue
> color sel light blue
> select #2/A:367-900
974 atoms, 829 bonds, 1 pseudobond, 255 residues, 2 models selected
> show #!2 models
> show #!3 models
> show #4 models
> show #!5 models
> hide #!5 models
> show #6 models
> show #!5 models
> show #7 models
> show #8 models
> select #2/A:367-900
974 atoms, 829 bonds, 1 pseudobond, 255 residues, 2 models selected
> color sel light blue
> hide #!1 models
> hide #!2 models
> select add #2
7501 atoms, 7414 bonds, 4 pseudobonds, 1187 residues, 3 models selected
> select subtract #2
Nothing selected
> select #3/A:524-900
847 atoms, 864 bonds, 1 pseudobond, 114 residues, 2 models selected
> color sel light blue
> select #4/A:470-900
787 atoms, 805 bonds, 100 residues, 1 model selected
> select #4/B:470-900
775 atoms, 793 bonds, 100 residues, 1 model selected
> color sel light blue
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #4
Nothing selected
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #4 models
> select #5/B:409-900
739 atoms, 750 bonds, 95 residues, 1 model selected
> select #5/A:409-900
728 atoms, 739 bonds, 95 residues, 1 model selected
> color sel light blue
> select add #5
8584 atoms, 7932 bonds, 5 pseudobonds, 1816 residues, 2 models selected
> select subtract #5
Nothing selected
> hide #!5 models
> select #7/A:580-900
326 atoms, 332 bonds, 41 residues, 1 model selected
> color sel light blue
> hide #8 models
> hide #6 models
> show #6 models
> show #8 models
> select #6/A:580-900
1052 atoms, 1071 bonds, 132 residues, 1 model selected
> color sel light blue
> select add #6
5553 atoms, 5667 bonds, 711 residues, 1 model selected
> select subtract #6
Nothing selected
> hide #6 models
> select #7/A:489-900
1055 atoms, 1077 bonds, 132 residues, 1 model selected
> color sel light blue
> select #8/A:489-900
1055 atoms, 1077 bonds, 132 residues, 1 model selected
> color sel light blue
> select add #8
4958 atoms, 5073 bonds, 620 residues, 1 model selected
> select subtract #8
Nothing selected
> hide #8 models
> hide #7 models
> show #!1 models
> select #1/A
4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 2 models selected
> select #1/A:
Expected an objects specifier or a keyword
> select #1/A:
Expected an objects specifier or a keyword
> select #1/A:455
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:455,367
13 atoms, 11 bonds, 2 residues, 1 model selected
> show #!2 models
> show #!3 models
> show #4 models
> show #!5 models
> show #6 models
> show #8 models
> show #7 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #1/A:455,367#2/A
3902 atoms, 3845 bonds, 2 pseudobonds, 624 residues, 3 models selected
> select #1/A:455,367#2/A:455,367
26 atoms, 22 bonds, 4 residues, 2 models selected
> select #1/A:455,367#2/A:455,367#3/A
5480 atoms, 5133 bonds, 7 pseudobonds, 1117 residues, 5 models selected
> select #1/A:455,367#2/A:455,367#3/A:609,524#4/A
4531 atoms, 4331 bonds, 836 residues, 4 models selected
> select #1/A:455,367#2/A:455,367#3/A:609,524#4/B
4363 atoms, 4306 bonds, 693 residues, 4 models selected
> select #1/A:455,367#2/A:455,367#3/A:609,524#4/B:557,470
46 atoms, 38 bonds, 8 residues, 4 models selected
> select #1/A:455,367#2/A:455,367#3/A:609,524#4/B:557,470#5/A
4307 atoms, 3991 bonds, 4 pseudobonds, 898 residues, 6 models selected
> select #1/A:455,367#2/A:455,367#3/A:609,524#4/B:557,470#5/A:492,409
55 atoms, 45 bonds, 10 residues, 5 models selected
> select
> #1/A:455,367#2/A:455,367#3/A:609,524#4/B:557,470#5/A:492,409#6/A:690,580#7/A:572,489
81 atoms, 67 bonds, 14 residues, 7 models selected
> select
> #1/A:455,367#2/A:455,367#3/A:609,524#4/B:557,470#5/A:492,409#6/A:690,580#7/A:572,489#8/A:572,489
94 atoms, 78 bonds, 16 residues, 8 models selected
> show sel atoms
> color sel magenta
> select clear
> hide #4,6-8#!1-3,5 target m
> show #!1 models
> hide #!1 models
> show #!1 models
> select #1/A:159,160,164,186,190,192,193,210,213,216,366,399,424,437,438
121 atoms, 112 bonds, 15 residues, 1 model selected
> color sel orange
> show sel atoms
> color sel byhetero
> select #1/A:424
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> color sel wheat
> color sel light blue
> select add #1
4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected
> select subtract #1
Nothing selected
> select #2/A:159,160,164,186,190,192,193,210,213,216,366,399,424,437,438
121 atoms, 112 bonds, 15 residues, 1 model selected
> show #!2 models
> hide #!1 models
> select #2/A:159,160,164,186,190,192,193,210,213,216,366,399,437,438
110 atoms, 102 bonds, 14 residues, 1 model selected
> show sel atoms
> color sel byhetero
> color sel orange
> color sel byhetero
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select add #2
7501 atoms, 7414 bonds, 4 pseudobonds, 1187 residues, 3 models selected
> select subtract #2
Nothing selected
> select #3/A:159,160,164,186,190,192,193,210,213,216,366,399,437,438
96 atoms, 89 bonds, 14 residues, 1 model selected
> select add #3
10837 atoms, 10248 bonds, 14 pseudobonds, 2134 residues, 4 models selected
> select subtract #3
Nothing selected
> select #3/A:163,191,194,196,164,165,305,306,309,357,335,360,523,584
111 atoms, 103 bonds, 14 residues, 1 model selected
> color sel byhetero
> color sel orange
> color sel byhetero
> select add #3
10837 atoms, 10248 bonds, 14 pseudobonds, 2134 residues, 4 models selected
> select subtract #3
Nothing selected
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #4 models
> hide #4 models
> show #4 models
> select #4/A:
Expected an objects specifier or a keyword
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #4
Nothing selected
> select #4/B
4328 atoms, 4277 bonds, 687 residues, 1 model selected
> select #4/B:137,138,139,261,262,265,249,290,311,469,532
84 atoms, 78 bonds, 11 residues, 1 model selected
> select #4/B:137,138,139,261,262,265,249,290,311,469,532
84 atoms, 78 bonds, 11 residues, 1 model selected
> show sel atoms
> color sel orange
> color sel byhetero
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #4
Nothing selected
> show #!5 models
> show #!3 models
> hide #!3 models
> hide #4 models
> select #5/A:137,138,139,261,262,265,249,290,311,469,532
80 atoms, 76 bonds, 10 residues, 1 model selected
> select #5/A:85,86,87,203,204,207,230,251,254,408,466
92 atoms, 88 bonds, 11 residues, 1 model selected
> color sel orange
> show sel atoms
> color sel byhetero
> select add #5
8584 atoms, 7932 bonds, 5 pseudobonds, 1816 residues, 2 models selected
> color sel byhetero
> select subtract #5
Nothing selected
> select add #5
8584 atoms, 7932 bonds, 5 pseudobonds, 1816 residues, 2 models selected
> select subtract #5
Nothing selected
> hide #!5 models
> show #6 models
> show #!5 models
> hide #!5 models
> show #6 models
> select #6/A:181,182,183,319,320,323,374,377,579,654,662
88 atoms, 83 bonds, 11 residues, 1 model selected
> show sel atoms
> color sel orange
> color sel byhetero
[Repeated 1 time(s)]
> show sel atoms
> color sel byhetero
> show #7 models
> select add #6
5553 atoms, 5667 bonds, 711 residues, 1 model selected
> hide #6 models
> select subtract #6
Nothing selected
> select #7/A:135,136,137,264,265,268,312,315,488,547,550
