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Opened 2 hours ago
#19939 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.3-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000000017a8ab000 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 331 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 629 in wait
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1399 in run
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1045 in _bootstrap_inner
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1002 in _bootstrap
Current thread 0x0000000208dbb080 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 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, PIL._imaging, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, 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, PIL._imagingmath (total: 56)
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"procLaunch" : "2026-03-05 09:44:52.5025 -0500",
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"appleIntelligenceStatus" : {"state":"available"},
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"bootProgressRegister" : "0x2f000000",
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"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
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"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"sleepWakeUUID" : "1E992554-33EE-4DDB-BCD6-7C3A85333358",
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"vmRegionInfo" : "0x8 is not in any region. Bytes before following region: 4362649592
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 10408c000-104090000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":49220},
"vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4362649592
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
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"path" : "\/Applications\/ChimeraX-1.11.1.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"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5311086592,
"size" : 376832,
"uuid" : "5d18d096-20ff-384b-84fb-bd6d8f5aaf40",
"path" : "\/Applications\/ChimeraX-1.11.1.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"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5309775872,
"size" : 180224,
"uuid" : "8e2ee74d-d576-3b31-9afa-bcb515675310",
"path" : "\/Applications\/ChimeraX-1.11.1.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"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5635325952,
"size" : 3768320,
"uuid" : "06082bf4-58c8-3f16-9f71-841cf9880fbe",
"path" : "\/Applications\/ChimeraX-1.11.1.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"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5310087168,
"size" : 131072,
"uuid" : "63b5bd02-9626-3588-a39c-88d4f882312b",
"path" : "\/Applications\/ChimeraX-1.11.1.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"
},
{
"source" : "P",
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"base" : 5176475648,
"size" : 32768,
"uuid" : "7c43df7b-5e3e-3a91-9bc6-b8f9ebd02ec2",
"path" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so",
"name" : "_imagingmath.cpython-311-darwin.so"
},
{
"source" : "P",
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"base" : 6923730944,
"size" : 246944,
"uuid" : "b809799c-0ec9-3ee1-b730-342bdbf14e03",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6923980800,
"size" : 51916,
"uuid" : "0596a7b6-bce2-3f06-a2e8-3eaab5371ed8",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6922481664,
"size" : 532552,
"uuid" : "eb569350-0696-3397-838e-0344948107c0",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6924034048,
