id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19939 Crash during window geometry change chimerax-bug-report@… Tom Goddard "{{{ 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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""\/Applications\/ChimeraX-1.11.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_csv.cpython-311-darwin.so"", ""name"" : ""_csv.cpython-311-darwin.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 5304565760, ""size"" : 753664, ""uuid"" : ""0d5e2b04-5266-3fcf-8917-51cab65a30b4"", ""path"" : ""\/Applications\/ChimeraX-1.11.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGL.abi3.so"", ""name"" : ""QtOpenGL.abi3.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 5300076544, ""size"" : 49152, ""uuid"" : ""6159a840-3c3a-3d9e-9af1-35dea6d209e4"", ""path"" : ""\/Applications\/ChimeraX-1.11.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGLWidgets.abi3.so"", ""name"" : ""QtOpenGLWidgets.abi3.so"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 5293522944, ""size"" : 49152, ""uuid"" : ""bdbfbc59-c41d-3a69-8112-739716f2e836"", ""path"" : ""\/Applications\/ChimeraX-1.11.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtOpenGLWidgets.framework\/Versions\/A\/QtOpenGLWidgets"", ""name"" : ""QtOpenGLWidgets"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 5299798016, ""size"" : 81920, ""uuid"" : ""d92182fe-4f0b-3c92-8bb7-0b79cd82503a"", ""path"" : ""\/Applications\/ChimeraX-1.11.1.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"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 5299978240, ""size"" : 16384, ""uuid"" : ""1cc9ad85-9303-310d-acec-456c2181bee3"", ""path"" : ""\/Applications\/ChimeraX-1.11.1.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"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 5303844864, ""size"" : 409600, ""uuid"" : ""3f1c3540-f7eb-3a3d-860e-c55452ccf717"", ""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"", ""arch"" : ""arm64"", ""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"", ""arch"" : ""arm64e"", ""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"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6919999488, ""size"" : 653076, ""uuid"" : ""bc4db5f4-1c64-3706-8006-73b78c3e1f1a"", ""path"" : ""\/usr\/lib\/dyld"", ""name"" : ""dyld"" }, { ""size"" : 0, ""source"" : ""A"", ""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 8589725696, ""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"", ""CFBundleVersion"" : ""993"" } ], ""sharedCache"" : { ""base"" : 6918914048, ""size"" : 5818417152, ""uuid"" : ""25ae5a2a-fe2a-3998-8d4e-f3c5c6e6ceb6"" }, ""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 "", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""9eed7e3f8f841d22c3ef07b94d34821a68f222a0"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""trmStatus"" : 8192, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6425c75e4327780c10cc4252"", ""factorPackIds"" : [ ""642600a457e7664b1698eb32"" ], ""deploymentId"" : 240000004 }, { ""rolloutId"" : ""654439cdafbf5b61207873a9"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000004 } ], ""experiments"" : [ ] } } ===== 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 }}} " defect closed normal Window Toolkit duplicate all ChimeraX