91 atoms, 86 bonds, 11 residues, 1 model selected
> show sel atoms
> color sel orange
> color sel byhetero
> show #8 models
> hide #7 models
> select add #7
4958 atoms, 5073 bonds, 620 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #8
4958 atoms, 5073 bonds, 620 residues, 1 model selected
> select subtract #8
Nothing selected
> select #8/A:135,136,137,264,265,268,312,315,488,547,550
91 atoms, 86 bonds, 11 residues, 1 model selected
> show sel atoms
> color sel orange
> color sel byhetero
> select add #8
4958 atoms, 5073 bonds, 620 residues, 1 model selected
> select subtract #8
Nothing selected
> show #7 models
> hide #8 models
> hide #7 models
> show #!1 models
> hide #!1 models
> show #8 models
> show #4 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #8 models
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
51872 atoms, 53103 bonds, 7 pseudobonds, 6662 residues, 11 models selected
> select
> ::name="01A"::name="8LE"::name="AMP"::name="BCO"::name="CL"::name="COA"::name="EDO"::name="HOH"::name="MG"::name="NO3"::name="PRX"
3355 atoms, 833 bonds, 11 pseudobonds, 2587 residues, 7 models selected
> select add #1
7103 atoms, 4677 bonds, 12 pseudobonds, 3064 residues, 9 models selected
> select subtract #1
3091 atoms, 727 bonds, 11 pseudobonds, 2420 residues, 6 models selected
> select add #2
10101 atoms, 7929 bonds, 15 pseudobonds, 3310 residues, 8 models selected
> select subtract #2
2600 atoms, 515 bonds, 11 pseudobonds, 2123 residues, 5 models selected
> select add #3
12416 atoms, 10592 bonds, 19 pseudobonds, 3395 residues, 7 models selected
> select subtract #3
1579 atoms, 344 bonds, 5 pseudobonds, 1261 residues, 3 models selected
> select add #5
9183 atoms, 8092 bonds, 5 pseudobonds, 2267 residues, 3 models selected
> select subtract #5
599 atoms, 160 bonds, 451 residues, 1 model selected
> select ~sel & ##selected
8225 atoms, 8419 bonds, 1066 residues, 1 model selected
> hide sel atoms
> undo
> hide sel cartoons
> hide sel atoms
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #4
Nothing selected
> undo
[Repeated 2 time(s)]
> hide #8 models
> style sel ball
Changed 8225 atom styles
> undo
> color sel byhetero
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #4
Nothing selected
> lighting soft
> show (#4 & sidechain) target ab
> undo
> show #4 cartoons
> undo
[Repeated 4 time(s)]
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #4
Nothing selected
> hide #8 models
> show #8 models
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> color sel cornflower blue
> color sel byhetero
> color sel byelement
> undo
> select subtract #4
Nothing selected
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #4
Nothing selected
> select
> ::name="01A"::name="8LE"::name="AMP"::name="BCO"::name="CL"::name="COA"::name="EDO"::name="HOH"::name="MG"::name="NO3"::name="PRX"
3355 atoms, 833 bonds, 11 pseudobonds, 2587 residues, 7 models selected
> color (#4 & sel) byelement
> select clear
> select C1
Nothing selected
> hide (#4,8 & (protein|nucleic)) target a
> cartoon hide #4,8
> show (#4,8 & backbone) target ab
> undo
[Repeated 2 time(s)]
> hide #4 models
> show #4 models
> hide #4,8 atoms
> undo
> select
> ::name="01A"::name="8LE"::name="AMP"::name="BCO"::name="CL"::name="COA"::name="EDO"::name="HOH"::name="MG"::name="NO3"::name="PRX"
3355 atoms, 833 bonds, 11 pseudobonds, 2587 residues, 7 models selected
> select ~sel & ##selected
36403 atoms, 37290 bonds, 13 pseudobonds, 4711 residues, 9 models selected
> hide sel & #4 atoms
> color sel & #4 byhetero
> select clear
> color #4,8 byhetero
[Repeated 1 time(s)]
> select sel :< 7
Nothing selected
> select ::name="BCO"
106 atoms, 110 bonds, 2 residues, 1 model selected
> select sel :< 7
4242 atoms, 4092 bonds, 4 pseudobonds, 606 residues, 9 models selected
> select sel :< 5
15531 atoms, 15168 bonds, 4 pseudobonds, 2317 residues, 9 models selected
> undo
[Repeated 1 time(s)]
> select sel :< 5
2572 atoms, 2451 bonds, 2 pseudobonds, 344 residues, 9 models selected
> show sel & #4,8 atoms
> undo
> select add #4
10756 atoms, 10420 bonds, 2 pseudobonds, 1783 residues, 9 models selected
> select subtract #4
1932 atoms, 1841 bonds, 2 pseudobonds, 266 residues, 8 models selected
> select add #1
5620 atoms, 5485 bonds, 3 pseudobonds, 864 residues, 10 models selected
> select subtract #1
1608 atoms, 1535 bonds, 2 pseudobonds, 220 residues, 7 models selected
> select add #2
8790 atoms, 8636 bonds, 6 pseudobonds, 1371 residues, 9 models selected
> select subtract #2
1289 atoms, 1222 bonds, 2 pseudobonds, 184 residues, 6 models selected
> select add #3
11838 atoms, 11202 bonds, 16 pseudobonds, 2274 residues, 9 models selected
> select subtract #3
1001 atoms, 954 bonds, 2 pseudobonds, 140 residues, 5 models selected
> select add #5
9284 atoms, 8614 bonds, 5 pseudobonds, 1903 residues, 5 models selected
> select subtract #5
700 atoms, 682 bonds, 87 residues, 3 models selected
> select add #6
6001 atoms, 6101 bonds, 765 residues, 3 models selected
> select subtract #6
448 atoms, 434 bonds, 54 residues, 2 models selected
> select add #7
5189 atoms, 5297 bonds, 647 residues, 2 models selected
> select subtract #7
231 atoms, 224 bonds, 27 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select add #8
4958 atoms, 5073 bonds, 620 residues, 1 model selected
> select subtract #8
Nothing selected
> color #4,8 byhetero
> graphics silhouettes false
> lighting flat
> lighting soft
> lighting full
> lighting simple
> lighting soft
[Repeated 3 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> hide #4 models
> show #4 models
> select ::name="COA"
240 atoms, 250 bonds, 5 residues, 3 models selected
> select ::name="BCO"
106 atoms, 110 bonds, 2 residues, 1 model selected
> select ~sel & ##selected
8718 atoms, 8469 bonds, 1515 residues, 1 model selected
> show sel cartoons
> ui mousemode right "move picked models"
> view matrix models
> #4,-0.62545,-0.2296,0.74572,19.831,0.65333,-0.67662,0.33964,94.363,0.42658,0.69962,0.5732,26.168
> undo
> ui mousemode right "translate selected atoms"
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #4
Nothing selected
> select #4/A
4496 atoms, 4302 bonds, 830 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #4/B
4328 atoms, 4277 bonds, 687 residues, 1 model selected
> ui tool show "Color Actions"
> color sel wheat
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #4
Nothing selected
> undo
[Repeated 9 time(s)]
> select #4/B
4328 atoms, 4277 bonds, 687 residues, 1 model selected
> select ::name="BCO"
106 atoms, 110 bonds, 2 residues, 1 model selected
> select ~sel & ##selected
8718 atoms, 8469 bonds, 1515 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> color sel byhetero
> ui mousemode right "move picked models"
> view matrix models #8,1,0,0,-5.6333,0,1,0,-3.5595,0,0,1,0.25735
> undo
> ui mousemode right translate
> open /Users/mk16/works/acyl-CoA_synthetase/3eq6_ACSM2A_bCoA_AMP.pdb
3eq6_ACSM2A_bCoA_AMP.pdb title:
Crystal structure of human acyl-coa synthetase medium-chain family member 2A
(L64P mutation) In A ternary complex with products [more info...]