"size" : 33968,
"uuid" : "62c9cd37-272d-3d2d-9a1c-6f4ef24f7ec7",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6924267520,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5542592,
"uuid" : "02762698-9950-3c66-8116-a3a565972a49",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "4302"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6949769216,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 16399392,
"uuid" : "d17ba2e6-fab3-33ad-9f98-d4e65847ea65",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "4302"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6995931136,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 24296416,
"uuid" : "07dcc67f-25b2-3f2c-b92e-6fc579455989",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2685.40.108"
},
{
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"size" : 653076,
"uuid" : "bc4db5f4-1c64-3706-8006-73b78c3e1f1a",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
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"uuid" : "00000000-0000-0000-0000-000000000000"
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"CFBundleShortVersionString" : "10",
"CFBundleIdentifier" : "com.apple.ScreenReaderCore",
"size" : 398496,
"uuid" : "a643bf2a-6d39-331d-a7d7-3eb9db28b12b",
"path" : "\/System\/Library\/PrivateFrameworks\/ScreenReaderCore.framework\/Versions\/A\/ScreenReaderCore",
"name" : "ScreenReaderCore",
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}
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},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)
Writable regions: Total=907.6M written=1301K(0%) resident=1301K(0%) swapped_out=0K(0%) unallocated=906.3M(100%)
VIRTUAL REGION
REGION TYPE SIZE COUNT (non-coalesced)
=========== ======= =======
.note.gnu.proper 320 1
Accelerate framework 128K 1
Activity Tracing 256K 1
AttributeGraph Data 1024K 1
CG image 1120K 8
ColorSync 96K 6
CoreAnimation 3920K 126
CoreGraphics 96K 6
CoreServices 624K 2
CoreUI image data 5344K 40
Foundation 16K 1
Kernel Alloc Once 32K 1
MALLOC 337.1M 149
MALLOC guard page 4096K 4
Mach message 64K 3
OpenGL GLSL 256K 3
PROTECTED_MEMORY 16K 1
STACK GUARD 688K 43
Stack 226.0M 44
Stack Guard 56.0M 1
VM_ALLOCATE 268.5M 198
VM_ALLOCATE (reserved) 64.0M 2 reserved VM address space (unallocated)
__AUTH 5948K 654
__AUTH_CONST 90.4M 1040
__CTF 824 1
__DATA 42.8M 1131
__DATA_CONST 59.6M 1179
__DATA_DIRTY 8492K 898
__FONT_DATA 2352 1
__GLSLBUILTINS 5176K 1
__INFO_FILTER 8 1
__LINKEDIT 619.4M 135
__OBJC_RO 78.4M 1
__OBJC_RW 2571K 1
__TEXT 1.3G 1122
__TEXT (graphics) 241.0M 79
__TPRO_CONST 128K 2
dyld private memory 432K 5
mapped file 618.6M 73
page table in kernel 1301K 1
shared memory 3792K 33
=========== ======= =======
TOTAL 4.0G 7000
TOTAL, minus reserved VM space 3.9G 7000
",
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}
},
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===== Log before crash start =====
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/ae811/Downloads/MUT Phex_G575R_rotamers+clashes_active
> highlighted.cxs"
Log from Thu Mar 5 08:26:52 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/ae811/Downloads/WT Phex_active highlighted.cxs"
Log from Wed Mar 4 19:12:26 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/andreaseckhard/Downloads/PHEX_WT_colored +mutant sites.pdb"
Chain information for PHEX_WT_colored +mutant sites.pdb #1
---
Chain | Description
A | No description available
> set bgColor white
> hide atoms
> undo
> lighting soft
> lighting flat
> color #1 #cfd9dbff
> color #1 #dbdbd9ff
