id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20383 ChimeraX bug report submission chimerax-bug-report@… "{{{ The following bug report has been submitted: Platform: macOS-26.4.1-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 Current thread 0x00000001ecbf98c0 (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, PIL._imaging, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, chimerax.map._map, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PIL._imagingmath, pyKVFinder._pyKVFinder, chimerax.mlp._mlp, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 56) {""app_name"":""ChimeraX"",""timestamp"":""2026-05-23 11:57:32.00 +0200"",""app_version"":""1.11.1"",""slice_uuid"":""c20e09a8-923e-3fb3-856b-3e765bcb267b"",""build_version"":""1.11.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 26.4.1 (25E253)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""EC6EED8D-6BAF-4B11-9239-7AABB8F8B28C""} { ""uptime"" : 1000000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 502, ""deployVersion"" : 210, ""modelCode"" : ""Mac17,2"", ""coalitionID"" : 7384, ""osVersion"" : { ""train"" : ""macOS 26.4.1"", ""build"" : ""25E253"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2026-05-23 11:57:24.9477 +0200"", ""codeSigningMonitor"" : 2, ""incident"" : ""EC6EED8D-6BAF-4B11-9239-7AABB8F8B28C"", ""pid"" : 98368, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""procLaunch"" : ""2026-05-20 12:23:02.8835 +0200"", ""procStartAbsTime"" : 20001059319764, ""procExitAbsTime"" : 26184949693870, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.11.1"",""CFBundleVersion"":""1.11.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""2B13CAE6-200B-5F32-AB52-F99A5D750900"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""8FA5886D-2DE9-9ED1-52BA-301AD4B7E1D3"", ""appleIntelligenceStatus"" : {""state"":""unavailable"",""reasons"":[""notOptedIn"",""assetIsNotReady""]}, ""developerMode"" : 1, ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""codeSigningAuxiliaryInfo"" : 0, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRCuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkf\/f\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""bootSessionUUID"" : ""C28089C1-A0CE-4352-9AD2-5B4BD0900103"", ""wakeTime"" : 266585, ""sleepWakeUUID"" : ""6C77CBCF-2581-4A50-BF70-3667001ACB7A"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x8 is not in any region. 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""uuid"" : ""83f39565-33c4-320a-ac75-81b90af76e46"", ""path"" : ""\/Applications\/ChimeraX-1.11.1.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"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 5331894272, ""size"" : 114688, ""uuid"" : ""f0372261-211e-32cf-83bb-119fbf49fb02"", ""path"" : ""\/Applications\/ChimeraX-1.11.1.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"" }, { ""source"" : ""P"", ""arch"" : ""arm64"", ""base"" : 5424349184, ""size"" : 114688, ""uuid"" : ""4054e3d0-2474-37de-901e-4c10afdac686"", ""path"" : ""\/Applications\/ChimeraX-1.11.1.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"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6456782848, ""size"" : 250512, ""uuid"" : ""51565b39-f595-3e96-a217-fef29815057a"", ""path"" : ""\/usr\/lib\/system\/libsystem_kernel.dylib"", ""name"" : ""libsystem_kernel.dylib"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6457036800, ""size"" : 52028, ""uuid"" : ""e7a73008-0c09-31e3-9dd9-0c61652f0e85"", ""path"" : ""\/usr\/lib\/system\/libsystem_pthread.dylib"", ""name"" : ""libsystem_pthread.dylib"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6455549952, ""size"" : 528120, ""uuid"" : ""66ebd321-6899-3863-ba24-5cfc3076a0cb"", ""path"" : ""\/usr\/lib\/system\/libsystem_c.dylib"", ""name"" : ""libsystem_c.dylib"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6457090048, ""size"" : 35060, ""uuid"" : ""d93ec420-f465-3a3a-916d-a04af9b023eb"", ""path"" : ""\/usr\/lib\/system\/libsystem_platform.dylib"", ""name"" : ""libsystem_platform.dylib"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6457323520, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.CoreFoundation"", ""size"" : 5626976, ""uuid"" : ""04941709-2330-3bf8-9213-6d33964db448"", ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"", ""name"" : ""CoreFoundation"", ""CFBundleVersion"" : ""4424.1.402"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6482931712, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.Foundation"", ""size"" : 16654816, ""uuid"" : ""8e9a5c62-7e95-3047-81e7-735ae1aee5f8"", ""path"" : ""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"", ""name"" : ""Foundation"", ""CFBundleVersion"" : ""4424.1.402"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6529081344, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.AppKit"", ""size"" : 24259264, ""uuid"" : ""59e23bd5-d01e-305a-b96f-a5790356049a"", ""path"" : ""\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit"", ""name"" : ""AppKit"", ""CFBundleVersion"" : ""2685.50.120"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 6453018624, ""size"" : 679624, ""uuid"" : ""9f682dcf-340c-3bfa-bcdd-dd702f30313e"", ""path"" : ""\/usr\/lib\/dyld"", ""name"" : ""dyld"" }, { ""size"" : 0, ""source"" : ""A"", ""base"" : 0, ""uuid"" : ""00000000-0000-0000-0000-000000000000"" } ], ""sharedCache"" : { ""base"" : 6451888128, ""size"" : 5978570752, ""uuid"" : ""2d40543a-792e-37b8-978d-3d7030e1aa81"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=2.1G resident=0K(0%) swapped_out_or_unallocated=2.1G(100%) Writable regions: Total=1.9G written=214.9M(11%) resident=1875K(0%) swapped_out=213.0M(11%) unallocated=1.7G(89%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 128K 1 Activity Tracing 256K 1 AttributeGraph Data 1024K 1 CG image 592K 20 ColorSync 144K 8 CoreAnimation 3152K 177 CoreGraphics 80K 5 CoreServices 704K 3 CoreUI image data 5856K 50 Foundation 48K 2 Kernel Alloc Once 48K 2 MALLOC 1.0G 368 MALLOC guard page 3840K 4 Mach message 64K 2 Memory Tag 22 64.0M 1 OpenGL GLSL 256K 3 PROTECTED_MEMORY 16K 1 STACK GUARD 672K 42 Stack 202.4M 43 Stack Guard 56.0M 1 VM_ALLOCATE 428.0M 341 VM_ALLOCATE (reserved) 192.0M 1 reserved VM address space (unallocated) __AUTH 6138K 646 __AUTH_CONST 91.3M 1043 __CTF 824 1 __DATA 42.5M 1129 __DATA_CONST 61.3M 1183 __DATA_DIRTY 8459K 897 __FONT_DATA 2352 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 604.3M 137 __OBJC_RO 79.1M 1 __OBJC_RW 2597K 1 __TEXT 1.5G 1205 __TPRO_CONST 128K 2 dyld private memory 304K 4 mapped file 659.0M 86 page table in kernel 1875K 1 shared memory 3200K 25 =========== ======= ======= TOTAL 4.9G 7440 TOTAL, minus reserved VM space 4.8G 7440 "", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""e4a52076704d666473c9a20fa90d29c8a51bf93c"", ""bug_type"" : ""309"", ""roots_installed"" : 0, ""trmStatus"" : 1, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6410af69ed1e1e7ab93ed169"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000011 }, { ""rolloutId"" : ""60186475825c62000ccf5450"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000083 } ], ""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. How to cite UCSF ChimeraX > open /Users/vatetaud/Downloads/pdb5ljo.ent format pdb pdb5ljo.ent title: E. Coli bam complex (bamabcde) by cryoem [more info...] Chain information for pdb5ljo.ent #1 --- Chain | Description | UniProt A | outer membrane protein assembly factor bama | BAMA_ECO45 24-806 B | outer membrane protein assembly factor bamb | BAMB_ECOLI 22-392 C | outer membrane protein assembly factor bamc | BAMC_ECOLI 25-189 D | outer membrane protein assembly factor bamd | BAMD_ECO57 26-243 E | outer membrane protein assembly factor bame | BAME_ECOL6 24-110 > hide #1 models > set bgColor white > open > /Users/vatetaud/Desktop/Protein/OM_biogenesis/Lpt_bridge_vp/fold_lptfg_lpta_lptc_lptd_sp_vp_model_0.cif Chain information for fold_lptfg_lpta_lptc_lptd_sp_vp_model_0.cif #2 --- Chain | Description A | . B | . C | . D | . Computing secondary structure > split #2 Split fold_lptfg_lpta_lptc_lptd_sp_vp_model_0.cif (#2) into 4 models Chain information for fold_lptfg_lpta_lptc_lptd_sp_vp_model_0.cif A #2.1 --- Chain | Description A | No description available Chain information for fold_lptfg_lpta_lptc_lptd_sp_vp_model_0.cif B #2.2 --- Chain | Description B | No description available Chain information for fold_lptfg_lpta_lptc_lptd_sp_vp_model_0.cif C #2.3 --- Chain | Description C | No description available Chain information for fold_lptfg_lpta_lptc_lptd_sp_vp_model_0.cif D #2.4 --- Chain | Description D | No description available > hide #2.1 models > show #2.1 models > hide #2.1 models > show #2.1 models > hide #2.2 models > hide #2.3 models > hide #2.4 models > select /A 14937 atoms, 15138 bonds, 1146 residues, 2 models selected > show #2.2 models > show #2.3 models > show #2.4 models > color (#2.1 & sel) #fffdeaff > color (#2.1 & sel) #fffde9ff > color (#2.1 & sel) #fffae7ff > color (#2.1 & sel) #fff7e4ff > color (#2.1 & sel) #fff3e1ff > color (#2.1 & sel) #fff2e0ff > color (#2.1 & sel) #fff1e0ff > color (#2.1 & sel) #fff1dfff > color (#2.1 & sel) #ffeedbff > color (#2.1 & sel) #ffebd7ff > color (#2.1 & sel) #ffe8d3ff > color (#2.1 & sel) #ffe5d1ff > color (#2.1 & sel) #ffe5d0ff > color (#2.1 & sel) #ffe4cfff > color (#2.1 & sel) #ffe2cdff > color (#2.1 & sel) #ffdfcbff > color (#2.1 & sel) #ffdac8ff > color (#2.1 & sel) #ffd7c5ff > color (#2.1 & sel) #ffd4c3ff > color (#2.1 & sel) #ffd3c2ff > color (#2.1 & sel) #ffd2c2ff > color (#2.1 & sel) #ffd2c1ff > color (#2.1 & sel) #ffd1c1ff > color (#2.1 & sel) #ffc8bbff > color (#2.1 & sel) #ffc1b8ff > color (#2.1 & sel) #ffbbb4ff > color (#2.1 & sel) #ffb8b3ff > color (#2.1 & sel) #ffb6b2ff > color (#2.1 & sel) #ffb7b1ff > color (#2.1 & sel) #ffbab1ff > color (#2.1 & sel) #ffbdb0ff > color (#2.1 & sel) #ffc0b0ff > color (#2.1 & sel) #ffc4afff > color (#2.1 & sel) #ffc5afff > color (#2.1 & sel) #ffc6afff > color (#2.1 & sel) #ffc7b0ff > color (#2.1 & sel) #ffc9b0ff > color (#2.1 & sel) #ffcab1ff > color (#2.1 & sel) #ffcbb2ff > color (#2.1 & sel) #ffceb4ff > color (#2.1 & sel) #ffd2b7ff > color (#2.1 & sel) #ffd8bbff > color (#2.1 & sel) #ffe2c2ff > color (#2.1 & sel) #ffe5c6ff > color (#2.1 & sel) #ffe7c7ff > color (#2.1 & sel) #ffe6c9ff > color (#2.1 & sel) #ffe3cbff > color (#2.1 & sel) #ffe1ccff > color (#2.1 & sel) #ffdfceff > color (#2.1 & sel) #ffdccfff > color (#2.1 & sel) #ffdbcfff > color (#2.1 & sel) #ffdacfff > color (#2.1 & sel) #ffd9cfff > color (#2.1 & sel) #ffd8cfff > color (#2.1 & sel) #ffd6d0ff > color (#2.1 & sel) #ffd5d0ff > color (#2.1 & sel) #ffd3d0ff > color (#2.1 & sel) #ffd1cfff > color (#2.1 & sel) #ffcfcfff > color (#2.1 & sel) #ffcfd1ff > color (#2.1 & sel) #ffced1ff > color (#2.1 & sel) #ffced2ff > color (#2.1 & sel) #ffcdd4ff > color (#2.1 & sel) #ffcdd6ff > color (#2.1 & sel) #ffccdaff > color (#2.1 & sel) #ffcbdcff > color (#2.1 & sel) #ffcaddff > color (#2.1 & sel) #ffcbdfff > color (#2.1 & sel) #ffd4e2ff > color (#2.1 & sel) #ffd9e4ff > color (#2.1 & sel) #ffdce4ff > color (#2.1 & sel) #ffdee5ff > color (#2.1 & sel) #ffdde4ff > color (#2.1 & sel) #ffdce4ff > color (#2.1 & sel) #ffdce3ff > color (#2.1 & sel) #ffdbe2ff > color (#2.1 & sel) #ffdae2ff > color (#2.1 & sel) #ffd8dfff > color (#2.1 & sel) #ffd6dcff > color (#2.1 & sel) #ffd3d9ff > color (#2.1 & sel) #ffd2d7ff > color (#2.1 & sel) #ffd1d6ff > color (#2.1 & sel) #ffd1d5ff > color (#2.1 & sel) #ffd0d4ff > color (#2.1 & sel) #ffcfd1ff > color (#2.1 & sel) #ffcdceff > color (#2.1 & sel) #ffcccbff > color (#2.1 & sel) #ffcccaff > color (#2.1 & sel) #ffccc9ff > color (#2.1 & sel) #ffccc8ff > color (#2.1 & sel) #ffccc6ff > color (#2.1 & sel) #ffccc3ff > color (#2.1 & sel) #ffcdc3ff > color (#2.1 & sel) #ffccc3ff > color (#2.1 & sel) #ffccc4ff > color (#2.1 & sel) #ffccc5ff > color (#2.1 & sel) #ffccc6ff > color (#2.1 & sel) #ffccc8ff > color (#2.1 & sel) #ffcdc9ff > color (#2.1 & sel) #ffcdcaff > color (#2.1 & sel) #ffcdccff > color (#2.1 & sel) #ffceccff > color (#2.1 & sel) #ffcfccff > color (#2.1 & sel) #ffd1ccff > color (#2.1 & sel) #ffd3cbff > color (#2.1 & sel) #ffd5cbff > color (#2.1 & sel) #ffd6cbff > color (#2.1 & sel) #ffd7cbff > color (#2.1 & sel) #ffd6cbff > color (#2.1 & sel) #ffd7cbff > color (#2.1 & sel) #ffd7caff > color (#2.1 & sel) #ffd8caff > select /B 7125 atoms, 7196 bonds, 586 residues, 2 models selected > select /C 3865 atoms, 3904 bonds, 343 residues, 2 models selected > color (#2.3 & sel) #ffb4b4ff > color (#2.3 & sel) #ffb6b6ff > color (#2.3 & sel) #ffb7b8ff > color (#2.3 & sel) #ffb9bbff > color (#2.3 & sel) #ffbbbdff > color (#2.3 & sel) #ffbcbfff > color (#2.3 & sel) #ffbcc0ff > color (#2.3 & sel) #ffbcc1ff > color (#2.3 & sel) #ffbcc2ff > color (#2.3 & sel) #ffbcc3ff > color (#2.3 & sel) #ffbdc5ff > color (#2.3 & sel) #ffbec8ff > color (#2.3 & sel) #ffbecaff > color (#2.3 & sel) #ffbfcbff > color (#2.3 & sel) #ffbfccff > color (#2.3 & sel) #ffbfcdff > color (#2.3 & sel) #ffc0ceff > color (#2.3 & sel) #ffc0d0ff > color (#2.3 & sel) #ffc1d1ff > color (#2.3 & sel) #ffc1d2ff > color (#2.3 & sel) #ffc1d3ff > color (#2.3 & sel) #ffc1d4ff > color (#2.3 & sel) #ffc2d6ff > color (#2.3 & sel) #ffc2d8ff > color (#2.3 & sel) #ffc3daff > color (#2.3 & sel) #ffc3dcff > color (#2.3 & sel) #ffc3ddff > color (#2.3 & sel) #ffc2deff > color (#2.3 & sel) #ffc1ddff > color (#2.3 & sel) #ffc0ddff > color (#2.3 & sel) #ffbfddff > color (#2.3 & sel) #ffbedcff > color (#2.3 & sel) #ffbdddff > color (#2.3 & sel) #ffbcdeff > color (#2.3 & sel) #ffbbdfff > color (#2.3 & sel) #ffbae0ff > color (#2.3 & sel) #ffb9e1ff > color (#2.3 & sel) #ffb9e2ff > color (#2.3 & sel) #ffb8e2ff > color (#2.3 & sel) #ffb7e3ff > color (#2.3 & sel) #ffb6e4ff > color (#2.3 & sel) #ffb7e3ff > color (#2.3 & sel) #ffb8e2ff > color (#2.3 & sel) #ffb9e2ff > color (#2.3 & sel) #ffb9e3ff > color (#2.3 & sel) #ffb9e4ff > color (#2.3 & sel) #ffb9e6ff > color (#2.3 & sel) #ffb9e7ff > color (#2.3 & sel) #ffb9e8ff > color (#2.3 & sel) #ffb8e9ff > color (#2.3 & sel) #ffb9eaff > color (#2.3 & sel) #ffbaebff > color (#2.3 & sel) #ffbaecff > color (#2.3 & sel) #ffbbedff > color (#2.3 & sel) #ffbceeff > color (#2.3 & sel) #ffbef0ff > color (#2.3 & sel) #ffbff1ff > color (#2.3 & sel) #ffbff2ff > select /B 7125 atoms, 7196 bonds, 586 residues, 2 models selected > color (#2.2 & sel) #ffccfcff > color (#2.2 & sel) #ffcdfcff > color (#2.2 & sel) #ffcefeff > color (#2.2 & sel) #fccfffff > color (#2.2 & sel) #f6cfffff > color (#2.2 & sel) #f0cdffff > color (#2.2 & sel) #eaccffff > color (#2.2 & sel) #e7caffff > color (#2.2 & sel) #e5c9ffff > color (#2.2 & sel) #e3c9ffff > color (#2.2 & sel) #e2c9ffff > color (#2.2 & sel) #e0c9ffff > color (#2.2 & sel) #ddc8ffff > color (#2.2 & sel) #d7c6ffff > color (#2.2 & sel) #d0c3ffff > color (#2.2 & sel) #cbc1ffff > color (#2.2 & sel) #c5bfffff > color (#2.2 & sel) #c4bfffff > color (#2.2 & sel) #c3beffff > color (#2.2 & sel) #c2beffff > color (#2.2 & sel) #c1beffff > color (#2.2 & sel) #bfbeffff > select /D 7427 atoms, 7573 bonds, 712 residues, 2 models selected > color (#2.4 & sel) #d1d0ffff > color (#2.4 & sel) #d1d2ffff > color (#2.4 & sel) #d1d4ffff > color (#2.4 & sel) #d1d6ffff > color (#2.4 & sel) #d1d7ffff > color (#2.4 & sel) #d1d8ffff > color (#2.4 & sel) #d2d9ffff > color (#2.4 & sel) #d2daffff > color (#2.4 & sel) #d3dbffff > color (#2.4 & sel) #d2ddffff > color (#2.4 & sel) #d2deffff > color (#2.4 & sel) #d2dfffff > color (#2.4 & sel) #d2e0ffff > color (#2.4 & sel) #d2e1ffff > color (#2.4 & sel) #d2e4ffff > color (#2.4 & sel) #d2e5ffff > color (#2.4 & sel) #d2e7ffff > color (#2.4 & sel) #d2e8ffff > color (#2.4 & sel) #d2e9ffff > color (#2.4 & sel) #d2eaffff > color (#2.4 & sel) #d2ebffff > color (#2.4 & sel) #d2ecffff > color (#2.4 & sel) #d1edffff > color (#2.4 & sel) #d1efffff > color (#2.4 & sel) #d0f2ffff > color (#2.4 & sel) #cff3ffff > color (#2.4 & sel) #cff4ffff > color (#2.4 & sel) #cef4ffff > color (#2.4 & sel) #cef5ffff > color (#2.4 & sel) #cdf7ffff > color (#2.4 & sel) #ccf9ffff > color (#2.4 & sel) #cbfbffff > color (#2.4 & sel) #cafdffff > color (#2.4 & sel) #cafeffff > color (#2.4 & sel) #c9feffff > color (#2.4 & sel) #c7ffffff > color (#2.4 & sel) #c6ffffff > select clear > show #2.1-4 surfaces > save /Users/vatetaud/Desktop/image8.png supersample 3 > hide #!2 models > open > /Users/vatetaud/Desktop/Protein/TIM/fold_lptd_petit_43595_hsaccharolyticum/fold_lptd_petit_43595_hsaccharolyticum_model_0.cif Chain information for fold_lptd_petit_43595_hsaccharolyticum_model_0.cif #3 --- Chain | Description A | . Computing secondary structure > hide #3 models > hide #!2.4 models > hide #!2.3 models > hide #!2.2 models > show #!2 models > hide #!2.1 models > show #!2.4 models > hide #!2.4 surfaces > select /D 7427 atoms, 7573 bonds, 712 residues, 2 models selected > color (#!2.4 & sel) #a7fff6ff > color (#!2.4 & sel) #a7fff9ff > color (#!2.4 & sel) #a8ffffff > color (#!2.4 & sel) #a5eaffff > color (#!2.4 & sel) #a4e7ffff > color (#!2.4 & sel) #a2e0ffff > color (#!2.4 & sel) #a1ddffff > color (#!2.4 & sel) #a0dbffff > color (#!2.4 & sel) #9fd8ffff > color (#!2.4 & sel) #9fd7ffff > color (#!2.4 & sel) #9ed6ffff > color (#!2.4 & sel) #9dd4ffff > color (#!2.4 & sel) #9cd3ffff > color (#!2.4 & sel) #9acfffff > color (#!2.4 & sel) #99ceffff > color (#!2.4 & sel) #97ccffff > color (#!2.4 & sel) #94c8ffff > color (#!2.4 & sel) #8abeffff > color (#!2.4 & sel) #87bbffff > color (#!2.4 & sel) #84b8ffff > color (#!2.4 & sel) #83b6ffff > color (#!2.4 & sel) #82b5ffff > color (#!2.4 & sel) #81b3ffff > color (#!2.4 & sel) #7faeffff > color (#!2.4 & sel) #7daaffff > color (#!2.4 & sel) #7aa2ffff > color (#!2.4 & sel) #789effff > color (#!2.4 & sel) #779cffff > color (#!2.4 & sel) #779affff > color (#!2.4 & sel) #789affff > color (#!2.4 & sel) #7899ffff > color (#!2.4 & sel) #7395ffff > color (#!2.4 & sel) #6f91ffff > color (#!2.4 & sel) #6c8dffff > color (#!2.4 & sel) #698bffff > color (#!2.4 & sel) #688affff > color (#!2.4 & sel) #678affff > color (#!2.4 & sel) #668affff > color (#!2.4 & sel) #658affff > color (#!2.4 & sel) #658bffff > color (#!2.4 & sel) #658dffff > color (#!2.4 & sel) #648fffff > color (#!2.4 & sel) #6490ffff > color (#!2.4 & sel) #6591ffff > color (#!2.4 & sel) #6592ffff > color (#!2.4 & sel) #6694ffff > color (#!2.4 & sel) #6795ffff > color (#!2.4 & sel) #6896ffff > color (#!2.4 & sel) #6997ffff > color (#!2.4 & sel) #6a98ffff > color (#!2.4 & sel) #6b99ffff > color (#!2.4 & sel) #6c9affff > color (#!2.4 & sel) #6d9affff > color (#!2.4 & sel) #6e9cffff > color (#!2.4 & sel) #709dffff > color (#!2.4 & sel) #709effff > color (#!2.4 & sel) #719fffff > color (#!2.4 & sel) #72a0ffff > color (#!2.4 & sel) #74a1ffff > color (#!2.4 & sel) #75a2ffff > color (#!2.4 & sel) #77a4ffff > color (#!2.4 & sel) #76a3ffff > color (#!2.4 & sel) #76a2ffff > color (#!2.4 & sel) #75a1ffff > color (#!2.4 & sel) #749fffff > color (#!2.4 & sel) #739effff > color (#!2.4 & sel) #719dffff > color (#!2.4 & sel) #6f9dffff > color (#!2.4 & sel) #6d9dffff > color (#!2.4 & sel) #6d9cffff > color (#!2.4 & sel) #6c9cffff > color (#!2.4 & sel) #6b9bffff > color (#!2.4 & sel) #6a9bffff > color (#!2.4 & sel) #679bffff > color (#!2.4 & sel) #669bffff > color (#!2.4 & sel) #659bffff > color (#!2.4 & sel) #659affff > color (#!2.4 & sel) #649affff > color (#!2.4 & sel) #6299ffff > color (#!2.4 & sel) #6198ffff > color (#!2.4 & sel) #6097ffff > color (#!2.4 & sel) #5f97ffff > color (#!2.4 & sel) #5d95ffff > color (#!2.4 & sel) #5c94ffff > color (#!2.4 & sel) #5b93ffff > color (#!2.4 & sel) #5a92ffff > color (#!2.4 & sel) #5991ffff > select clear > select #2.4/D:227 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select #2.4/D:226 6 atoms, 5 bonds, 1 residue, 1 model selected > select /D:44-226 4373 atoms, 4441 bonds, 366 residues, 2 models selected > color (#!2.4 & sel) #76acffff > color (#!2.4 & sel) #75acffff > color (#!2.4 & sel) #76acffff > color (#!2.4 & sel) #77acffff > color (#!2.4 & sel) #78abffff > color (#!2.4 & sel) #79abffff > color (#!2.4 & sel) #79aaffff > color (#!2.4 & sel) #79a6ffff > color (#!2.4 & sel) #779bffff > color (#!2.4 & sel) #7695ffff > color (#!2.4 & sel) #7591ffff > color (#!2.4 & sel) #738dffff > color (#!2.4 & sel) #7289ffff > color (#!2.4 & sel) #7185ffff > color (#!2.4 & sel) #7082ffff > color (#!2.4 & sel) #6f7fffff > color (#!2.4 & sel) #6e7bffff > color (#!2.4 & sel) #6e79ffff > color (#!2.4 & sel) #6e76ffff > color (#!2.4 & sel) #6d74ffff > color (#!2.4 & sel) #6d71ffff > color (#!2.4 & sel) #6e6fffff > color (#!2.4 & sel) #706effff > color (#!2.4 & sel) #766fffff > color (#!2.4 & sel) #7d70ffff > color (#!2.4 & sel) #8371ffff > color (#!2.4 & sel) #9073ffff > color (#!2.4 & sel) #9473ffff > color (#!2.4 & sel) #9873ffff > color (#!2.4 & sel) #9a72ffff > color (#!2.4 & sel) #9e71ffff > color (#!2.4 & sel) #9f71ffff > color (#!2.4 & sel) #a171ffff > color (#!2.4 & sel) #a372ffff > color (#!2.4 & sel) #a572ffff > color (#!2.4 & sel) #a872ffff > color (#!2.4 & sel) #ab73ffff > color (#!2.4 & sel) #af72ffff > color (#!2.4 & sel) #b271ffff > color (#!2.4 & sel) #b770ffff > color (#!2.4 & sel) #ba6effff > color (#!2.4 & sel) #bd6dffff > color (#!2.4 & sel) #bf6cffff > color (#!2.4 & sel) #c26cffff > color (#!2.4 & sel) #c16cffff > color (#!2.4 & sel) #c06cffff > color (#!2.4 & sel) #bf6bffff > color (#!2.4 & sel) #bd6affff > color (#!2.4 & sel) #b969ffff > color (#!2.4 & sel) #b369ffff > color (#!2.4 & sel) #ad68ffff > color (#!2.4 & sel) #a867ffff > color (#!2.4 & sel) #a567ffff > color (#!2.4 & sel) #a367ffff > color (#!2.4 & sel) #a267ffff > color (#!2.4 & sel) #a167ffff > color (#!2.4 & sel) #a066ffff > color (#!2.4 & sel) #9e66ffff > color (#!2.4 & sel) #9d65ffff > color (#!2.4 & sel) #9b64ffff > color (#!2.4 & sel) #9a63ffff > color (#!2.4 & sel) #9963ffff > color (#!2.4 & sel) #9962ffff > color (#!2.4 & sel) #9862ffff > color (#!2.4 & sel) #9762ffff > color (#!2.4 & sel) #9662ffff > select clear > save /Users/vatetaud/Desktop/image9.png supersample 3 > hide #!2.4 models > show #3 models > select clear Drag select of 1 residues > select #3/A:591 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > select #3:209-591 3217 atoms, 3305 bonds, 383 residues, 1 model selected > color (#!2.4 & sel) #5991ffff > color (#!2.4 & sel) #5991ffff selectedOnly Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color (#!2.4 & sel) #5991ffff SelectedOnly Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color SelectedOnly #5991ffff Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #5991ffff > color #5991ffff selectedOnly Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #5991ffff selectedo\nly Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #5991ffff selectedonly Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #5991ffff select Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel #5991ffff > close #3 > open > /Users/vatetaud/Desktop/Protein/TIM/LptD/fold_lptd_petit_sp_43595_hsaccharolyticum/fold_lptd_petit_sp_43595_hsaccharolyticum_model_0.cif Chain information for fold_lptd_petit_sp_43595_hsaccharolyticum_model_0.cif #3 --- Chain | Description A | . Computing secondary structure > select #3/A:178 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select #3:37-208 1375 atoms, 1411 bonds, 172 residues, 1 model selected > select #3:37-208 1375 atoms, 1411 bonds, 172 residues, 1 model selected > select #3:178-557 3192 atoms, 3278 bonds, 380 residues, 1 model selected > color sel #9662ffff > select clear > select #3/A:178 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:1 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3:178-557 3192 atoms, 3278 bonds, 380 residues, 1 model selected > color sel #9662ffff > select :1-177 17585 atoms, 17812 bonds, 1587 residues, 6 models selected > color sel #5991ffff > color sel #9662ffff > select #3:178-557 3192 atoms, 3278 bonds, 380 residues, 1 model selected > color sel #5991ffff > select clear > hide #!2 models > show #!2 models > hide #!2 models > show #!2.4 models > hide #!2.4 models > show #!2.4 models > hide #!2.4 models > save /Users/vatetaud/Desktop/image10.png supersample 3 > hide #3 models > show #!2.4 models > save /Users/vatetaud/Desktop/image11.png supersample 3 > hide #!2.4 models > open > /Users/vatetaud/Desktop/Protein/TIM/LptD/fold_lptd_grand_sp_43595_hsaccharolyticum/fold_lptd_grand_sp_43595_hsaccharolyticum_model_0.cif Chain information for fold_lptd_grand_sp_43595_hsaccharolyticum_model_0.cif #4 --- Chain | Description A | . Computing secondary structure > select #4/A:343 14 atoms, 15 bonds, 1 residue, 1 model selected > shape rectangle width 80 height 80 color lightblue modelId #10 > shape rectangle width 80 height 80 Thickness 80color lightblue modelId #10 Expected a keyword > shape rectangle width 80 height 80 Thickness 80 color lightblue modelId #10 Expected a keyword > shape rectangle width 80 height 80 Thick 80 color lightblue modelId #10 Expected a keyword > shape rectangle width 80 height 80 thick 80 color lightblue modelId #10 Expected a keyword > shape rectangle width 80 height 80 thickness 80 color lightblue modelId #10 Expected a keyword > hide #4 models > moove z 60 #10 Unknown command: moove z 60 #10 > move z 60 #10 Expected an integer >= 1 or