Chain information for 3eq6_ACSM2A_bCoA_AMP.pdb #9
---
Chain | Description | UniProt
A B | acyl-coenzyme A synthetase ACSM2A | ACS2A_HUMAN 32-577
Non-standard residues in 3eq6_ACSM2A_bCoA_AMP.pdb #9
---
AMP — adenosine monophosphate
BCO — butyryl coenzyme A
(S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3Λ~5~,5Λ~5~-diphosphaheptadecan-17-yl}
butanethioate (non-preferred name))
28 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> matchmaker #4,6-9#!2-3,5 to #1
Computing secondary structure
[Repeated 8 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#4), sequence alignment score = 290.3
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_acsl4_model_0.cif, chain A (#6), sequence alignment score = 181.7
RMSD between 80 pruned atom pairs is 1.286 angstroms; (across all 430 pairs:
23.367)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_fatp2_model_0.cif, chain A (#7), sequence alignment score = 179.1
RMSD between 56 pruned atom pairs is 1.119 angstroms; (across all 410 pairs:
23.522)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8), sequence alignment score =
189.9
RMSD between 73 pruned atom pairs is 1.213 angstroms; (across all 410 pairs:
19.742)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#9), sequence alignment score = 290.3
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
6he2_openConformatin_2-HIB-AMP_CoA.pdb, chain A (#2), sequence alignment score
= 2511
RMSD between 355 pruned atom pairs is 0.323 angstroms; (across all 456 pairs:
14.640)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
1pg4_AcetylCoASynthetase_Salmonella.pdb, chain A (#3), sequence alignment
score = 279.5
RMSD between 81 pruned atom pairs is 1.236 angstroms; (across all 444 pairs:
18.441)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3cw9_Alcaligenes_ChlorobenzoylCoA.pdb, chain B (#5), sequence alignment score
= 323.5
RMSD between 64 pruned atom pairs is 1.175 angstroms; (across all 400 pairs:
15.376)
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.63144,-0.10227,0.76865,-11.141,0.61652,-0.66743,0.41766,18.391,0.47031,0.73761,0.48449,-79.835
> undo
[Repeated 2 time(s)]
> select #4/B
4328 atoms, 4277 bonds, 687 residues, 1 model selected
> hide sel atoms
> select #9/A
4496 atoms, 4302 bonds, 830 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> view matrix models
> #9,-0.63144,-0.10227,0.76865,31.62,0.61652,-0.66743,0.41766,84.912,0.47031,0.73761,0.48449,-23.225
> undo
> view matrix models
> #9,-0.63144,-0.10227,0.76865,32.675,0.61652,-0.66743,0.41766,90.596,0.47031,0.73761,0.48449,-17.236
> undo
> ui mousemode right "move picked models"
> view matrix models
> #9,-0.63144,-0.10227,0.76865,15.223,0.61652,-0.66743,0.41766,93.645,0.47031,0.73761,0.48449,41.798
> view matrix models
> #9,-0.63144,-0.10227,0.76865,10.46,0.61652,-0.66743,0.41766,101.22,0.47031,0.73761,0.48449,70.451
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> select add #4
13320 atoms, 12881 bonds, 2347 residues, 2 models selected
> show sel cartoons
> undo
> select subtract #4
4496 atoms, 4302 bonds, 830 residues, 1 model selected
> select add #4
13320 atoms, 12881 bonds, 2347 residues, 2 models selected
> select subtract #4
4496 atoms, 4302 bonds, 830 residues, 1 model selected
> select add #9
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #9
Nothing selected
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> show sel cartoons
> undo
[Repeated 1 time(s)]
> ui tool show Matchmaker
> matchmaker #4,6-9#!2-3,5 to #1
Computing secondary structure
[Repeated 8 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#4), sequence alignment score = 290.3
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_acsl4_model_0.cif, chain A (#6), sequence alignment score = 181.7
RMSD between 80 pruned atom pairs is 1.286 angstroms; (across all 430 pairs:
23.367)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_fatp2_model_0.cif, chain A (#7), sequence alignment score = 179.1
RMSD between 56 pruned atom pairs is 1.119 angstroms; (across all 410 pairs:
23.522)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8), sequence alignment score =
189.9
RMSD between 73 pruned atom pairs is 1.213 angstroms; (across all 410 pairs:
19.742)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#9), sequence alignment score = 290.3
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
6he2_openConformatin_2-HIB-AMP_CoA.pdb, chain A (#2), sequence alignment score
= 2511
RMSD between 355 pruned atom pairs is 0.323 angstroms; (across all 456 pairs:
14.640)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
1pg4_AcetylCoASynthetase_Salmonella.pdb, chain A (#3), sequence alignment
score = 279.5
RMSD between 81 pruned atom pairs is 1.236 angstroms; (across all 444 pairs:
18.441)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3cw9_Alcaligenes_ChlorobenzoylCoA.pdb, chain B (#5), sequence alignment score
= 323.5
RMSD between 64 pruned atom pairs is 1.175 angstroms; (across all 400 pairs:
15.376)
> view matrix models
> #9,-0.63144,-0.10227,0.76865,4.7933,0.61652,-0.66743,0.41766,97.428,0.47031,0.73761,0.48449,56.96
> hide #4 models
> show #4 models
> hide #4 models
> undo
[Repeated 2 time(s)]
> show #4,8-9 cartoons
> undo
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select ::name="BCO"
212 atoms, 220 bonds, 4 residues, 2 models selected
> show sel atoms
[Repeated 1 time(s)]
> show sel cartoons
[Repeated 1 time(s)]
> select add #4
8930 atoms, 8689 bonds, 1519 residues, 2 models selected
> select subtract #4
106 atoms, 110 bonds, 2 residues, 1 model selected
> select add #9
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #9
Nothing selected
> select add #9
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #9
Nothing selected
> select add #9
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #9
Nothing selected
> select
> ::name="01A"::name="8LE"::name="AMP"::name="BCO"::name="CL"::name="COA"::name="EDO"::name="HOH"::name="MG"::name="NO3"::name="PRX"
3954 atoms, 993 bonds, 11 pseudobonds, 3038 residues, 8 models selected
> color (#4,9 & sel) byelement
> style sel & #4,9 ball
Changed 1198 atom styles
> select #9/A
4496 atoms, 4302 bonds, 830 residues, 1 model selected
> hide sel atoms
> select add #9
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #9
Nothing selected
> select add #3
10837 atoms, 10248 bonds, 14 pseudobonds, 2134 residues, 4 models selected
> select add #4
19661 atoms, 18827 bonds, 14 pseudobonds, 3651 residues, 5 models selected
> select subtract #3
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #4
Nothing selected
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #4
Nothing selected
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select ::name="BCO"
212 atoms, 220 bonds, 4 residues, 2 models selected
> select add #9
8930 atoms, 8689 bonds, 1519 residues, 2 models selected
> select subtract #9
106 atoms, 110 bonds, 2 residues, 1 model selected
> show sel atoms
[Repeated 6 time(s)]
> ui tool show Matchmaker
> matchmaker #4,6-9#!2-3,5 to #1
Computing secondary structure
[Repeated 8 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#4), sequence alignment score = 290.3
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_acsl4_model_0.cif, chain A (#6), sequence alignment score = 181.7
RMSD between 80 pruned atom pairs is 1.286 angstroms; (across all 430 pairs:
23.367)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_fatp2_model_0.cif, chain A (#7), sequence alignment score = 179.1
RMSD between 56 pruned atom pairs is 1.119 angstroms; (across all 410 pairs:
23.522)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8), sequence alignment score =
189.9
RMSD between 73 pruned atom pairs is 1.213 angstroms; (across all 410 pairs:
19.742)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#9), sequence alignment score = 290.3
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
6he2_openConformatin_2-HIB-AMP_CoA.pdb, chain A (#2), sequence alignment score
= 2511
RMSD between 355 pruned atom pairs is 0.323 angstroms; (across all 456 pairs:
14.640)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
1pg4_AcetylCoASynthetase_Salmonella.pdb, chain A (#3), sequence alignment
score = 279.5
RMSD between 81 pruned atom pairs is 1.236 angstroms; (across all 444 pairs:
18.441)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3cw9_Alcaligenes_ChlorobenzoylCoA.pdb, chain B (#5), sequence alignment score
= 323.5
RMSD between 64 pruned atom pairs is 1.175 angstroms; (across all 400 pairs:
15.376)
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #4
Nothing selected
> close #4
> view matrix models
> #8,1,-1.0888e-15,6.5046e-16,-11.075,1.0888e-15,1,-5.4026e-16,-8.7467,-6.5046e-16,5.4026e-16,1,-65.524
> undo
[Repeated 1 time(s)]Undo failed, probably because structures have been
modified.