> color #1 #cecdccff
> color #1 lightgrey
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> select /A:642
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel purple
> color sel #fffffdff
> color sel #fffefdff
> color sel #fffcfdff
> color sel #fffbfdff
> color sel #fffafdff
> color sel #fff8fdff
> color sel #fff7fdff
> color sel #fff5fcff
> color sel #fff4fcff
> color sel #fff3fbff
> color sel #fff2fbff
> color sel #fff1fbff
> color sel #fff0fbff
> color sel #ffeffaff
> color sel #ffeefaff
[Repeated 1 time(s)]
> color sel #ffedfaff
> color sel #ffecfaff
[Repeated 1 time(s)]
> color sel #ffebf9ff
> color sel #ffeaf9ff
> color sel #ffe8f8ff
> color sel #ffe6f7ff
> color sel #ffe2f7ff
> color sel #ffddf7ff
> color sel #ffd9f7ff
> color sel #ffd6f6ff
> color sel #ffd4f6ff
> color sel #ffd3f6ff
> color sel #ffd2f5ff
> color sel #ffd1f5ff
> color sel #ffd0f5ff
[Repeated 1 time(s)]
> color sel #ffcff5ff
> color sel #ffcff6ff
> color sel #ffcef6ff
> color sel #ffcdf7ff
> color sel #ffcbf8ff
> color sel #ffc9f9ff
> color sel #ffc7fbff
> color sel #ffc5fcff
> color sel #ffc5feff
> color sel #fec6ffff
> color sel #fcc7ffff
> color sel #fac8ffff
> color sel #f9c9ffff
> color sel #f8c9ffff
[Repeated 1 time(s)]
> color sel #f8caffff
> color sel #f9caffff
[Repeated 1 time(s)]
> color sel #f8c7ffff
> color sel #f7c2ffff
> color sel #f7bdffff
> color sel #f8b8ffff
> color sel #f8b4ffff
> color sel #f8b1ffff
> color sel #f7adffff
> color sel #f7abffff
> color sel #f7a8ffff
> color sel #f7a6ffff
> color sel #f7a5ffff
> color sel #f8a5ffff
> color sel #f8a6ffff
> color sel #f9a8ffff
> color sel #f9aaffff
> color sel #faabffff
> color sel #fbadffff
[Repeated 1 time(s)]
> color sel #fbaeffff
> color sel #fcafffff
> color sel #fcb1ffff
> color sel #fcb1fffe
> color sel #fcb1fffc
> color sel #fcb1fff7
> color sel #fcb1ffd4
> color sel #fcb1ffd1
> color sel #fcb1ffce
> color sel #fcb1ffcc
> color sel #fcb1ffca
> color sel #fcb1ffc8
> color sel #fcb1ffc5
> color sel #fcb1ffc1
> color sel #fcb1ffbd
> color sel #fcb1ffba
> color sel #fcb1ffb7
> color sel #fcb1ffb5
> color sel #fcb1ffb4
> color sel #fcb1ffb3
> color sel #fcb1ffb1
> color sel #fcb1ffb0
> color sel #fcb1ffaf
> color sel #fcb1ffae
> color sel #fcb1ffaf
[Repeated 1 time(s)]
> color sel #fcb1ffb1
> color sel #fcb1ffb4
> color sel #fcb1ffbb
> color sel #fcb1ffc5
> color sel #fcb1ffd1
> color sel #fcb1ffe0
> color sel #fcb1fff0
> color sel #fcb1ffff
[Repeated 1 time(s)]
> color sel #fbb0feff
> color sel #f9affcff
> color sel #f6acf9ff
> color sel #f3aaf5ff
> color sel #f0a8f2ff
> color sel #eea6f0ff
> color sel #eca5eeff
> color sel #eba4edff
> color sel #eaa4edff
> color sel #e9a3ecff
> color sel #e9a3ebff
> color sel #e8a3ebff
> color sel #e8a2eaff
> color sel #e7a2eaff
> color sel #e7a2e9ff
> color sel #e6a1e9ff
> color sel #e5a1e8ff
> color sel #e5a0e7ff
> color sel #e4a0e7ff
> color sel #e39fe6ff
> color sel #e29ee4ff
> color sel #e19de3ff
> color sel #e09de2ff
> color sel #df9ce2ff
> color sel #df9ce1ff
> color sel #de9ce1ff
[Repeated 1 time(s)]
> color sel #de9be0ff
> color sel #dd9be0ff
> color sel #dc9adeff
> color sel #da99ddff
> color sel #d897daff
> color sel #d596d8ff
> color sel #d394d6ff
> color sel #d193d4ff
> color sel #d091d2ff
> color sel #cf91d1ff
> color sel #ce90d0ff
[Repeated 1 time(s)]
> color sel #cd90d0ff
[Repeated 1 time(s)]
> color sel #cd8fcfff
> color sel #cc8fceff
> color sel #cb8eceff
> color sel #ca8ecdff
> color sel #c98dccff
> color sel #c78ccaff
> color sel #c58ac8ff
> color sel #c388c5ff
> color sel #c086c2ff
> color sel #bd84bfff