a keyword > move z 60 models #10 > show #4 models > hide #10 models > break 343@N 344@C Unknown command: break 343@N 344@C > delete bound: 343@C 344@N Missing or invalid ""atoms"" argument: invalid atoms specifier > delete bound: 343@C 344@N Missing or invalid ""atoms"" argument: invalid atoms specifier > delete bond: 343@C 344@N Missing or invalid ""atoms"" argument: invalid atoms specifier > delete bond: 343@C :344@N Missing or invalid ""atoms"" argument: invalid atoms specifier > delete bonds :250@C :251@N > undo > hide #10 models > hide #4.1 models > close #4.1 > select :250 65 atoms, 60 bonds, 6 residues, 5 models selected > select :250-260 701 atoms, 697 bonds, 5 pseudobonds, 66 residues, 9 models selected > select clear > select #4/A:343 14 atoms, 15 bonds, 1 residue, 1 model selected > delete bonds :343@C :344@N > hide #4.1 models > show #4.1 models > hide #4.1 models > show #4.1 models > split #4 Did not split fold_lptd_grand_sp_43595_hsaccharolyticum_model_0.cif, has only one piece > hide #4.1 models > select clear > open > /Users/vatetaud/Desktop/Protein/TIM/LptD/fold_lptd_grand_sp_43595_hsaccharolyticum/fold_lptd_grand_sp_43595_hsaccharolyticum_model_1.cif > /Users/vatetaud/Desktop/Protein/TIM/LptD/fold_lptd_grand_sp_43595_hsaccharolyticum/fold_lptd_grand_sp_43595_hsaccharolyticum_model_2.cif > /Users/vatetaud/Desktop/Protein/TIM/LptD/fold_lptd_grand_sp_43595_hsaccharolyticum/fold_lptd_grand_sp_43595_hsaccharolyticum_model_3.cif > /Users/vatetaud/Desktop/Protein/TIM/LptD/fold_lptd_grand_sp_43595_hsaccharolyticum/fold_lptd_grand_sp_43595_hsaccharolyticum_model_4.cif Chain information for fold_lptd_grand_sp_43595_hsaccharolyticum_model_1.cif #5 --- Chain | Description A | . Chain information for fold_lptd_grand_sp_43595_hsaccharolyticum_model_2.cif #6 --- Chain | Description A | . Chain information for fold_lptd_grand_sp_43595_hsaccharolyticum_model_3.cif #7 --- Chain | Description A | . Chain information for fold_lptd_grand_sp_43595_hsaccharolyticum_model_4.cif #8 --- Chain | Description A | . Computing secondary structure > hide #8 models > hide #7 models > hide #6 models > hide #!4 models > show #6 models > hide #5 models > show #7 models > hide #6 models > show #8 models > hide #7 models > close #5-7 > hide #8 models > close #8 > show #!4 models > select #4/A:248 11 atoms, 11 bonds, 1 residue, 1 model selected > select #4/A:250 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > select #4/A:251 6 atoms, 5 bonds, 1 residue, 1 model selected > select #4/A:342 11 atoms, 11 bonds, 1 residue, 1 model selected > select #4/A:343 14 atoms, 15 bonds, 1 residue, 1 model selected > select #4/A:344 11 atoms, 10 bonds, 1 residue, 1 model selected > delete bonds :343@C :344@N > select clear > show #4.1 models > hide #4.1 models > show #4.1 models > close #4 > open > /Users/vatetaud/Desktop/Protein/TIM/LptD/fold_lptd_grand_sp_43595_hsaccharolyticum/fold_lptd_grand_sp_43595_hsaccharolyticum_model_0.cif Chain information for fold_lptd_grand_sp_43595_hsaccharolyticum_model_0.cif #4 --- Chain | Description A | . Computing secondary structure > delete bonds :343@C :344@N > split #4 Did not split fold_lptd_grand_sp_43595_hsaccharolyticum_model_0.cif, has only one piece > select add #4.1 1 pseudobond, 1 model selected > select subtract #4.1 Nothing selected > select add #10 1 model selected > select subtract #10 Nothing selected > select add #4.1 1 pseudobond, 1 model selected > select up 8793 atoms, 9015 bonds, 1 pseudobond, 1056 residues, 2 models selected > select down 1 pseudobond, 1 model selected > select up 8793 atoms, 9015 bonds, 1 pseudobond, 1056 residues, 2 models selected > select down 1 pseudobond, 1 model selected > select up 8793 atoms, 9015 bonds, 1 pseudobond, 1056 residues, 2 models selected > select down 1 pseudobond, 1 model selected > select down 1 pseudobond, 1 model selected > delete bonds :343@C :344@N > select ~sel & ##selected 1 pseudobond, 1 model selected > show #!1 models > hide #!1 models > delete bonds #4:343@C :344@N > select #4 /a 8793 atoms, 9015 bonds, 1 pseudobond, 1056 residues, 2 models selected > select #4 /A 8793 atoms, 9015 bonds, 1 pseudobond, 1056 residues, 2 models selected > delete bonds :343@C :344@N > select up 8793 atoms, 9015 bonds, 1 pseudobond, 1056 residues, 2 models selected > select up 38337 atoms, 38948 bonds, 1 pseudobond, 3237 residues, 6 models selected > select up 38337 atoms, 38948 bonds, 1 pseudobond, 3237 residues, 6 models selected > delete bonds :343@C :344@N > select clear > move z 60 > select : 1-343 31020 atoms, 31462 bonds, 5 pseudobonds, 2877 residues, 11 models selected > hide #!2 models > select add #3 32809 atoms, 33302 bonds, 6 pseudobonds, 3091 residues, 15 models selected > select add #2.4 34079 atoms, 34609 bonds, 7 pseudobonds, 3242 residues, 15 models selected > select subtract #3 29482 atoms, 29892 bonds, 5 pseudobonds, 2685 residues, 13 models selected > select subtract #2.4 25516 atoms, 25822 bonds, 3 pseudobonds, 2191 residues, 11 models selected > select add #2 29641 atoms, 30054 bonds, 6 pseudobonds, 2705 residues, 13 models selected > select subtract #2 19882 atoms, 20100 bonds, 2 pseudobonds, 1455 residues, 7 models selected > select add #1 27703 atoms, 28031 bonds, 4 pseudobonds, 1967 residues, 3 models selected > select subtract #1 2756 atoms, 2815 bonds, 343 residues, 1 model selected > turn y 90 models #4 > delete bonds #4 :343@C :344@N > select clear > delete bonds #4 :250@C :251@N > select :250-260 701 atoms, 697 bonds, 6 pseudobonds, 66 residues, 10 models selected > select add #1 25307 atoms, 25573 bonds, 8 pseudobonds, 1668 residues, 12 models selected > select subtract #1 360 atoms, 357 bonds, 4 pseudobonds, 44 residues, 10 models selected > select add #2 9936 atoms, 10128 bonds, 6 pseudobonds, 1272 residues, 13 models selected > select subtract #2 177 atoms, 174 bonds, 2 pseudobonds, 22 residues, 8 models selected > delete bonds #4 :250@C :251@N > hide #4.1 models > select clear > select add #4.1 2 pseudobonds, 1 model selected > select subtract #4.1 Nothing selected > select add #4.1 2 pseudobonds, 1 model selected > select subtract #4.1 Nothing selected > select add #4.1 2 pseudobonds, 1 model selected > select subtract #4.1 Nothing selected > select add #4.1 2 pseudobonds, 1 model selected > select subtract #4.1 Nothing selected > show #4.1 models > hide #4.1 models > show #4.1 models > hide #4.1 models > delete bonds :250@C :251@N > move x 30 models #4 > move z 50 models #4 > ui mousemode right ""tape measure"" > ui mousemode right ""move planes"" > ui mousemode right ""rotate slab"" > ui tool show Distances > select #4/A:82 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 4 atom styles > hide sel cartoons > select clear > select #4/A:82@O 1 atom, 1 residue, 1 model selected > select #4/A:203 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #4/A:203@OE1 1 atom, 1 residue, 1 model selected > select add #4/A:82@O 2 atoms, 2 residues, 1 model selected > distance #4/A:203@OE1 #4/A:82@O Distance between fold_lptd_grand_sp_43595_hsaccharolyticum_model_0.cif #4/A GLN 203 OE1 and GLY 82 O: 90.213Å > select #4/A:393 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #4/A:1026 14 atoms, 12 bonds, 2 residues, 1 model selected > show sel atoms > select clear > select #4/A:393@OG 1 atom, 1 residue, 1 model selected > select add #4/A:1026@CD1 2 atoms, 2 residues, 1 model selected > distance #4/A:393@OG #4/A:1026@CD1 Distance between fold_lptd_grand_sp_43595_hsaccharolyticum_model_0.cif #4/A SER 393 OG and LEU 1026 CD1: 28.809Å > select #4/A:157 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #4/A:157@NZ 1 atom, 1 residue, 1 model selected > select clear > select #4/A:157@NZ 1 atom, 1 residue, 1 model selected > select add #4/A:203@CD 2 atoms, 1 bond, 2 residues, 1 model selected > select add #4/A:203@OE1 3 atoms, 2 residues, 1 model selected Exactly two atoms must be selected! > select clear > select #4/A:203@OE1 1 atom, 1 residue, 1 model selected > select add #4/A:157@NZ 2 atoms, 2 residues, 1 model selected > distance #4/A:203@OE1 #4/A:157@NZ Distance between fold_lptd_grand_sp_43595_hsaccharolyticum_model_0.cif #4/A GLN 203 OE1 and LYS 157 NZ: 47.913Å > show #!2 models > show #!2.1 models > show #!2.2 models > show #!2.3 models > show #!2.4 models > hide #!4 models > select all 48096 atoms, 48901 bonds, 15 pseudobonds, 4487 residues, 16 models selected > hide sel & #!2.1-4 surfaces > select clear > hide #!2 models > show #!2 models > select #2.1/A:153 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #2.4/D:227 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #2.4/D:227@CD1 1 atom, 1 residue, 1 model selected > select add #2.1/A:153@NZ 2 atoms, 2 residues, 3 models selected > distance #2.4/D:227@CD1 #2.1/A:153@NZ Distance between fold_lptfg_lpta_lptc_lptd_sp_vp_model_0.cif D #2.4/D ILE 227 CD1 and fold_lptfg_lpta_lptc_lptd_sp_vp_model_0.cif A #2.1/A LYS 153 NZ: 159.382Å > ~distance #4/A:203@OE1 #4/A:82@O > show #!4 models > distance style color #fa1104 > distance style color #790802 > distance style color #780802 > distance style color #770802 > distance style color #710802 > distance style color #6d0802 > distance style color #680702 > distance style color #630701 > distance style color #5e0701 > distance style color #580601 > distance style color #530601 > distance style color #440501 > distance style color #3d0401 > distance style color #350401 > distance style color #270301 > distance style color #1a0200 > distance style color #160200 > distance style color #100100 > distance style color #0e0100 > distance style color #0d0100 > distance style color #0c0100 > distance style color #0a0100 > distance style color #050000 > distance style color #020000 > distance style color black > distance style color #0a0100 > distance style color #1c0200 > distance style color #250301 > distance style color #2c0301 > distance style color #330401 > distance style color #3d0401 > distance style color #430501 > distance style color #460501 > distance style color #490501 > distance style color #4c0501 > distance style color #4e0501 > distance style color #520601 > distance style color #540601 > distance style color #550601 > distance style color #560601 > distance style color #570601 > distance style color #590601 > distance style color #600701 > distance style color #650701 > distance style color #680702 > distance style color #6b0802 > distance style color #6e0802 > distance style color #730802 > distance style color #760802 > distance style color #790802 > distance style color #7d0902 > distance style color #810902 > distance style color #850902 > distance style color #920a02 > distance style color #9a0b02 > distance style color #a20b02 > distance style color #b20c03 > distance style color #ba0d03 > distance style color #c10d03 > distance style color #ce0e03 > distance style color #d30f03 > hide #!4 models > show #!4 models > hide #!2 models > select #4/A:377 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/A:376 6 atoms, 5 bonds, 1 residue, 1 model selected > select #4/A:377 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #4/A:376 11 atoms, 9 bonds, 2 residues, 1 model selected > ui mousemode right rotate > ui mousemode right select > ui mousemode right pivot Drag select of 1 residues > select #4/A:375 4 atoms, 3 bonds, 1 residue, 1 model selected Drag select of 1 residues > ui tool show ""Find Cavities"" pyKVFinder module not installed; fetching from PyPi repository... Errors may have occurred when running pip: pip standard error: \--- ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. nptyping 2.5.0 requires numpy=1.20.0; python_version >= ""3.8"", but you have numpy 2.4.6 which is incompatible. scipy 1.14.0 requires numpy=1.23.5, but you have numpy 2.4.6 which is incompatible. \--- pip standard output: \--- \--- pyKVFinder module installed from PyPi repository. > hide sel atoms > show sel cartoons > select clear > ui tool show Rotamers Populating font family aliases took 52 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > select #4/A:493 9 atoms, 8 bonds, 1 residue, 1 model selected > hide #!2.1 models > hide #!2.2 models > hide #!2.3 models > hide #!2.4 models > select clear > select #4/A:1056 9 atoms, 8 bonds, 1 residue, 1 model selected > select #4/A:493-1056 4825 atoms, 4959 bonds, 564 residues, 1 model selected > color sel #5991ffff > select up 4833 atoms, 4967 bonds, 565 residues, 1 model selected > select clear > select #4/A:377 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/A:377-492 955 atoms, 979 bonds, 116 residues, 1 model selected > color sel 9662ffff Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel #9662ffff > select clear > select #4/A:157@CE 1 atom, 1 residue, 1 model selected > show sel cartoons > hide sel atoms > select #4/A:157@CD 1 atom, 1 residue, 1 model selected > hide #5.1 models > show #5.1 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > select #4/A:157@NZ 1 atom, 1 residue, 1 model selected > hide sel atoms > select clear > select #4/A:157 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select #4/A:203 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select #4/A:220 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/A:133 7 atoms, 7 bonds, 1 residue, 1 model selected > select #4/A:133-220 740 atoms, 756 bonds, 1 pseudobond, 88 residues, 2 models selected > color sel #9662ffff > select #4/A:794 11 atoms, 11 bonds, 1 residue, 1 model selected > select #4/A:376 6 atoms, 5 bonds, 1 residue, 1 model selected > select clear > select #4/A:359 4 atoms, 3 bonds, 1 residue, 1 model selected > select clear > select #4/A:221 8 atoms, 7 bonds, 1 residue, 1 model selected > select #4/A:221-359 1121 atoms, 1144 bonds, 2 pseudobonds, 139 residues, 2 models selected > distance style color #d31409 > distance style color #d3160b > distance style color #d31b14 > distance style color #d32424 > distance style color #d33640 > distance style color #d3495d > distance style color #d35976 > distance style color #d3688a > distance style color #d3749b > distance style color #d37da8 > distance style color #d383b0 > distance style color #d386b5 > distance style color #d387b7 > distance style color #d386b7 > distance style color #d386b6 > distance style color #d385b5 > distance style color #d384b4 > distance style color #d383b3 > distance style color #d382b2 > distance style color #d381b1 > distance style color #d380b2 > distance style color #d37fb2 > distance style color #d37db3 > distance style color #d379b6 > distance style color #d374b9 > distance style color #d36dbe > distance style color #d367c4 > distance style color #d362cb > distance style color #d360d0 > distance style color #d35ed3 > distance style color #d25ed3 > distance style color #d25fd3 > distance style color #d35ed3 > distance style color #d35fd3 > distance style color #d35fd2 > distance style color #d35fcf > distance style color #d35eca > distance style color #d35cc3 > distance style color #d359bc > distance style color #d356b5 > distance style color #d353ae > distance style color #d351a8 > distance style color #d34fa4 > distance style color #d34ea1 > distance style color #d34d9f > distance style color #d34c9e > distance style color #d34d9d > distance style color #d34d9c > distance style color #d34d9a > distance style color #d34e98 > distance style color #d34e95 > distance style color #d34e92 > distance style color #d34e90 > distance style color #d34e8d > distance style color #d34e8b > distance style color #d34e8a > distance style color #d34f89 > distance style color #d34f88 > distance style color #d35087 > distance style color #d35186 > distance style color #d35285 > distance style color #d35283 > distance style color #d35382 > distance style color #d35381 > distance style color #d35380 > distance style color #d3547f > distance style color #d3547e > distance style color #d3547d > distance style color #d3547b > distance style color #d35478 > distance style color #d35476 > distance style color #d35573 > distance style color #d35571 > distance style color #d3556f > distance style color #d3566e > distance style color #d3566d > distance style color #d3566c > distance style color #d3566d > distance style color #d3576d > distance style color #d3566e > distance style color #d3566f > distance style color #d35670 > distance style color #d35771 > distance style color #d35772 > distance style color #d35873 > distance style color #d35874 > distance style color #d35875 > distance style color #d35975 > distance style color #d35976 > distance style color #d35a77 > color (#!4 & sel) #d35a77ff > color (#!4 & sel) #d35f76ff > color (#!4 & sel) #d36076ff > color (#!4 & sel) #d36177ff > color (#!4 & sel) #d36178ff > color (#!4 & sel) #d36278ff > color (#!4 & sel) #d36577ff > color (#!4 & sel) #d36875ff > color (#!4 & sel) #d36c73ff > color (#!4 & sel) #d36f71ff > color (#!4 & sel) #d36f70ff > color (#!4 & sel) #d37070ff > color (#!4 & sel) #d37071ff > color (#!4 & sel) #d37171ff > color (#!4 & sel) #d37672ff > color (#!4 & sel) #d37e75ff > color (#!4 & sel) #d38678ff > color (#!4 & sel) #d38d7aff > color (#!4 & sel) #d3937cff > color (#!4 & sel) #d3967cff > color (#!4 & sel) #d3977dff > color (#!4 & sel) #d3967cff > color (#!4 & sel) #d3957cff > color (#!4 & sel) #d3937cff > color (#!4 & sel) #d3927bff > color (#!4 & sel) #d3917bff > color (#!4 & sel) #d38f7aff > color (#!4 & sel) #d38e7aff > color (#!4 & sel) #d38d7aff > color (#!4 & sel) #d38c7aff > color (#!4 & sel) #d38b7aff > color (#!4 & sel) #d38a7aff > color (#!4 & sel) #d3897aff > color (#!4 & sel) #d3887aff > color (#!4 & sel) #d3877aff > color (#!4 & sel) #d3867aff > color (#!4 & sel) #d3857aff > color (#!4 & sel) #d3847bff > color (#!4 & sel) #d3827aff > color (#!4 & sel) #d3817aff > color (#!4 & sel) #d37e7aff > color (#!4 & sel) #d37f7aff > color (#!4 & sel) #d3807aff > color (#!4 & sel) #d3847aff > color (#!4 & sel) #d3867bff > color (#!4 & sel) #d3877bff > color (#!4 & sel) #d3887bff > color (#!4 & sel) #d3897bff > color (#!4 & sel) #d38a7cff > color (#!4 & sel) #d38b7cff > select #4/A:132 8 atoms, 7 bonds, 1 residue, 1 model selected > select #4/A:1 9 atoms, 8 bonds, 1 residue, 1 model selected > select #4/A:1-132 1033 atoms, 1052 bonds, 132 residues, 1 model selected > color sel #d38b7cff > select clear > select #4/A:359 4 atoms, 3 bonds, 1 residue, 1 model selected > select #4/A:378 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #4/A:359 13 atoms, 11 bonds, 2 residues, 1 model selected > show sel atoms > style sel ball Changed 13 atom styles > style sel stick Changed 13 atom styles > show sel atoms > select clear > select #4/A:359 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > hide sel cartoons > select clear > select #4/A:361 6 atoms, 5 bonds, 1 residue, 1 model selected > select #4/A:139 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select #4/A:359@N 1 atom, 1 residue, 1 model selected > select #4/A:378@OE1 1 atom, 1 residue, 1 model selected > select add #4/A:359@N 2 atoms, 2 residues, 1 model selected > ui mousemode right distance > distance #4/A:378@OE1 #4/A:359@N Distance between fold_lptd_grand_sp_43595_hsaccharolyticum_model_0.cif #4/A GLU 378 OE1 and GLY 359 N: 40.862Å > hide #!5 models > hide #!4 models > open ""/Users/vatetaud/Desktop/Protein/Deletion > /lap1/fold_lap1x2_sp/fold_lap1x2_sp_model_0.cif"" Chain information for fold_lap1x2_sp_model_0.cif #6 --- Chain | Description A B | . Computing secondary structure Drag select of 244 residues > ui tool show ""Find Cavities"" > kvfinder #6 17 cavities found for fold_lap1x2_sp_model_0.cif #6 fold_lap1x2_sp_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 6.1.1 | | 221.18 | 231.18 | 1024 | 6.43 | 2.87 6.1.8 | | 47.74 | 54.97 | 221 | 1.9 | 0.54 6.1.17 | | 27.43 | 41.55 | 127 | 1.7 | 0.38 6.1.2 | | 24.41 | 51.37 | 113 | 4.02 | 1.92 6.1.11 | | 20.95 | 26.85 | 97 | 1.34 | 0.41 6.1.16 | | 20.95 | 33.49 | 97 | 2.4 | 0.83 6.1.6 | | 19.01 | 38.34 | 88 | 0 | 0 6.1.10 | | 17.5 | 38.05 | 81 | 0.6 | 0.13 6.1.7 | | 17.28 | 36.68 | 80 | 0 | 0 6.1.4 | | 16.85 | 32.3 | 78 | 0 | 0 6.1.5 | | 16.85 | 32.3 | 78 | 0 | 0 6.1.14 | | 16.85 | 32.3 | 78 | 0 | 0 6.1.9 | | 13.82 | 22.69 | 64 | 1.8 | 0.58 6.1.3 | | 8.64 | 16.79 | 40 | 1.2 | 0.34 6.1.13 | | 7.34 | 15.07 | 34 | 0.85 | 0.28 6.1.15 | | 6.48 | 10.96 | 30 | 0.85 | 0.24 6.1.12 | | 6.05 | 14.22 | 28 | 0.6 | 0.02 Populating font family aliases took 7 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > color byattribute a:kvfinder_depth #6.1.1-3,8-13,15-17 1956 atoms, 12 residues, atom kvfinder_depth range 0 to 6.43 > color byattribute a:kvfinder_depth #6.1.1-3,8-13,15-17 1956 atoms, 12 residues, atom kvfinder_depth range 0 to 6.43 > view #6.1.1 @ zoom 0.75 moved plane near -31.125958660103066 [-0.85750559 -0.51428789 -0.01386201] moved plane far -31.125958660103066 [-0.85750559 -0.51428789 -0.01386201] > surface #6.1.1-17 transparency 50 > color #6.1.1-17 fromatoms transparency 50 > ~surface #6.1 > surface #6.1.1 > show #!6/A-B:43-45,67-69,108-113 > view #!6.1.8 @ zoom 0.75 moved plane near -15.791274704106833 [-0.22357886 0.80593182 0.5481664 ] moved plane far -15.791274704106833 [-0.22357886 0.80593182 0.5481664 ] > ~surface #6.1 > surface #!6.1.8 > show #!6/A:86-87,89-90/B:20,24,28,120-122 > undo > select add #6 4092 atoms, 1752 bonds, 261 residues, 21 models selected > select subtract #6 17 models selected > show #!1 models > hide #!1 models > mlp #!6#!6.1.1-17 Map values for surface ""fold_lap1x2_sp_model_0.cif_A SES surface"": minimum -28.33, mean -3.789, maximum 23.03 Map values for surface ""fold_lap1x2_sp_model_0.cif_B SES surface"": minimum -28.26, mean -3.676, maximum 23.02 To also show corresponding color key, enter the above mlp command and add key true > hide #!6#!6.1.1-17 surfaces > ui tool show ""Find Cavities"" > kvfinder #6 17 cavities found for fold_lap1x2_sp_model_0.cif #6 fold_lap1x2_sp_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 6.1.1 | | 221.18 | 231.18 | 1024 | 6.43 | 2.87 6.1.8 | | 47.74 | 54.97 | 221 | 1.9 | 0.54 6.1.17 | | 27.43 | 41.55 | 127 | 1.7 | 0.38 6.1.2 | | 24.41 | 51.37 | 113 | 4.02 | 1.92 6.1.11 | | 20.95 | 26.85 | 97 | 1.34 | 0.41 6.1.16 | | 20.95 | 33.49 | 97 | 2.4 | 0.83 6.1.6 | | 19.01 | 38.34 | 88 | 0 | 0 6.1.10 | | 17.5 | 38.05 | 81 | 0.6 | 0.13 6.1.7 | | 17.28 | 36.68 | 80 | 0 | 0 6.1.4 | | 16.85 | 32.3 | 78 | 0 | 0 6.1.5 | | 16.85 | 32.3 | 78 | 0 | 0 6.1.14 | | 16.85 | 32.3 | 78 | 0 | 0 6.1.9 | | 13.82 | 22.69 | 64 | 1.8 | 0.58 6.1.3 | | 8.64 | 16.79 | 40 | 1.2 | 0.34 6.1.13 | | 7.34 | 15.07 | 34 | 0.85 | 0.28 6.1.15 | | 6.48 | 10.96 | 30 | 0.85 | 0.24 6.1.12 | | 6.05 | 14.22 | 28 | 0.6 | 0.02 > view #6.1.1 @ zoom 0.75 moved plane near -22.604134716996935 [ 0.90306323 0.37409084 -0.21102814] moved plane far -22.604134716996935 [ 0.90306323 0.37409084 -0.21102814] > surface #6.1.1-17 transparency 50 > ~surface #6.1 > surface #6.1.1 > show #!6/A-B:43-45,67-69,108-113 > color byattribute a:kvfinder_depth #!6.1.1-3,8-13,15-17 1956 atoms, 12 residues, 12 surfaces, atom kvfinder_depth range 0 to 6.43 > view #!6.1.8 @ zoom 0.75 moved plane near -13.107169384330069 [ 0.9464462 0.00509193 -0.32282146] moved plane far -13.107169384330069 [ 0.9464462 0.00509193 -0.32282146] > ~surface #6.1 > surface #!6.1.8 > show #!6/A:86-87,89-90/B:20,24,28,120-122 > view #!6.1.1 @ zoom 0.75 moved plane near -24.177055707893413 [ 0.9464462 0.00509193 -0.32282146] moved plane far -24.177055707893413 [ 0.9464462 0.00509193 -0.32282146] > ~surface #6.1 > surface #!6.1.1 > show #!6/A-B:43-45,67-69,108-113 > close #6 > open ""/Users/vatetaud/Desktop/Protein/Deletion > /lap1/fold_lap1x2_sp/fold_lap1x2_sp_model_0.cif"" Chain information for fold_lap1x2_sp_model_0.cif #6 --- Chain | Description A B | . Computing secondary structure > select #6 1734 atoms, 1752 bonds, 244 residues, 1 model selected > color sel #d38b7cff > view > graphics silhouettes true > lighting full > ui mousemode right ""mark surface"" > ui mousemode right ""bond rotation"" > ui tool show ""Find Cavities"" > ui tool show ViewDock > ui tool show ""Find Cavities"" > kvfinder #6 17 cavities found for fold_lap1x2_sp_model_0.cif #6 fold_lap1x2_sp_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 6.1.1 | | 221.18 | 231.18 | 1024 | 6.43 | 2.87 6.1.8 | | 47.74 | 54.97 | 221 | 1.9 | 0.54 6.1.17 | | 27.43 | 41.55 | 127 | 1.7 | 0.38 6.1.2 | | 24.41 | 51.37 | 113 | 4.02 | 1.92 6.1.11 | | 20.95 | 26.85 | 97 | 1.34 | 0.41 6.1.16 | | 20.95 | 33.49 | 97 | 2.4 | 0.83 6.1.6 | | 19.01 | 38.34 | 88 | 0 | 0 6.1.10 | | 17.5 | 38.05 | 81 | 0.6 | 0.13 6.1.7 | | 17.28 | 36.68 | 80 | 0 | 0 6.1.4 | | 16.85 | 32.3 | 78 | 0 | 0 6.1.5 | | 16.85 | 32.3 | 78 | 0 | 0 6.1.14 | | 16.85 | 32.3 | 78 | 0 | 0 6.1.9 | | 13.82 | 22.69 | 64 | 1.8 | 0.58 6.1.3 | | 8.64 | 16.79 | 40 | 1.2 | 0.34 6.1.13 | | 7.34 | 15.07 | 34 | 0.85 | 0.28 6.1.15 | | 6.48 | 10.96 | 30 | 0.85 | 0.24 6.1.12 | | 6.05 | 14.22 | 28 | 0.6 | 0.02 > color byattribute a:kvfinder_depth #6.1.1-3,8-13,15-17 1956 atoms, 12 residues, atom kvfinder_depth range 0 to 6.43 > view #6.1.1 @ zoom 0.75 moved plane near -27.061409246234735 [0.84900576 0.17622275 0.4981313 ] moved plane far -27.061409246234735 [0.84900576 0.17622275 0.4981313 ] > surface #6.1.1-17 transparency 50 > color #6.1.1-17 