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> select
> ::name="01A"::name="8LE"::name="AMP"::name="BCO"::name="CL"::name="COA"::name="EDO"::name="HOH"::name="MG"::name="NO3"::name="PRX"
3355 atoms, 833 bonds, 11 pseudobonds, 2587 residues, 7 models selected
> select ~sel & ##selected
36403 atoms, 37290 bonds, 13 pseudobonds, 4711 residues, 9 models selected
> select add #9
37002 atoms, 37450 bonds, 13 pseudobonds, 5162 residues, 9 models selected
> select subtract #9
28178 atoms, 28871 bonds, 13 pseudobonds, 3645 residues, 8 models selected
> select add #9
37002 atoms, 37450 bonds, 13 pseudobonds, 5162 residues, 9 models selected
> select subtract #9
28178 atoms, 28871 bonds, 13 pseudobonds, 3645 residues, 8 models selected
> select ::name="BCO"
106 atoms, 110 bonds, 2 residues, 1 model selected
> select add #9
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #9
Nothing selected
> color wheat
> undo
> select add #9
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> color sel wheat
> hide #8 models
> rename #9 id #4
> view matrix models
> #4,-0.63144,-0.10227,0.76865,17.743,0.61652,-0.66743,0.41766,86.782,0.47031,0.73761,0.48449,2.3275
> select #4/A
4496 atoms, 4302 bonds, 830 residues, 1 model selected
> select #4/B
4328 atoms, 4277 bonds, 687 residues, 1 model selected
> select #4/B:470-900
775 atoms, 793 bonds, 100 residues, 1 model selected
> color sel light blue
> select
> ::name="01A"::name="8LE"::name="AMP"::name="BCO"::name="CL"::name="COA"::name="EDO"::name="HOH"::name="MG"::name="NO3"::name="PRX"
3355 atoms, 833 bonds, 11 pseudobonds, 2587 residues, 7 models selected
> color (#4 & sel) byelement
> select ::name="HOH"
2551 atoms, 2551 residues, 5 models selected
> hide sel & #4 atoms
> color sel & #4 byhetero
[Repeated 1 time(s)]
> select clear
> color #4 byhetero
> view matrix models
> #4,-0.63144,-0.10227,0.76865,5.0026,0.61652,-0.66743,0.41766,100.71,0.47031,0.73761,0.48449,69.138
> show #!3 models
> hide #!3 models
> show #!3 models
> view matrix models
> #4,-0.63144,-0.10227,0.76865,-2.3827,0.61652,-0.66743,0.41766,95.152,0.47031,0.73761,0.48449,63.671
> hide #!3 models
> show #8 models
> open /Users/mk16/works/acyl-CoA_synthetase/AF-O14975-F1-model_v4_FATP2.pdb
AF-O14975-F1-model_v4_FATP2.pdb title:
Alphafold monomer V2.0 prediction for very long-chain acyl-coa synthetase
(O14975) [more info...]
Chain information for AF-O14975-F1-model_v4_FATP2.pdb #9
---
Chain | Description | UniProt
A | very long-chain acyl-coa synthetase | S27A2_HUMAN 1-620
Computing secondary structure
> select ::name="BCO"
106 atoms, 110 bonds, 2 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #4,6-9#!2-3,5 to #1
Computing secondary structure
[Repeated 8 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#4), sequence alignment score = 290.3
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_acsl4_model_0.cif, chain A (#6), sequence alignment score = 181.7
RMSD between 80 pruned atom pairs is 1.286 angstroms; (across all 430 pairs:
23.367)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_fatp2_model_0.cif, chain A (#7), sequence alignment score = 179.1
RMSD between 56 pruned atom pairs is 1.119 angstroms; (across all 410 pairs:
23.522)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8), sequence alignment score =
189.9
RMSD between 73 pruned atom pairs is 1.213 angstroms; (across all 410 pairs:
19.742)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
AF-O14975-F1-model_v4_FATP2.pdb, chain A (#9), sequence alignment score =
189.9
RMSD between 73 pruned atom pairs is 1.213 angstroms; (across all 410 pairs:
19.742)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
6he2_openConformatin_2-HIB-AMP_CoA.pdb, chain A (#2), sequence alignment score
= 2511
RMSD between 355 pruned atom pairs is 0.323 angstroms; (across all 456 pairs:
14.640)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
1pg4_AcetylCoASynthetase_Salmonella.pdb, chain A (#3), sequence alignment
score = 279.5
RMSD between 81 pruned atom pairs is 1.236 angstroms; (across all 444 pairs:
18.441)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3cw9_Alcaligenes_ChlorobenzoylCoA.pdb, chain B (#5), sequence alignment score
= 323.5
RMSD between 64 pruned atom pairs is 1.175 angstroms; (across all 400 pairs:
15.376)
> view matrix models
> #4,-0.63144,-0.10227,0.76865,-2.948,0.61652,-0.66743,0.41766,99.232,0.47031,0.73761,0.48449,61.83
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #4
Nothing selected
> select add #9
4958 atoms, 5073 bonds, 620 residues, 1 model selected
> select subtract #9
Nothing selected
> select add #9
4958 atoms, 5073 bonds, 620 residues, 1 model selected
> select ::name="BCO"
106 atoms, 110 bonds, 2 residues, 1 model selected
> close #9
> open /Users/mk16/works/acyl-CoA_synthetase/3eq6_ACSM2A_bCoA_AMP.pdb
3eq6_ACSM2A_bCoA_AMP.pdb title:
Crystal structure of human acyl-coa synthetase medium-chain family member 2A
(L64P mutation) In A ternary complex with products [more info...]