> color sel #bb83bdff
> color sel #b982bbff
> color sel #b881baff
[Repeated 1 time(s)]
> color sel #b780b9ff
[Repeated 3 time(s)]
> color sel #b67fb8ff
> color sel #b47eb6ff
> color sel #b37db5ff
> color sel #b27db4ff
> color sel #b17cb3ff
> color sel #b07cb2ff
> color sel #b07bb2ff
[Repeated 1 time(s)]
> color sel #b17cb3ff
> color sel #b27db4ff
> color sel #b47eb6ff
> color sel #b67fb8ff
> color sel #b780b9ff
> color sel #b881baff
> lighting shadows false
> lighting shadows true
> lighting shadows false
> color sel #b881baff
> color sel #b982bbff
> color sel #bc84bfff
> color sel #bf86c1ff
> color sel #c288c5ff
> color sel #c58ac8ff
> color sel #c88ccaff
> color sel #ca8dccff
> color sel #cb8ecdff
[Repeated 1 time(s)]
> color sel #cc90cdff
> color sel #cc91cdff
[Repeated 1 time(s)]
> color sel #cb91cdff
> color sel #ca92cdff
> color sel #c893cdff
> color sel #c793cdff
> color sel #c694cdff
> color sel #c594cdff
> color sel #c493cdff
> color sel #c393cdff
[Repeated 1 time(s)]
> color sel #c293cdff
> color sel #c192cdff
> color sel #c092cdff
> color sel #bf92cdff
> color sel #be91cdff
[Repeated 1 time(s)]
> color sel #bd91cdff
> color sel #bc91cdff
> color sel #bb91cdff
> color sel #ba91cdff
> color sel #b990cdff
> color sel #b890cdff
[Repeated 1 time(s)]
> color sel #b78fcdff
> color sel #b68ecdff
> color sel #b58ecdff
> color sel #b48dcdff
[Repeated 2 time(s)]
> color sel #b58ccdff
> color sel #b68ccdff
[Repeated 1 time(s)]
> color sel #b78ccdff
> color sel #b88ccdff
> color sel #b98ccdff
> color sel #bb8ccdff
> color sel #bd8ccdff
> color sel #c08ccdff
> color sel #c28bcdff
> color sel #c48bcdff
> color sel #c68acdff
> color sel #c78acdff
> color sel #c889cdff
> color sel #c989cdff
[Repeated 1 time(s)]
> color sel #ca89cdff
> color sel #cc88cdff
> color sel #cd86ccff
> color sel #cd84c8ff
> color sel #cd82c4ff
> color sel #cd80bfff
> color sel #cd7fbcff
> color sel #cd7fb9ff
> color sel #cd7eb8ff
> color sel #cd7fb8ff
> color sel #cd7fb9ff
> color sel #cd81bbff
> color sel #cd82bdff
> color sel #cd83bfff
> color sel #cd84c1ff
> color sel #cd85c2ff
> color sel #cd86c3ff
> color sel #cd87c3ff
[Repeated 1 time(s)]
> color sel #cd88c4ff
> color sel #cd8ac4ff
> color sel #cd8cc4ff
> color sel #cd8dc5ff
> color sel #cd8fc5ff
> color sel #cd90c6ff
> color sel #cd91c6ff
> color sel #cd92c6ff
[Repeated 1 time(s)]
> color sel #cd93c6ff
> color sel #cd93c7ff
> color sel #cd94c7ff
> color sel #cd94c8ff
> color sel #cd95c8ff
> color sel #cd96c9ff
> color sel #cd96caff
> color sel #cd97caff
> color sel #cd98caff
[Repeated 3 time(s)]
> color sel #cd97caff
> color sel #cd97cbff
> color sel #cd97caff
> color sel #c993c6ff
> color sel #c18ebfff
> color sel #be8bbbff
> color sel #bb89b8ff
> color sel #b887b6ff
> color sel #b686b4ff
> color sel #b484b2ff
> color sel #b283b0ff
> color sel #b182aeff
> color sel #af81adff
> color sel #ae80acff
> color sel #ad7fabff
> color sel #ad7faaff
> color sel #ac7ea9ff
> color sel #ab7da8ff
> color sel #aa7da8ff
> color sel #aa7ca7ff
> color sel #a97ca7ff
> color sel #a97ca6ff
> color sel #a87ba6ff
> color sel #a478a2ff
> color sel #9a7198ff
> color sel #956e93ff
> color sel #926b90ff
> color sel #906a8eff
> color sel #8f698dff
[Repeated 3 time(s)]
> color sel #916a8fff
> color sel #976f95ff
> color sel #9b7198ff
> color sel #9e749cff
> color sel #a1769eff
> color sel #a277a0ff
> color sel #a478a2ff
> color sel #a479a2ff
> color sel #a579a3ff
> color sel #a67aa4ff
> color sel #a77ba5ff
> color sel #a97ca7ff
> color sel #aa7da8ff
> color sel #ae80abff
> color sel #af81adff
> color sel #b081aeff
> color sel #b182afff
> color sel #b282afff
[Repeated 2 time(s)]
> color sel #b182afff
> color sel #b182aeff
[Repeated 1 time(s)]
> color sel #b081aeff
[Repeated 1 time(s)]
> select clear
> select /A:580
17 atoms, 17 bonds, 1 residue, 1 model selected
> color sel #b081aeff
> select clear
> select /A:582
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select clear
> select /A:584
17 atoms, 17 bonds, 1 residue, 1 model selected
> color sel #b081aeff
> select clear
> select @@serial_number=12156
1 atom, 1 residue, 1 model selected
> color sel #b081aeff
> hide #1.1 models
> select /A:584@NE2
1 atom, 1 residue, 1 model selected
> select add @@serial_number=12156
2 atoms, 2 residues, 1 model selected
> distance sel
Distance between /A HIS 584 NE2 and ZN2 701 ZN+2: 2.168Å
> ui tool show Distances
> select clear
> select /A:642@OE2
1 atom, 1 residue, 1 model selected
> select @@serial_number=12156
1 atom, 1 residue, 1 model selected
> select add /A:642@OE2
2 atoms, 2 residues, 1 model selected
> distance sel
Distance between /A ZN2 701 ZN+2 and GLU 642 OE2: 1.902Å
> select clear
> select /A:580@NE2
1 atom, 1 residue, 1 model selected
> select add @@serial_number=12156
2 atoms, 2 residues, 1 model selected
> distance sel
Distance between /A HIS 580 NE2 and ZN2 701 ZN+2: 2.071Å
> select clear
> select /A:581
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #b085adff
[Repeated 1 time(s)]
> color sel #b084adff
> color sel #b083aeff
> color sel #b082aeff
> color sel #b081afff
[Repeated 1 time(s)]
> color sel #b080afff
> color sel #b07fb0ff
> color sel #b07db0ff
> color sel #b07bb0ff
> color sel #b07ab0ff
> color sel #af79b0ff
> color sel #af78b0ff
> color sel #ae76b0ff
> color sel #ae75b0ff
> color sel #ad73b0ff
> color sel #ac72b0ff
> color sel #ac71b0ff
> color sel #ab70b0ff
> color sel #ab6fb0ff
> color sel #aa6eb0ff
> color sel #a96cb0ff
> color sel #a96bb0ff
> color sel #a86ab0ff
> color sel #a469b0ff
> color sel #a268b0ff
> color sel #a068b0ff
> color sel #9e67b0ff
> color sel #9968b0ff
> color sel #9466b0ff
> color sel #8f66b0ff
> color sel #8c65b0ff
> color sel #8965b0ff
> color sel #8765b0ff
[Repeated 1 time(s)]
> color sel #8665b0ff
> color sel #8565b0ff
> color sel #8465b0ff
[Repeated 1 time(s)]
> color sel #8365b0ff
> color sel #8265b0ff
> color sel #8367b0ff
> color sel #856ab0ff
> color sel #866db0ff
> color sel #8870b0ff
> color sel #8972b0ff
> color sel #8a73b0ff
> color sel #8a74b0ff
[Repeated 1 time(s)]
> color sel #8974b0ff
> color sel #8873b0ff
> color sel #8672b0ff
> label delete pseudobonds
> color #2 #fed6ffff models
> color #2 #f6b0ffff models
> select clear
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting shadows true
> set bgColor gray
> set bgColor white
> save "/Users/andreaseckhard/Desktop/WT Phex_active highlighted.cxs"
——— End of log from Wed Mar 4 19:12:26 2026 ———
> view name session-start
opened ChimeraX session
> sequence chain #1/A
Alignment identifier is 1/A
> swapaa #1/A:575 Arg
Using Dunbrack library
/A GLY 575: phi -61.8, psi -41.7 trans
Applying ARG rotamer (chi angles: -179.4 64.9 178.1 175.7) to /A ARG 575
> select #1/A:575
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show Rotamers
Populating font family aliases took 106 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> swapaa interactive sel ARG rotLib Dunbrack
/A ARG 575: phi -61.8, psi -41.7 trans
Changed 600 bond radii
> color sel #ff8f81ff
> color sel #ff8c83ff
> color sel #ff8b83ff
> color sel #ff8b84ff
> color sel #ff8a84ff
> color sel #ff8884ff
> color sel #ff8784ff
> color sel #ff8684ff