Chain information for 3eq6_ACSM2A_bCoA_AMP.pdb #9
---
Chain | Description | UniProt
A B | acyl-coenzyme A synthetase ACSM2A | ACS2A_HUMAN 32-577
Non-standard residues in 3eq6_ACSM2A_bCoA_AMP.pdb #9
---
AMP — adenosine monophosphate
BCO — butyryl coenzyme A
(S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3Λ~5~,5Λ~5~-diphosphaheptadecan-17-yl}
butanethioate (non-preferred name))
28 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> matchmaker #4,6-9#!2-3,5 to #1
Computing secondary structure
[Repeated 8 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#4), sequence alignment score = 290.3
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_acsl4_model_0.cif, chain A (#6), sequence alignment score = 181.7
RMSD between 80 pruned atom pairs is 1.286 angstroms; (across all 430 pairs:
23.367)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_fatp2_model_0.cif, chain A (#7), sequence alignment score = 179.1
RMSD between 56 pruned atom pairs is 1.119 angstroms; (across all 410 pairs:
23.522)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8), sequence alignment score =
189.9
RMSD between 73 pruned atom pairs is 1.213 angstroms; (across all 410 pairs:
19.742)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#9), sequence alignment score = 290.3
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
6he2_openConformatin_2-HIB-AMP_CoA.pdb, chain A (#2), sequence alignment score
= 2511
RMSD between 355 pruned atom pairs is 0.323 angstroms; (across all 456 pairs:
14.640)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
1pg4_AcetylCoASynthetase_Salmonella.pdb, chain A (#3), sequence alignment
score = 279.5
RMSD between 81 pruned atom pairs is 1.236 angstroms; (across all 444 pairs:
18.441)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3cw9_Alcaligenes_ChlorobenzoylCoA.pdb, chain B (#5), sequence alignment score
= 323.5
RMSD between 64 pruned atom pairs is 1.175 angstroms; (across all 400 pairs:
15.376)
> view matrix models
> #8,1,-1.0792e-15,6.9772e-16,-26.958,1.0792e-15,1,-5.1093e-16,23.071,-6.9772e-16,5.1093e-16,1,82.515
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #4
Nothing selected
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #4
Nothing selected
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #4
Nothing selected
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #4
Nothing selected
> hide #9 models
> show #9 models
> hide #9 models
> ui tool show Matchmaker
> matchmaker #4,6-9#!2-3,5 to #1
Computing secondary structure
[Repeated 8 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#4), sequence alignment score = 290.3
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_acsl4_model_0.cif, chain A (#6), sequence alignment score = 181.7
RMSD between 80 pruned atom pairs is 1.286 angstroms; (across all 430 pairs:
23.367)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_fatp2_model_0.cif, chain A (#7), sequence alignment score = 179.1
RMSD between 56 pruned atom pairs is 1.119 angstroms; (across all 410 pairs:
23.522)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8), sequence alignment score =
189.9
RMSD between 73 pruned atom pairs is 1.213 angstroms; (across all 410 pairs:
19.742)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#9), sequence alignment score = 290.3
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
6he2_openConformatin_2-HIB-AMP_CoA.pdb, chain A (#2), sequence alignment score
= 2511
RMSD between 355 pruned atom pairs is 0.323 angstroms; (across all 456 pairs:
14.640)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
1pg4_AcetylCoASynthetase_Salmonella.pdb, chain A (#3), sequence alignment
score = 279.5
RMSD between 81 pruned atom pairs is 1.236 angstroms; (across all 444 pairs:
18.441)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3cw9_Alcaligenes_ChlorobenzoylCoA.pdb, chain B (#5), sequence alignment score
= 323.5
RMSD between 64 pruned atom pairs is 1.175 angstroms; (across all 400 pairs:
15.376)
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #4
Nothing selected
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> view matrix models
> #4,-0.63144,-0.10227,0.76865,2.611,0.61652,-0.66743,0.41766,93.529,0.47031,0.73761,0.48449,59.378
> select subtract #4
Nothing selected
> select add #4
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #4
Nothing selected
> show #9 models
> hide #9 models
> show #9 models
> select ::name="BCO"
212 atoms, 220 bonds, 4 residues, 2 models selected
> select ~sel & ##selected
17436 atoms, 16938 bonds, 3030 residues, 2 models selected
> select add #4
17542 atoms, 17048 bonds, 3032 residues, 2 models selected
> select subtract #4
8718 atoms, 8469 bonds, 1515 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #9/A
4496 atoms, 4302 bonds, 830 residues, 1 model selected
> hide sel atoms
> select add #9
8824 atoms, 8579 bonds, 1517 residues, 1 model selected
> select subtract #9
Nothing selected
> select
> ::name="01A"::name="8LE"::name="AMP"::name="BCO"::name="CL"::name="COA"::name="EDO"::name="HOH"::name="MG"::name="NO3"::name="PRX"
3954 atoms, 993 bonds, 11 pseudobonds, 3038 residues, 8 models selected
> color (#4,9 & sel) byelement
> style sel & #4,9 ball
Changed 1198 atom styles
> select clear
> view matrix models
> #4,-0.63144,-0.10227,0.76865,-12.792,0.61652,-0.66743,0.41766,80.371,0.47031,0.73761,0.48449,44.336
> view matrix models
> #4,-0.63144,-0.10227,0.76865,-8.8339,0.61652,-0.66743,0.41766,79.275,0.47031,0.73761,0.48449,38.312
> select ::name="LYS"
3571 atoms, 3187 bonds, 417 residues, 9 models selected
> view matrix models
> #8,1,-9.0489e-16,6.1096e-16,-4.9505,9.0489e-16,1,-4.8312e-16,-8.8155,-6.1096e-16,4.8312e-16,1,14.889
> undo
> select clear
> color #4,8-9 byhetero
> hide #4 models
> hide #8 models
> hide #9 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!3 models
> show #!5 models
> hide #!3 models
> hide #!5 models
> show #9 models
> show #8 models
> ui mousemode right translate
> hide #8 models
> show #8 models
> show #!3 models
> show #4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #8 models
> hide #9 models
> show #8 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> select ::name="COA"
240 atoms, 250 bonds, 5 residues, 3 models selected
> select add #2
7645 atoms, 7564 bonds, 4 pseudobonds, 1190 residues, 5 models selected
> select subtract #2
144 atoms, 150 bonds, 3 residues, 2 models selected
> select add #3
10885 atoms, 10298 bonds, 14 pseudobonds, 2135 residues, 5 models selected
> select subtract #3
48 atoms, 50 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
3964 atoms, 3900 bonds, 1 pseudobond, 643 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> undo
[Repeated 1 time(s)]
> hide #4 models
> show #4 models
> hide #4 models
> show #9 models
> hide #8 models
> hide #9 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> select add #1
4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> hide #8 models
> show #8 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #!5 models
> select #5/A
4261 atoms, 3953 bonds, 4 pseudobonds, 890 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select #5/B
4323 atoms, 3979 bonds, 1 pseudobond, 926 residues, 2 models selected
> show sel atoms
> show sel cartoons
> undo
[Repeated 1 time(s)]
> show sel cartoons
> select #5/B:409-900
739 atoms, 750 bonds, 95 residues, 1 model selected
> color sel light blue
[Repeated 1 time(s)]
> select add #5
8584 atoms, 7932 bonds, 5 pseudobonds, 1816 residues, 2 models selected
> select subtract #5
Nothing selected
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #8 models
> hide #!5 models
> show #!5 models
> select
> ::name="01A"::name="8LE"::name="AMP"::name="BCO"::name="CL"::name="COA"::name="EDO"::name="HOH"::name="MG"::name="NO3"::name="PRX"
3954 atoms, 993 bonds, 11 pseudobonds, 3038 residues, 8 models selected
> select add #1
7702 atoms, 4837 bonds, 12 pseudobonds, 3515 residues, 10 models selected
> select add #2
14712 atoms, 12039 bonds, 16 pseudobonds, 4405 residues, 12 models selected
> select subtract #1
10700 atoms, 8089 bonds, 15 pseudobonds, 3761 residues, 9 models selected
> select subtract #2