[Repeated 1 time(s)]
> color sel #ff8583ff
> color sel #ff8483ff
> color sel #ff8383ff
> color sel #ff8382ff
> color sel #ff8281ff
> color sel #ff8180ff
[Repeated 1 time(s)]
> color sel #ff817fff
> color sel #ff807fff
[Repeated 3 time(s)]
> color sel #ff807eff
[Repeated 1 time(s)]
> color sel #ff807fff
> color sel #ff817fff
> color sel #ff8180ff
> color sel #ff8280ff
> color sel #ff8180ff
> color sel #fc807eff
> color sel #f37b7aff
> color sel #f07a79ff
> color sel #ef7978ff
> color sel #ee7978ff
[Repeated 2 time(s)]
> color sel #ec7877ff
> color sel #df7170ff
> color sel #de716fff
> color sel #de7170ff
[Repeated 1 time(s)]
> color sel #df7170ff
> color sel #e17271ff
[Repeated 2 time(s)]
> color sel #e27371ff
> color sel #e77574ff
> color sel #eb7776ff
[Repeated 1 time(s)]
> color sel #eb7876ff
> color sel #eb7676ff
> select clear
> select add #1.2.1/A:1@N
1 atom, 1 bond, 1 residue, 1 model selected
> select add #1.2.5/A:1@NH1
2 atoms, 13 bonds, 2 residues, 5 models selected
> select add #1.2.5/A:1@NH2
3 atoms, 13 bonds, 2 residues, 5 models selected
> select add #1.2.1/A:1@NH1
4 atoms, 17 bonds, 2 residues, 5 models selected
> select add #1.2.2/A:1@NH2
5 atoms, 19 bonds, 3 residues, 5 models selected
> select add #1.2.4/A:1@NH1
6 atoms, 20 bonds, 4 residues, 5 models selected
> select add #1.2.3/A:1@NH2
7 atoms, 20 bonds, 5 residues, 5 models selected
> select add #1.2.1/A:1@NH2
8 atoms, 20 bonds, 5 residues, 5 models selected
> select add #1.2.4/A:1@NH2
9 atoms, 20 bonds, 5 residues, 5 models selected
> select add #1.2.2/A:1@NH1
10 atoms, 23 bonds, 5 residues, 5 models selected
> select add #1.2.3/A:1@NH1
11 atoms, 24 bonds, 5 residues, 5 models selected
> color (#1.2.1-5 & sel) #eb7876ff
[Repeated 2 time(s)]
> color (#1.2.1-5 & sel) #ea7875ff
> color (#1.2.1-5 & sel) #ea7775ff
[Repeated 2 time(s)]
> color (#1.2.1-5 & sel) #e97775ff
[Repeated 1 time(s)]
> color (#1.2.1-5 & sel) #e97774ff
[Repeated 4 time(s)]
> color (#1.2.1-5 & sel) #e87774ff
> color (#1.2.1-5 & sel) #e97774ff
[Repeated 1 time(s)]
> color (#1.2.1-5 & sel) #e97775ff
[Repeated 1 time(s)]
> show sel atoms
> show sel cartoons
[Repeated 1 time(s)]
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> style sel stick
Changed 11 atom styles
> style sel sphere
Changed 11 atom styles
> style sel ball
Changed 11 atom styles
> style sel stick
Changed 11 atom styles
> show sel surfaces
> hide sel surfaces
> graphics silhouettes false
> graphics silhouettes true
> select clear
> select #!1/A:575
14 atoms, 13 bonds, 1 residue, 1 model selected
> clashes sel makePseudobonds true
2635 clashes
> select clear
[Repeated 1 time(s)]
> select add #1.2.2/A:1@NH1
1 atom, 4 bonds, 1 residue, 1 model selected
> select add #1.2.2/A:1@NH2
2 atoms, 4 bonds, 1 residue, 2 models selected
> select add #1.2.3/A:1@NH2
3 atoms, 5 bonds, 2 residues, 3 models selected
> select add #1.2.1/A:1@NH1
4 atoms, 5 bonds, 3 residues, 5 models selected
> select add #1.2.1/A:1@NH2
5 atoms, 6 bonds, 3 residues, 6 models selected
> select add #!1/A:655
29 atoms, 34 bonds, 4 residues, 9 models selected
> select subtract #!1/A:655
5 atoms, 11 bonds, 3 residues, 8 models selected
> select add #1.2.5/A:1@NH1
6 atoms, 11 bonds, 4 residues, 8 models selected
> select add #1.2.4/A:1@NH2
7 atoms, 11 bonds, 5 residues, 9 models selected
> select add #1.2.5/A:1@NH2
8 atoms, 12 bonds, 5 residues, 10 models selected
> select add #1.2.4/A:1@NH1
9 atoms, 13 bonds, 5 residues, 10 models selected
> select add #1.2.3/A:1@NH1
10 atoms, 22 bonds, 3 pseudobonds, 5 residues, 11 models selected