3199 atoms, 675 bonds, 11 pseudobonds, 2574 residues, 6 models selected
> select add #2
10700 atoms, 8089 bonds, 15 pseudobonds, 3761 residues, 9 models selected
> select add #3
20516 atoms, 18166 bonds, 23 pseudobonds, 5033 residues, 11 models selected
> select subtract #3
9679 atoms, 7918 bonds, 9 pseudobonds, 2899 residues, 7 models selected
> select subtract #2
2178 atoms, 504 bonds, 5 pseudobonds, 1712 residues, 4 models selected
> select add #2
9679 atoms, 7918 bonds, 9 pseudobonds, 2899 residues, 7 models selected
> select subtract #2
2178 atoms, 504 bonds, 5 pseudobonds, 1712 residues, 4 models selected
> select add #4
10403 atoms, 8923 bonds, 5 pseudobonds, 2778 residues, 4 models selected
> select subtract #4
1579 atoms, 344 bonds, 5 pseudobonds, 1261 residues, 3 models selected
> select add #9
9804 atoms, 8763 bonds, 5 pseudobonds, 2327 residues, 3 models selected
> select subtract #9
980 atoms, 184 bonds, 5 pseudobonds, 810 residues, 2 models selected
> show sel atoms
> select ::name="HOH"
2998 atoms, 2998 residues, 6 models selected
> hide sel & #!5 atoms
> select #5/A
4261 atoms, 3953 bonds, 4 pseudobonds, 890 residues, 2 models selected
> hide sel atoms
> select add #5
8584 atoms, 7932 bonds, 5 pseudobonds, 1816 residues, 2 models selected
> select subtract #5
Nothing selected
> show #8 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #8 models
> show #!5 models
> select ::name="COA"
240 atoms, 250 bonds, 5 residues, 3 models selected
> select ::name="8LE"
87 atoms, 93 bonds, 3 residues, 2 models selected
> select ::name="PRX"
52 atoms, 56 bonds, 2 residues, 1 model selected
> select ::name="01A"
116 atoms, 122 bonds, 2 residues, 1 model selected
> select sel :< 5
2861 atoms, 2743 bonds, 5 pseudobonds, 398 residues, 9 models selected
> show sel & #!5 atoms
> select ::name="HOH"
2998 atoms, 2998 residues, 6 models selected
> hide sel & #!5 atoms
> color sel & #!5 byhetero
[Repeated 1 time(s)]
> select clear
> color #!5 byhetero
> hide #!5 models
> show #!5 models
> show #7 models
> hide #7 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #7 models
> hide #7 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #7 models
> hide #7 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #8 models
> select ::name="01A"
116 atoms, 122 bonds, 2 residues, 1 model selected
> select ~sel & ##selected
8468 atoms, 7810 bonds, 5 pseudobonds, 1814 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select add #5
8584 atoms, 7932 bonds, 5 pseudobonds, 1816 residues, 2 models selected
> select subtract #5
Nothing selected
> undo
[Repeated 3 time(s)]
> select add #5
8584 atoms, 7932 bonds, 5 pseudobonds, 1816 residues, 2 models selected
> select subtract #5
Nothing selected
> hide #!5 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #!5 models
> hide #!5 models
> show #9 models
> hide #8 models
> show #8 models
> show #!1 models
> hide #8 models
> hide #9 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #8 models
> hide #8 models
> show #!2 models
> hide #!1 models
> select
> ::name="01A"::name="8LE"::name="AMP"::name="BCO"::name="CL"::name="COA"::name="EDO"::name="HOH"::name="MG"::name="NO3"::name="PRX"
3954 atoms, 993 bonds, 11 pseudobonds, 3038 residues, 8 models selected
> color (#!2 & sel) byelement
> select clear
> show #!1 models
> hide #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #2/A #2/B
Alignment identifier is 1
> select #1/A:158 #2/A-B:158
15 atoms, 12 bonds, 3 residues, 2 models selected
> select #1/A:158-159 #2/A-B:158-159
30 atoms, 27 bonds, 6 residues, 2 models selected
2-Hydroxyisobutyryl-Coa Synthetase [ID: 1] region 3 chains [169-170] RMSD:
0.246
> select add #2
7511 atoms, 7423 bonds, 4 pseudobonds, 1189 residues, 4 models selected
> select subtract #2
10 atoms, 9 bonds, 2 residues, 1 model selected
> select add #1
4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> show #!1 models
> show #8 models
> select #8/A:
Expected an objects specifier or a keyword
> select #8/A:269
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/A:159 #2/A-B:159
15 atoms, 12 bonds, 3 residues, 2 models selected
> select #1/A:159 #2/A-B:159
15 atoms, 12 bonds, 3 residues, 2 models selected
2-Hydroxyisobutyryl-Coa Synthetase [ID: 1] region 3 chains [170] RMSD: 0.235
> select #8/A:269#1/A:159
11 atoms, 9 bonds, 2 residues, 2 models selected
> select #8/A:323#1/A:159
12 atoms, 11 bonds, 2 residues, 2 models selected
> select #8/A:268#1/A:159
15 atoms, 14 bonds, 2 residues, 2 models selected
> select #8/A:124
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> open /Users/mk16/works/acyl-CoA_synthetase/acyl-
> CoA_synthetase_homolog/mustang/2-HIBA_FATP2/results.afasta
Summary of feedback from opening /Users/mk16/works/acyl-CoA_synthetase/acyl-
CoA_synthetase_homolog/mustang/2-HIBA_FATP2/results.afasta
---
notes | Alignment identifier is results.afasta
Associated 6he0_Thioesterification_2-HIB-AMP_CoA.pdb chain A to
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb with 18 mismatches
Associated 6he2_openConformatin_2-HIB-AMP_CoA.pdb chain A to
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb with 18 mismatches
Associated 6he2_openConformatin_2-HIB-AMP_CoA.pdb chain B to
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb with 18 mismatches
Associated fold_fatp2_model_0.cif chain A to AF-O14975-F1-model_v4_FATP2.pdb
with 0 mismatches
Associated AF-O14975-F1-model_v4_FATP2.pdb chain A to
AF-O14975-F1-model_v4_FATP2.pdb with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment results.afasta
Opened 2 sequences from results.afasta
> select #1/A:24-25 #2/A-B:24-25
54 atoms, 57 bonds, 6 residues, 2 models selected
> select #1/A:24-29 #2/A-B:24-29
168 atoms, 171 bonds, 18 residues, 2 models selected
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb [41-46] RMSD: 0.157
> select #7/A:20 #8/A:20
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #7/A:20 #8/A:20
16 atoms, 14 bonds, 2 residues, 2 models selected
Results.afasta [ID: results.afasta] region AF-O14975-F1-model_v4_FATP2.pdb
[45] RMSD: 2.166
> select #1/A:27 #2/A-B:27
33 atoms, 30 bonds, 3 residues, 2 models selected
> select #1/A:27-28 #2/A-B:27-28
60 atoms, 57 bonds, 6 residues, 2 models selected
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb [44-45] RMSD: 0.083
> select #1/A:-1 #2/A-B:-1
18 atoms, 15 bonds, 3 residues, 2 models selected
> select #1/A:-1-12 #2/A-B:-1-12
363 atoms, 375 bonds, 42 residues, 2 models selected
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb [1-14] RMSD: 0.157
> select #1/A:46 #2/A-B:46
21 atoms, 18 bonds, 3 residues, 2 models selected
> select #1/A:46 #2/A-B:46 #7/A:43 #8/A:43
35 atoms, 30 bonds, 5 residues, 4 models selected
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-
AMP_CoA.pdb..AF-O14975-F1-model_v4_FATP2.pdb [68] RMSD: 11.142
> select #1/A:104 #2/A-B:104
18 atoms, 15 bonds, 3 residues, 2 models selected
> select #1/A:104 #2/A-B:104
18 atoms, 15 bonds, 3 residues, 2 models selected
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb [126] RMSD: 0.289
> select clear
[Repeated 1 time(s)]
> select #1/A:133 #2/A-B:133
42 atoms, 45 bonds, 3 residues, 2 models selected
> select #1/A:133 #2/A-B:133
42 atoms, 45 bonds, 3 residues, 2 models selected
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb [160] RMSD: 0.119
> select #1/A:304-305 #2/A-B:304-305
66 atoms, 63 bonds, 6 residues, 2 models selected
> select #1/A:304-306 #2/A-B:304-306
87 atoms, 84 bonds, 9 residues, 2 models selected
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb [508-510] RMSD: 0.269
> select #1/A:227 #2/A-B:227
24 atoms, 21 bonds, 3 residues, 2 models selected
> select #1/A:227-233 #2/A-B:227-233
171 atoms, 174 bonds, 21 residues, 2 models selected
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb [411-417] RMSD: 0.413
> sequence header results.afasta consensus show
Showing consensus header ("seq_consensus" residue attribute) for alignment
results.afasta
> undo
> sequence refseq results.afasta:extracted_6he0_Thioesterification_2-HIBA-
> AMP_CoA.pdb
> select #1/A:154 #2/A:154 #2/B:154 #7/A:105 #8/A:105