> clashes sel makePseudobonds true
66 clashes
> select add #!1/A:575@NH2
11 atoms, 22 bonds, 6 residues, 11 models selected
> select add #!1/A:575@NH1
12 atoms, 24 bonds, 6 residues, 11 models selected
> clashes sel makePseudobonds true
129 clashes
> save "/Users/ae811/Downloads/MUT Phex_G575R_rotamers+clashes_active
> highlighted.cxs" includeMaps true
> show sel atoms
> show sel cartoons
> hide sel atoms
> show sel atoms
> show sel cartoons
> style sel stick
Changed 12 atom styles
> select clear
> select add #!1/A:444
24 atoms, 25 bonds, 1 pseudobond, 1 residue, 2 models selected
> select subtract #!1/A:444
1 pseudobond, 1 model selected
No visible atoms or bonds selected
> color #3 #d66053ff models
> color #3 #d6a09fff models
> color #3 #d6a9a8ff models
> color #3 #d6a8abff models
> color #3 #d6a8aaff models
> color #3 #dbacafff models
> color #3 #dba6a9ff models
Drag select of 5 residues
> select clear
[Repeated 1 time(s)]
> select #!1/A:575
14 atoms, 13 bonds, 1 residue, 1 model selected
> select clear
> select #!1/A:575
14 atoms, 13 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
6 hydrogen bonds found
> select clear
> hbonds sel reveal true
Atom specifier selects no atoms
> select clear
> hbonds sel reveal true
Atom specifier selects no atoms
> select clear
> color #4 #aaf6faff models
> color #4 #a0f7faff models
> color #4 #affaf5ff models
> color #4 #92d0ccff models
> color #4 #90cecaff models
> save "/Users/ae811/Downloads/MUT Phex_G575R_rotamers+clashes_active
> highlighted.cxs"
> select #!1/A:441
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #!1/A:442
23 atoms, 21 bonds, 2 residues, 1 model selected
> select add #!1/A:438
42 atoms, 39 bonds, 3 residues, 1 model selected
> select add #!1/A:656
52 atoms, 48 bonds, 4 residues, 1 model selected
> select add #!1/A:657
73 atoms, 69 bonds, 5 residues, 1 model selected
> select add #!1/A:653
83 atoms, 78 bonds, 6 residues, 1 model selected
> select add #!1/A:654
103 atoms, 98 bonds, 7 residues, 1 model selected
> select add #!1/A:571
124 atoms, 119 bonds, 8 residues, 1 model selected
> select add #!1/A:570
135 atoms, 129 bonds, 9 residues, 1 model selected
> select add #!1/A:567
159 atoms, 152 bonds, 10 residues, 1 model selected
> color sel #91cec8ff
[Repeated 1 time(s)]
> color sel #92cec6ff
> color sel #99cec1ff
> color sel #a2cebaff
> color sel #a4ceb7ff
> color sel #a8ceafff
> color sel #a9ceabff
> color sel #aecea9ff
> color sel #afcea9ff
> color sel #b1cea9ff
> color sel #b4cea9ff
> color sel #bdcea9ff
> color sel #bfcea7ff
> color sel #c1cea5ff
> color sel #c2cea4ff
> color sel #c4cea2ff
> color sel #c5cea1ff
> color sel #c6cea0ff
> color sel #c7ce9fff
> color sel #cace9bff
> color sel #cbce99ff
> color sel #cdce97ff
> color sel #cece95ff
> color sel #cecd93ff
> color sel #cecd92ff
[Repeated 1 time(s)]
> color sel #cecc91ff
> color sel #cecb8fff
> color sel #ceca8dff
> color sel #cec788ff
> color sel #cec484ff
> color sel #cec382ff
> color sel #cec280ff
> color sel #cec17fff
> color sel #cec07dff
> color sel #cebf7bff
[Repeated 4 time(s)]
> color sel #cebe7cff
> color sel #cebc7fff
> color sel #cebb82ff
> color sel #cebb83ff
> color sel #cebb85ff
> color sel #cebb87ff
> color sel #cebb89ff
> color sel #cebe92ff
> color sel #cebf96ff
> color sel #cec099ff
[Repeated 1 time(s)]
> color sel #cec09aff
> color sel #cec29cff
> color sel #cec49fff
> color sel #cec6a1ff
> color sel #cec7a3ff
[Repeated 3 time(s)]
> color sel #cec5a1ff
> color sel #cec4a0ff
> color sel #cec19eff
> color sel #cebb99ff
> color sel #ceb997ff
> color sel #ceb896ff
> color sel #ceb696ff
> color sel #ceb597ff
> color sel #ceb198ff
> color sel #ceac99ff
> color sel #ceaa99ff
[Repeated 1 time(s)]
> color sel #ceaa98ff
> color sel #cea998ff
[Repeated 1 time(s)]
> color sel #ceaa98ff
> color sel #ceab98ff
> color sel #ceab97ff
> color sel #ceac97ff
> color sel #cead97ff
> color sel #ceae97ff
> color sel #ceaf97ff
[Repeated 3 time(s)]
> color sel #ceaf96ff
[Repeated 2 time(s)]
> color sel #ceb096ff
> color sel #ceb196ff
[Repeated 4 time(s)]
> color sel #ceb296ff
[Repeated 3 time(s)]
> color sel #ceb196ff
[Repeated 1 time(s)]
> color sel #ceb197ff
> color sel #ceaf97ff
[Repeated 2 time(s)]
> color sel #ceae98ff
> color sel #cead98ff
> color sel #ceac99ff
[Repeated 5 time(s)]
> color sel #ceab99ff
> color sel #cead9bff
> color sel #ceaf9dff
> color sel #ceb09fff
> color sel #ceb2a1ff
> color sel #ceb2a3ff
> color sel #ceb3a4ff
[Repeated 3 time(s)]
> color sel #ceb3a6ff
> color sel #ceb3a8ff
> color sel #ceb2a9ff
> color sel #ceb1aaff
> color sel #ceb0abff
> color sel #ceafabff
> color sel #ceaeabff
> color sel #ceacabff
> color sel #ceabacff
> color sel #ceabadff
[Repeated 2 time(s)]
> color sel #ceaaadff
> color sel #ceaaacff
> color sel #cea9acff
[Repeated 2 time(s)]
> color sel #cea8acff
> color sel #cea7acff
> color sel #cea6abff
[Repeated 1 time(s)]
> color sel #cea6aaff
> color sel #cea3a8ff
> color sel #cea1a6ff
> color sel #cea0a5ff
> color sel #ce9ea2ff
> color sel #ce9da2ff
> color sel #ce9ea2ff
> color sel #ce9fa3ff
> color sel #cea0a4ff
[Repeated 1 time(s)]
> color sel #cea0a5ff
> color sel #cea1a5ff
[Repeated 1 time(s)]
> color sel #cea1a6ff
> color sel #cea2a6ff
[Repeated 2 time(s)]
> color sel #cea4a8ff
> color sel #ceaaaeff
> color sel #ceaaafff
[Repeated 1 time(s)]
> color sel #ceabafff
> color sel #ceacb1ff
> color sel #ceaeb2ff
> color sel #ceb0b4ff
[Repeated 2 time(s)]
> color sel #ceafb3ff
> color sel #ceaeb3ff
> color sel #ceaeb2ff
[Repeated 1 time(s)]
> color sel #ceadb1ff
[Repeated 3 time(s)]
> select clear
> save "/Users/ae811/Downloads/MUT Phex_G575R_rotamers+clashes_active
> highlighted.cxs"
——— End of log from Thu Mar 5 08:26:52 2026 ———
> view name session-start
opened ChimeraX session
> color #1.2 #bf9896ff models
> color #1.2 #bfa4a3ff models
> color #1.2 #bf7a7eff models
> color #1.2 #bf7a7e9a models
> color #1.2 #bf7a7e5c models
> color #1.2 #bf7a7e95 models
> color #1.2 #bf7a7e98 models
> hide #4 models
> save "/Users/ae811/Downloads/MUT Phex_G575R_rotamers+clashes_active
> highlighted.cxs"
> close session
> open "/Users/ae811/Downloads/MUT Phex_A645T_rotamers+clashes_active
> highlighted.cxs"
> view name session-start
opened ChimeraX session
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac21,1
Model Number: Z12R000LXLL/A
Chip: Apple M1
Total Number of Cores: 8 (4 Performance and 4 Efficiency)
Memory: 16 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3 (25D125)
Kernel Version: Darwin 25.3.0
Time since boot: 2 days, 2 hours, 36 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 4.5K (4480 x 2520)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.19.1
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: 2.5.2
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
narwhals: 2.16.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 2.4.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
plotly: 6.5.2
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pyKVFinder: 0.9.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tomlkit: 0.14.0
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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