40 atoms, 35 bonds, 5 residues, 4 models selected
> select #1/A:155 #2/A:155 #2/B:155 #7/A:106 #8/A:106
33 atoms, 28 bonds, 5 residues, 4 models selected
> select #1/A:158 #2/A-B:158
15 atoms, 12 bonds, 3 residues, 2 models selected
> select #1/A:158 #2/A-B:158
15 atoms, 12 bonds, 3 residues, 2 models selected
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb [186] RMSD: 0.256
> select #1/A:159-160 #2/A-B:159-160
36 atoms, 33 bonds, 6 residues, 2 models selected
> select #1/A:159 #2/A-B:159
15 atoms, 12 bonds, 3 residues, 2 models selected
> select #1/A:159 #2/A-B:159
15 atoms, 12 bonds, 3 residues, 2 models selected
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb [187] RMSD: 0.235
> select #1/A:159 #2/A-B:159
15 atoms, 12 bonds, 3 residues, 2 models selected
> select #1/A:159 #2/A-B:159 #7/A:110 #8/A:110
31 atoms, 26 bonds, 5 residues, 4 models selected
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-
AMP_CoA.pdb..AF-O14975-F1-model_v4_FATP2.pdb [187] RMSD: 12.926
> select #1/A:159 #2/A-B:159
15 atoms, 12 bonds, 3 residues, 2 models selected
> select #1/A:159 #2/A-B:159 #7/A:110 #8/A:110
31 atoms, 26 bonds, 5 residues, 4 models selected
Results.afasta [ID: results.afasta] region
extracted_6he0_Thioesterification_2-HIBA-
AMP_CoA.pdb..AF-O14975-F1-model_v4_FATP2.pdb [187] RMSD: 12.926
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #7/A #8/A
Alignment identifier is 2
> select #7/A:264 #8/A:264
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #7/A:264 #8/A:264
16 atoms, 14 bonds, 2 residues, 2 models selected
. [ID: 2] region 2 chains [264] RMSD: 1.127
> select #1/A:159 #2/A-B:159
15 atoms, 12 bonds, 3 residues, 2 models selected
> open /Users/mk16/works/acyl-CoA_synthetase/acyl-
> CoA_synthetase_homolog/mustang/2-HIBA_FATP2/results.pdb
Summary of feedback from opening /Users/mk16/works/acyl-CoA_synthetase/acyl-
CoA_synthetase_homolog/mustang/2-HIBA_FATP2/results.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Produced by MUSTANG v3.2.4
Ignored bad PDB record found on line 2
REMARK Authors: A S Konagurthu, J C Whisstock, P J Stuckey, and A M Lesk
Ignored bad PDB record found on line 4
REMARK Structures: extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb
AF-O14975-F1-model_v4_FATP2.pdb
Ignored bad PDB record found on line 6
REMARK All structures were superposed on the coordinate frame of:
extracted_6he0_Thioesterification_2-HIBA-AMP_CoA.pdb
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
3759 messages similar to the above omitted
Ignored bad PDB record found on line 8733
Chain information for results.pdb #10
---
Chain | Description
A | No description available
B | No description available
16 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> hide #!1 models
> select add #1
4022 atoms, 3958 bonds, 1 pseudobond, 646 residues, 4 models selected
> select subtract #1
10 atoms, 8 bonds, 2 residues, 1 model selected
> select add #2
7501 atoms, 7414 bonds, 4 pseudobonds, 1187 residues, 3 models selected
> select subtract #2
Nothing selected
> hide #8 models
> select add #10
8706 atoms, 8917 bonds, 1 pseudobond, 1097 residues, 2 models selected
> rainbow sel
> select subtract #10
Nothing selected
> select add #10
8706 atoms, 8917 bonds, 1 pseudobond, 1097 residues, 2 models selected
> close #10
> ui tool show Matchmaker
> matchmaker #8 to #1 showAlignment true
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8), sequence alignment score =
189.9
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: 6he0_Thioesterification_2-HIB-
AMP_CoA.pdb #1/A, AF-O14975-F1-model_v4_FATP2.pdb #8/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 73 pruned atom pairs is 1.213 angstroms; (across all 410 pairs:
19.742)
> show #8 models
> show #!1 models
> sequence refseq "3:6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A"
> select #1/A:159
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:159
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #8/A:264
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:264
8 atoms, 7 bonds, 1 residue, 1 model selected
> save /Users/mk16/works/acyl-CoA_synthetase/acyl-
> CoA_synthetase_homolog/2-HIBA_FATP2_matchmaker.aln.fa format fasta alignment
> 3
> select #1/A:173
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:173-174
9 atoms, 8 bonds, 2 residues, 1 model selected
> select #1/A:181
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:181
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:186
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/A:186
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #8/A:292
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/A:186 #8/A:292
16 atoms, 15 bonds, 2 residues, 2 models selected
MatchMaker Alignment [ID: 3] region 6he0_Thioesterification_2-HIB-AMP_CoA.pdb,
chain A..AF-O14975-F1-model_v4_FATP2.pdb, chain A [318] RMSD: 3.521
> select #1/A:165-166
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #1/A:165-169
36 atoms, 37 bonds, 5 residues, 1 model selected
> select #1/A:199-202 #8/A:299-302
64 atoms, 62 bonds, 8 residues, 2 models selected
> select #1/A:199-203 #8/A:299-304
94 atoms, 93 bonds, 11 residues, 2 models selected
MatchMaker Alignment [ID: 3] region 6he0_Thioesterification_2-HIB-AMP_CoA.pdb,
chain A..AF-O14975-F1-model_v4_FATP2.pdb, chain A [331-336] RMSD: 5.198
> select #1/A:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:197-201 #8/A:297-301
93 atoms, 96 bonds, 10 residues, 2 models selected
MatchMaker Alignment [ID: 3] region 6he0_Thioesterification_2-HIB-AMP_CoA.pdb,
chain A..AF-O14975-F1-model_v4_FATP2.pdb, chain A [329-333] RMSD: 5.871
> select #1/A:196-197
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #1/A:196-200
46 atoms, 47 bonds, 5 residues, 1 model selected
> select #1/A:152
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:152
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:166
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:166
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:190
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:190
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/A:296
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:190 #8/A:296
13 atoms, 11 bonds, 2 residues, 2 models selected
MatchMaker Alignment [ID: 3] region 6he0_Thioesterification_2-HIB-AMP_CoA.pdb,
chain A..AF-O14975-F1-model_v4_FATP2.pdb, chain A [322] RMSD: 8.166
> select #1/A:190
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:190 #8/A:296
13 atoms, 11 bonds, 2 residues, 2 models selected
MatchMaker Alignment [ID: 3] region 6he0_Thioesterification_2-HIB-AMP_CoA.pdb,
chain A..AF-O14975-F1-model_v4_FATP2.pdb, chain A [322] RMSD: 8.166
> show sel atoms
> undo
> select add #1
4021 atoms, 3958 bonds, 1 pseudobond, 645 residues, 4 models selected
> select subtract #1
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #!1 models
> select add #8
4958 atoms, 5073 bonds, 620 residues, 1 model selected
> select subtract #8
Nothing selected
> show #!1 models
> select ::name="01A"
116 atoms, 122 bonds, 2 residues, 1 model selected
> select ::name="COA"
240 atoms, 250 bonds, 5 residues, 3 models selected
> select ~sel & ##selected
22110 atoms, 21362 bonds, 19 pseudobonds, 3960 residues, 7 models selected
> hide sel & #!1 atoms
> hide sel & #!1 cartoons
> select add #1
22158 atoms, 21412 bonds, 19 pseudobonds, 3961 residues, 8 models selected
> select subtract #1
18146 atoms, 17462 bonds, 18 pseudobonds, 3317 residues, 5 models selected
> select add #2
18242 atoms, 17562 bonds, 18 pseudobonds, 3319 residues, 6 models selected
> select subtract #2
10741 atoms, 10148 bonds, 14 pseudobonds, 2132 residues, 3 models selected
> select add #3
10837 atoms, 10248 bonds, 14 pseudobonds, 2134 residues, 4 models selected
> select subtract #3
Nothing selected
> hide #!1 models
> show #!1 models
> close #9
> open /Users/mk16/works/acyl-
> CoA_synthetase/Aquincola_tertiaricarbonis/6he0_Thioesterification_2-HIB-
> AMP_CoA.pdb
6he0_Thioesterification_2-HIB-AMP_CoA.pdb title:
Crystal structure of 2-hydroxyisobutyryl-coa ligase (HCL) In complex with
2-hib-amp and coa In the thioesterfication state [more info...]
Chain information for 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9
---
Chain | Description | UniProt
A | 2-hydroxyisobutyryl-coa synthetase | I3VE75_9BURK 1-477
Non-standard residues in 6he0_Thioesterification_2-HIB-AMP_CoA.pdb #9
---
8LE —
[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-
oxidanyl-phosphoryl]2-methyl-2-oxidanyl-propanoate
AMP — adenosine monophosphate
COA — coenzyme A
116 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> matchmaker #4,6-8#!2-3,5,9 to #1 showAlignment true
Computing secondary structure
[Repeated 8 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3eq6_ACSM2A_bCoA_AMP.pdb, chain B (#4), sequence alignment score = 290.3
RMSD between 84 pruned atom pairs is 1.140 angstroms; (across all 418 pairs:
18.347)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_acsl4_model_0.cif, chain A (#6), sequence alignment score = 181.7
RMSD between 80 pruned atom pairs is 1.286 angstroms; (across all 430 pairs:
23.367)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
fold_fatp2_model_0.cif, chain A (#7), sequence alignment score = 179.1
RMSD between 56 pruned atom pairs is 1.119 angstroms; (across all 410 pairs:
23.522)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
AF-O14975-F1-model_v4_FATP2.pdb, chain A (#8), sequence alignment score =
189.9
RMSD between 73 pruned atom pairs is 1.213 angstroms; (across all 410 pairs:
19.742)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
6he2_openConformatin_2-HIB-AMP_CoA.pdb, chain A (#2), sequence alignment score
= 2511
RMSD between 355 pruned atom pairs is 0.323 angstroms; (across all 456 pairs:
14.640)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
1pg4_AcetylCoASynthetase_Salmonella.pdb, chain A (#3), sequence alignment
score = 279.5
RMSD between 81 pruned atom pairs is 1.236 angstroms; (across all 444 pairs:
18.441)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
3cw9_Alcaligenes_ChlorobenzoylCoA.pdb, chain B (#5), sequence alignment score
= 323.5
RMSD between 64 pruned atom pairs is 1.175 angstroms; (across all 400 pairs:
15.376)
Matchmaker 6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#1) with
6he0_Thioesterification_2-HIB-AMP_CoA.pdb, chain A (#9), sequence alignment
score = 2593.8
RMSD between 477 pruned atom pairs is 0.000 angstroms; (across all 477 pairs:
0.000)
> ui mousemode right "move picked models"
> view matrix models
> #9,0.78064,-0.60853,-0.14245,-13.659,0.51267,0.75386,-0.41094,-55.023,0.35745,0.24776,0.90047,-84.152
> select add #9
4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected
> color (#!9 & sel) light gray
> select
> ::name="01A"::name="8LE"::name="AMP"::name="BCO"::name="CL"::name="COA"::name="EDO"::name="HOH"::name="MG"::name="NO3"::name="PRX"
3619 atoms, 939 bonds, 11 pseudobonds, 2754 residues, 8 models selected
> color (#!1,9 & sel) byelement
> style sel & #!1,9 ball
Changed 528 atom styles
> select ::name="HOH"
2715 atoms, 2715 residues, 6 models selected
> hide sel & #!1,9 atoms
> select clear
> color #8#!1,9 byhetero
> select #8/A:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/A
4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 2 models selected
> select #9/A:159,160,164,186,190,192,193,210,213,216,366,399,437,438
110 atoms, 102 bonds, 14 residues, 1 model selected
> color sel forest green
> color sel byhetero
> select add #9
4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected
> select subtract #9
Nothing selected
> select #9/A:360-900
902 atoms, 911 bonds, 1 pseudobond, 116 residues, 2 models selected
> rainbow sel
> select #9/A:159,160,164,186,190,192,193,210,213,216,366,399,437,438
110 atoms, 102 bonds, 14 residues, 1 model selected
> color sel forest green
> color sel byhetero
> select add #9
4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected
> select subtract #9
Nothing selected
> select #8/A:482-900
1119 atoms, 1144 bonds, 139 residues, 1 model selected
> rainbow sel
> color sel byhetero
> select add #8
4958 atoms, 5073 bonds, 620 residues, 1 model selected
> select subtract #8
Nothing selected
> view matrix models
> #8,1,-1.1256e-15,6.5835e-16,0.24975,1.1256e-15,1,-5.5169e-16,-1.821,-6.5835e-16,5.5169e-16,1,-0.7586
> undo
> ui mousemode right select
Drag select of 1 bonds, 1 atoms
Drag select of 1 atoms
Drag select of 2 residues
> select clear
[Repeated 1 time(s)]Drag select of 1 atoms
> select sel :< 5
415 atoms, 415 bonds, 35 residues, 8 models selected
> show sel & #8#!1 atoms
> undo
> select add #8
5356 atoms, 5471 bonds, 653 residues, 8 models selected
> select subtract #8
398 atoms, 398 bonds, 33 residues, 7 models selected
> undo
[Repeated 1 time(s)]
> select add #1
4361 atoms, 4300 bonds, 1 pseudobond, 674 residues, 10 models selected
> select subtract #1
349 atoms, 350 bonds, 30 residues, 7 models selected
> select add #2
7768 atoms, 7683 bonds, 4 pseudobonds, 1209 residues, 9 models selected
> select subtract #2
267 atoms, 269 bonds, 22 residues, 6 models selected
> select add #3
11070 atoms, 10484 bonds, 14 pseudobonds, 2152 residues, 9 models selected
> select subtract #3
233 atoms, 236 bonds, 18 residues, 5 models selected
> select add #4
8973 atoms, 8728 bonds, 1530 residues, 5 models selected
> select subtract #4
149 atoms, 149 bonds, 13 residues, 4 models selected
> select add #5
8644 atoms, 7990 bonds, 5 pseudobonds, 1823 residues, 5 models selected
> select subtract #5
60 atoms, 58 bonds, 7 residues, 3 models selected
> select add #6
5581 atoms, 5695 bonds, 714 residues, 3 models selected
> select subtract #6
28 atoms, 28 bonds, 3 residues, 2 models selected
> select add #7
4975 atoms, 5090 bonds, 622 residues, 2 models selected
> select subtract #7
17 atoms, 17 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select add #8
4958 atoms, 5073 bonds, 620 residues, 1 model selected
> select subtract #8
Nothing selected
> select clear
> ui mousemode right translate
> ui tool show Matchmaker
> select #8/A
4958 atoms, 5073 bonds, 620 residues, 1 model selected
> show sel atoms
> select clear
> select #9/A:
Expected an objects specifier or a keyword
> select #9/A
4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 2 models selected
> select #9/A:190,192,193,216
25 atoms, 23 bonds, 4 residues, 1 model selected
> color sel byhetero
> select #9/A:159
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #9/A:159,160,210
19 atoms, 17 bonds, 3 residues, 1 model selected
> show sel atoms
> hide #!1 models
> hide #8 models
> show #8 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> show #!1 models
> hide #!9 models
> select add #9
4012 atoms, 3950 bonds, 1 pseudobond, 644 residues, 3 models selected
> select subtract #9
Nothing selected
> select add #8
4958 atoms, 5073 bonds, 620 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 4958 atom styles
> style sel ball
Changed 4958 atom styles
> undo
[Repeated 1 time(s)]
> select subtract #8
Nothing selected
> select add #8
4958 atoms, 5073 bonds, 620 residues, 1 model selected
> select add #1
8970 atoms, 9023 bonds, 1 pseudobond, 1264 residues, 4 models selected
> select clear
> open /Users/mk16/Desktop/2pv7_model.cif
Summary of feedback from opening /Users/mk16/Desktop/2pv7_model.cif
---
note | Fetching CCD COA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/COA/COA.cif
Chain information for 2pv7_model.cif #10
---
Chain | Description
A B | .
No chain in structure corresponds to chain ID given in local score info (chain
'C')
Computing secondary structure
> open /Users/mk16/Desktop/2pv7_model.cif
Chain information for 2pv7_model.cif #11
---
Chain | Description
A B | .
No chain in structure corresponds to chain ID given in local score info (chain
'C')
Computing secondary structure
> close #11
> hide #8 models
> hide #!1 models
> close #10
> show #!1 models
> show #8 models
> show #!9 models
> save /Users/mk16/Desktop/220250214.cxs
——— End of log from Fri Feb 14 11:22:12 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: MRX43J/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 11881.81.2
OS Loader Version: 11881.81.2
Software:
System Software Overview:
System Version: macOS 15.3 (24D60)
Kernel Version: Darwin 24.3.0
Time since boot: 9日 6時間 36分
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Studio Display:
Display Type: Retina LCD
Resolution: 5120 x 2880 Retina
Display Serial Number: KCR2L4HL0M
Display Firmware Version: Version 17.0 (Build 21A329)
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 8 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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