fromatoms transparency 50 > ~surface #6.1 > surface #6.1.1 > select #!6 & (#6.1.1 @ select #6.1.1 1024 atoms, 1 residue, 1 model selected > show #!6/A-B:43-45,67-69,108-113 > select #!6/A:108@NH2 1 atom, 1 residue, 1 model selected > select #!6/B:108@NE 1 atom, 1 residue, 1 model selected > select add #!6/A:108@NE 2 atoms, 2 residues, 1 model selected Populating font family aliases took 19 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > distance #!6/B:108@NE #!6/A:108@NE Distance between fold_lap1x2_sp_model_0.cif #!6/B ARG 108 NE and /A ARG 108 NE: 17.856Å > show #!5 models > view #!6.1.8 @ zoom 0.75 moved plane near -12.708402947190232 [-0.97254267 -0.02950377 -0.23084693] moved plane far -12.708402947190232 [-0.97254267 -0.02950377 -0.23084693] > ~surface #6.1 > surface #!6.1.8 > select #!6 & (#!6.1.8 @ select #!6.1.8 221 atoms, 1 residue, 1 model selected > show #!6/A:86-87,89-90/B:20,24,28,120-122 > view #!6.1.17 @ zoom 0.75 moved plane near -12.54223349163726 [-0.97254267 -0.02950377 -0.23084693] moved plane far -12.54223349163726 [-0.97254267 -0.02950377 -0.23084693] > ~surface #6.1 > surface #!6.1.17 > select #!6 & (#!6.1.17 @ select #!6.1.17 127 atoms, 1 residue, 1 model selected > show #!6/A:20,24,28,120-122/B:86-87,89-90 > view #!6.1.8 @ zoom 0.75 moved plane near -16.484699224597843 [-0.75061338 0.09693522 -0.6535925 ] moved plane far -16.484699224597843 [-0.75061338 0.09693522 -0.6535925 ] > ~surface #6.1 > surface #!6.1.8 > select #!6 & (#!6.1.8 @ select #!6.1.8 221 atoms, 1 residue, 1 model selected > show #!6/A:86-87,89-90/B:20,24,28,120-122 > view #!6.1.2 @ zoom 0.75 moved plane near -15.013868880771149 [-0.97376724 0.22747395 -0.00574465] moved plane far -15.013868880771149 [-0.97376724 0.22747395 -0.00574465] > ~surface #6.1 > surface #!6.1.2 > select #!6 & (#!6.1.2 @ select #!6.1.2 113 atoms, 1 residue, 1 model selected > show #!6/A:108/B:33,36-37,41-43,47,65,67,115 > select #!6/B:114 7 atoms, 6 bonds, 1 residue, 1 model selected > view #!6.1.17 @ zoom 0.75 moved plane near -16.946234935351 [-0.98172148 -0.18688865 -0.03599449] moved plane far -16.946234935351 [-0.98172148 -0.18688865 -0.03599449] > ~surface #6.1 > surface #!6.1.17 > select #!6 & (#!6.1.17 @ select #!6.1.17 127 atoms, 1 residue, 1 model selected > show #!6/A:20,24,28,120-122/B:86-87,89-90 > view #!6.1.10 @ zoom 0.75 moved plane near -19.171909757717312 [-0.81757263 -0.39502928 -0.4189593 ] moved plane far -19.171909757717312 [-0.81757263 -0.39502928 -0.4189593 ] > ~surface #6.1 > surface #!6.1.10 > select #!6 & (#!6.1.10 @ select #!6.1.10 81 atoms, 1 residue, 1 model selected > show #!6/A:117/B:52,61-63,81,93,95,117 > view #!6.1.16 @ zoom 0.75 moved plane near -14.539305096435362 [-0.88383786 0.03768197 -0.46627324] moved plane far -14.539305096435362 [-0.88383786 0.03768197 -0.46627324] > ~surface #6.1 > surface #!6.1.16 > select #!6 & (#!6.1.16 @ select #!6.1.16 97 atoms, 1 residue, 1 model selected > show #!6/A:53-54,57-60,101,103 > view #!6.1.10 @ zoom 0.75 moved plane near -18.865586300966005 [-0.68486202 0.37056163 -0.62741384] moved plane far -18.865586300966005 [-0.68486202 0.37056163 -0.62741384] > ~surface #6.1 > surface #!6.1.10 > select #!6 & (#!6.1.10 @ select #!6.1.10 81 atoms, 1 residue, 1 model selected > show #!6/A:117/B:52,61-63,81,93,95,117 > color #6.1.10 #c6f5b6 > color #6.1.10 #c6f5b5 > color #6.1.10 #c3f5af > color #6.1.10 #c1f5ab > color #6.1.10 #c0f5a9 > color #6.1.10 #b4f5a1 > color #6.1.10 #a7f597 > color #6.1.10 #a5f596 > color #6.1.10 #a3f595 > view #!6.1.11 @ zoom 0.75 moved plane near -14.547969793325057 [-0.68486202 0.37056163 -0.62741384] moved plane far -14.547969793325057 [-0.68486202 0.37056163 -0.62741384] > ~surface #6.1 > surface #!6.1.11 > select #!6 & (#!6.1.11 @ select #!6.1.11 97 atoms, 1 residue, 1 model selected > show #!6/A:52,81,93,95,117/B:117 > color #6.1.10 #8ff583 > color #6.1.11 #6af59e > color #6.1.11 #6bf59d > color #6.1.11 #70f59c > color #6.1.11 #7bf59b > color #6.1.11 #82f599 > color #6.1.11 #86f598 > color #6.1.11 #8af592 > view #!6.1.4-5,7,10-11,14,16 @ zoom 0.75 moved plane near -37.804762223557084 [-0.68486202 0.37056163 -0.62741384] moved plane far -37.804762223557084 [-0.68486202 0.37056163 -0.62741384] > ~surface #6.1 > surface #!6.1.4-5,7,10-11,14,16 > select #!6 & (#!6.1.4-5,7,10-11,14,16 @ select #!6.1.4-5,7,10-11,14,16 589 atoms, 7 residues, 7 models selected > show > #!6/A:20-21,28,49,52-54,57-60,63,67,81,93,95-97,101,103,108,112-115,117-118,120/B:20-21,28,49,52,61-63,67,81,93,95-97,108,112-115,117-118,120 > view #!6.1.4-5,10-11,14,16 @ zoom 0.75 moved plane near -35.38763134015136 [-0.6514393 0.5791903 -0.4900668] moved plane far -35.38763134015136 [-0.6514393 0.5791903 -0.4900668] > ~surface #6.1 > surface #!6.1.4-5,10-11,14,16 > select #!6 & (#!6.1.4-5,10-11,14,16 @ select #!6.1.4-5,10-11,14,16 509 atoms, 6 residues, 6 models selected > show > #!6/A:20-21,28,49,52-54,57-60,63,67,81,93,95-97,101,103,108,112-115,117-118,120/B:52,61-63,67,81,93,95-97,108,112-115,117 > view #!6.1.4-5,10-11,14 @ zoom 0.75 moved plane near -32.36504218306514 [-0.6514393 0.5791903 -0.4900668] moved plane far -32.36504218306514 [-0.6514393 0.5791903 -0.4900668] > ~surface #6.1 > surface #!6.1.4-5,10-11,14 > select #!6 & (#!6.1.4-5,10-11,14 @ select #!6.1.4-5,10-11,14 412 atoms, 5 residues, 5 models selected > show > #!6/A:20-21,28,49,52,63,67,81,93,95-97,108,112-115,117-118,120/B:52,61-63,67,81,93,95-97,108,112-115,117 > view #!6.1.4-5,10-11 @ zoom 0.75 moved plane near -27.410047439647958 [-0.6514393 0.5791903 -0.4900668] moved plane far -27.410047439647958 [-0.6514393 0.5791903 -0.4900668] > ~surface #6.1 > surface #!6.1.4-5,10-11 > select #!6 & (#!6.1.4-5,10-11 @ select #!6.1.4-5,10-11 334 atoms, 4 residues, 4 models selected > show > #!6/A:52,67,81,93,95-97,108,112-115,117/B:52,61-63,67,81,93,95-97,108,112-115,117 > view #!6.1.4,10-11 @ zoom 0.75 moved plane near -26.91733395136454 [-0.6514393 0.5791903 -0.4900668] moved plane far -26.91733395136454 [-0.6514393 0.5791903 -0.4900668] > ~surface #6.1 > surface #!6.1.4,10-11 > select #!6 & (#!6.1.4,10-11 @ select #!6.1.4,10-11 256 atoms, 3 residues, 3 models selected > show #!6/A:52,67,81,93,95,114-115,117/B:52,61-63,81,93,95-97,108,112-114,117 > view #!6.1.10-11 @ zoom 0.75 moved plane near -21.82197918501174 [-0.6514393 0.5791903 -0.4900668] moved plane far -21.82197918501174 [-0.6514393 0.5791903 -0.4900668] > ~surface #6.1 > surface #!6.1.10-11 > select #!6 & (#!6.1.10-11 @ select #!6.1.10-11 178 atoms, 2 residues, 2 models selected > show #!6/A:52,81,93,95,117/B:52,61-63,81,93,95,117 > select #!6/B:53 8 atoms, 7 bonds, 1 residue, 1 model selected Drag select of 16 atoms, 3 residues, 8 bonds > select #!6/A:81@OE1 1 atom, 1 residue, 1 model selected > select #!6/B:52@CG2 1 atom, 1 residue, 1 model selected > select add #!6/A:81@OE1 2 atoms, 1 bond, 2 residues, 1 model selected > select subtract #!6/A:81@OE1 1 atom, 1 residue, 1 model selected > select add #!6/A:81@OE1 2 atoms, 2 residues, 1 model selected > distance #!6/B:52@CG2 #!6/A:81@OE1 Distance between fold_lap1x2_sp_model_0.cif #!6/B ILE 52 CG2 and /A GLN 81 OE1: 15.435Å > color #6.1.11 #88f5b9 > color #6.1.11 #93f5b8 > color #6.1.11 #9bf5bc > color #6.1.11 #bff5db > color #6.1.11 #cef5ef > color #6.1.11 #daebf5 > color #6.1.11 #dce3f5 > color #6.1.11 #e9cff5 > color #6.1.11 #e9cef5 > color #6.1.11 #e8cef5 > color #6.1.11 #e6cdf5 > color #6.1.11 #ddc5f5 > color #6.1.11 #d1baf5 > color #6.1.11 #cfb7f5 > color #6.1.11 #ceb5f5 > color #6.1.11 #c7abf5 > color #6.1.11 #c7aaf5 > color #6.1.11 #c6aaf5 > color #6.1.11 #c3a9f5 > color #6.1.11 #c2a9f5 > color #6.1.11 #c0a9f5 > color #6.1.11 #bfa8f5 > color #6.1.11 #bea6f5 > color #6.1.11 #bca3f5 > color #6.1.11 #bba3f5 > color #6.1.11 #9b93f5 > color #6.1.11 #958ff5 > color #6.1.11 #958df5 > color #6.1.11 #9188f5 > color #6.1.11 #7f74f5 > color #6.1.11 #7e73f5 > color #6.1.11 #7b6ff5 > color #6.1.11 #7b70f5 > color #6.1.11 #7b71f5 > color #6.1.11 #7670f5 > color #6.1.11 #636cf5 > color #6.1.11 #5963f5 > color #6.1.11 #527af5 > color #6.1.11 #537ff5 > color #6.1.11 #547ff5 > color #6.1.11 #5580f5 > color #6.1.11 #567ff5 > color #6.1.11 #577ff5 > color #6.1.11 #587ff5 > color #6.1.11 #5b7ef5 > color #6.1.11 #5c7bf5 > color #6.1.11 #5c7af5 > color #6.1.10 #b2f1b4 > color #6.1.10 #b4f1b8 > color #6.1.10 #cff0f1 > color #6.1.10 #bdc7f1 > color #6.1.10 #a8a1f1 > color #6.1.10 #9f8ff1 > color #6.1.10 #9985f1 > color #6.1.10 #9882f1 > color #6.1.10 #9782f1 > color #6.1.10 #957ff1 > color #6.1.10 #9177f1 > color #6.1.10 #8d77f1 > color #6.1.10 #8b7df1 > color #6.1.10 #8b82f1 > color #6.1.10 #8a86f1 > color #6.1.10 #8a88f1 > color #6.1.10 #8a89f1 > color #6.1.10 #8c8ff1 > color #6.1.10 #939df1 > color #6.1.10 #95a1f1 > color #6.1.10 #9babf1 > color #6.1.10 #a1bcf1 > color #6.1.10 #a1bdf1 > color #6.1.10 #a0baf1 > color #6.1.10 #9eb8f1 > color #6.1.10 #96b5f1 > color #6.1.10 #95b5f1 > color #6.1.10 #91c8f1 > color #6.1.10 #90c8f1 > color #6.1.10 #88bdf1 > color #6.1.10 #7eb4f1 > color #6.1.10 #77abf1 > color #6.1.10 #76aaf1 > color #6.1.10 #74b9f1 > color #6.1.10 #73bef1 > color #6.1.10 #74b8f1 > color #6.1.10 #73a0f1 > color #6.1.10 #7399f1 > color #6.1.10 #7497f1 > color #6.1.10 #7590f1 > color #6.1.10 #758df1 > color #6.1.10 #768cf1 > color #6.1.10 #778cf1 > color #6.1.10 #7989f1 > color #6.1.10 #7988f1 > color #6.1.10 #7a8af1 > color #6.1.10 #7f91f1 > color #6.1.10 #8093f1 > color #6.1.10 #8194f1 > color #6.1.10 #849af1 > color #6.1.10 #89a3f1 > color #6.1.10 #8aa8f1 > color #6.1.10 #8ba9f1 > color #6.1.10 #8cacf1 > color #6.1.10 #8eb1f1 > color #6.1.10 #8faef1 > color #6.1.10 #8fabf1 > color #6.1.10 #90a5f1 > color #6.1.10 #8d9ef1 > color #6.1.10 #8895f1 > color #6.1.10 #838cf1 > color #6.1.10 #817ff1 > color #6.1.10 #807ef1 > color #6.1.10 #7e7df1 > color #6.1.10 #7c7df1 > color #6.1.10 #797ef1 > color #6.1.10 #7988f1 > color #6.1.10 #798df1 > color #6.1.10 #7a90f1 > color #6.1.10 #7b91f1 > color #6.1.10 #7c90f1 > color #6.1.10 #7e90f1 > color #6.1.10 #7f91f1 > color #6.1.10 #7f93f1 > color #6.1.10 #8094f1 > color #6.1.10 #8197f1 > color #6.1.10 #829cf1 > color #6.1.10 #819bf1 > color #6.1.10 #829af1 > color #6.1.10 #8299f1 > color #6.1.10 #8296f1 > color #6.1.10 #8394f1 > color #6.1.10 #8493f1 > color #6.1.10 #8492f1 > color #6.1.10 #8491f1 > view #!6.1.1 @ zoom 0.75 moved plane near -23.72298270621744 [ 0.49951015 -0.11965271 0.85800516] moved plane far -23.72298270621744 [ 0.49951015 -0.11965271 0.85800516] > ~surface #6.1 > surface #!6.1.1 > select #!6 & (#!6.1.1 @ select #!6.1.1 1024 atoms, 1 residue, 1 model selected > show #!6/A-B:43-45,67-69,108-113 > mlp sel mlp: no amino acids specified > mlp sel mlp: no amino acids specified > view #!6.1.16 @ zoom 0.75 moved plane near -16.011671135320736 [-0.96200577 0.18018354 -0.20513124] moved plane far -16.011671135320736 [-0.96200577 0.18018354 -0.20513124] > ~surface #6.1 > surface #!6.1.16 > select #!6 & (#!6.1.16 @ select #!6.1.16 97 atoms, 1 residue, 1 model selected > show #!6/A:53-54,57-60,101,103 > view #!6.1.10 @ zoom 0.75 moved plane near -20.180647625910392 [-0.96200577 0.18018354 -0.20513124] moved plane far -20.180647625910392 [-0.96200577 0.18018354 -0.20513124] > ~surface #6.1 > surface #!6.1.10 > select #!6 & (#!6.1.10 @ select #!6.1.10 81 atoms, 1 residue, 1 model selected > show #!6/A:117/B:52,61-63,81,93,95,117 > view #!6.1.11 @ zoom 0.75 moved plane near -17.11213269306369 [-0.96200577 0.18018354 -0.20513124] moved plane far -17.11213269306369 [-0.96200577 0.18018354 -0.20513124] > ~surface #6.1 > surface #!6.1.11 > select #!6 & (#!6.1.11 @ select #!6.1.11 97 atoms, 1 residue, 1 model selected > show #!6/A:52,81,93,95,117/B:117 > view #!6.1.10-11 @ zoom 0.75 moved plane near -25.187514522114487 [-0.96200577 0.18018354 -0.20513124] moved plane far -25.187514522114487 [-0.96200577 0.18018354 -0.20513124] > ~surface #6.1 > surface #!6.1.10-11 > select #!6 & (#!6.1.10-11 @ select #!6.1.10-11 178 atoms, 2 residues, 2 models selected > show #!6/A:52,81,93,95,117/B:52,61-63,81,93,95,117 > mlp sel mlp: no amino acids specified > mlp sel mlp: no amino acids specified > mlp sel mlp: no amino acids specified > view #!6.1.1 @ zoom 0.75 moved plane near -27.33729251885039 [-0.96200577 0.18018354 -0.20513124] moved plane far -27.33729251885039 [-0.96200577 0.18018354 -0.20513124] > ~surface #6.1 > surface #!6.1.1 > select #!6 & (#!6.1.1 @ select #!6.1.1 1024 atoms, 1 residue, 1 model selected > show #!6/A-B:43-45,67-69,108-113 > select #6 4092 atoms, 1752 bonds, 2 pseudobonds, 261 residues, 20 models selected > mlp sel Map values for surface ""fold_lap1x2_sp_model_0.cif_A SES surface"": minimum -28.33, mean -3.789, maximum 23.03 Map values for surface ""fold_lap1x2_sp_model_0.cif_B SES surface"": minimum -28.26, mean -3.676, maximum 23.02 To also show corresponding color key, enter the above mlp command and add key true > view > hide #!5 models > close #10 > close #6 > open ""/Users/vatetaud/Desktop/Protein/Deletion > /Lap2/fold_lap2_sp/fold_lap2_sp_model_0.cif"" Chain information for fold_lap2_sp_model_0.cif #6 --- Chain | Description A | . Computing secondary structure > select #6 2579 atoms, 2606 bonds, 351 residues, 1 model selected > color sel medium blue > ui tool show ""Find Cavities"" > kvfinder #6 12 cavities found for fold_lap2_sp_model_0.cif #6 fold_lap2_sp_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 6.1.11 | | 283.61 | 276.99 | 1313 | 3.84 | 1.03 6.1.6 | | 110.16 | 129.26 | 510 | 3.39 | 0.84 6.1.2 | | 77.76 | 99.51 | 360 | 3.29 | 1.45 6.1.10 | | 66.96 | 85.65 | 310 | 2.68 | 0.77 6.1.12 | | 57.89 | 90.17 | 268 | 0 | 0 6.1.4 | | 43.42 | 69.87 | 201 | 0 | 0 6.1.1 | | 38.02 | 44.71 | 176 | 1.7 | 0.5 6.1.3 | | 33.05 | 42.59 | 153 | 1.47 | 0.43 6.1.9 | | 25.49 | 40.78 | 118 | 0 | 0 6.1.7 | | 17.93 | 27.97 | 83 | 1.34 | 0.5 6.1.8 | | 15.77 | 29.32 | 73 | 1.2 | 0.38 6.1.5 | | 11.45 | 24.03 | 53 | 1.2 | 0.23 > color byattribute a:kvfinder_depth #6.1.1-3,5-8,10-11 3031 atoms, 9 residues, atom kvfinder_depth range 0 to 3.84 > ui tool show ""Find Cavities"" > kvfinder #6 12 cavities found for fold_lap2_sp_model_0.cif #6 fold_lap2_sp_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 6.1.11 | | 283.61 | 276.99 | 1313 | 3.84 | 1.03 6.1.6 | | 110.16 | 129.26 | 510 | 3.39 | 0.84 6.1.2 | | 77.76 | 99.51 | 360 | 3.29 | 1.45 6.1.10 | | 66.96 | 85.65 | 310 | 2.68 | 0.77 6.1.12 | | 57.89 | 90.17 | 268 | 0 | 0 6.1.4 | | 43.42 | 69.87 | 201 | 0 | 0 6.1.1 | | 38.02 | 44.71 | 176 | 1.7 | 0.5 6.1.3 | | 33.05 | 42.59 | 153 | 1.47 | 0.43 6.1.9 | | 25.49 | 40.78 | 118 | 0 | 0 6.1.7 | | 17.93 | 27.97 | 83 | 1.34 | 0.5 6.1.8 | | 15.77 | 29.32 | 73 | 1.2 | 0.38 6.1.5 | | 11.45 | 24.03 | 53 | 1.2 | 0.23 > color byattribute a:kvfinder_depth #6.1.1-3,5-8,10-11 3031 atoms, 9 residues, atom kvfinder_depth range 0 to 3.84 > view #6.1.11 @ zoom 0.75 moved plane near -27.71425943727883 [-0.83940726 -0.44868236 -0.306724 ] moved plane far -27.71425943727883 [-0.83940726 -0.44868236 -0.306724 ] > surface #6.1.1-12 transparency 50 > color #6.1.1-12 fromatoms transparency 50 > ~surface #6.1 > surface #6.1.11 > select #!6 & (#6.1.11 @ select #6.1.11 1313 atoms, 1 residue, 1 model selected > show #!6/A:195-199,224,227-228,231,235-247,256-262 Populating font family aliases took 10 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > mlp sel mlp: no amino acids specified > select #6 6197 atoms, 2606 bonds, 363 residues, 14 models selected > mlp sel Map values for surface ""fold_lap2_sp_model_0.cif_A SES surface"": minimum -28.04, mean -6.596, maximum 22.28 To also show corresponding color key, enter the above mlp command and add key true > movie record > turn y 2 180 > wait 180 > movie encode /Users/vatetaud/Desktop/movie3.mp4 Movie saved to /Users/vatetaud/Desktop/movie3.mp4 > movie record > turn y 2 180 > wait 180 > movie encode /Users/vatetaud/Desktop/movie4.mp4 Movie saved to /Users/vatetaud/Desktop/movie4.mp4 > hide sel surfaces > view #!6.1.6 @ zoom 0.75 moved plane near -20.842152079924887 [-0.46155622 0.78009523 -0.42239472] moved plane far -20.842152079924887 [-0.46155622 0.78009523 -0.42239472] > ~surface #6.1 > surface #!6.1.6 > select #!6 & (#!6.1.6 @ select #!6.1.6 510 atoms, 1 residue, 1 model selected > show #!6/A:12,57,61,70,74,84-87,92,175-176,178-180,208-212,214 > view > view #!6.1.6,11 @ zoom 0.75 moved plane near -56.705825757454456 [-0.27091912 -0.31354876 -0.9101044 ] moved plane far -56.705825757454456 [-0.27091912 -0.31354876 -0.9101044 ] > ~surface #6.1 > surface #!6.1.6,11 > select #!6 & (#!6.1.6,11 @ select #!6.1.6,11 1823 atoms, 2 residues, 2 models selected > show > #!6/A:12,57,61,70,74,84-87,92,175-176,178-180,195-199,208-212,214,224,227-228,231,235-247,256-262 > view > movie record > turn y 2 180 > wait 180 > movie encode /Users/vatetaud/Desktop/movie5.mp4 Movie saved to /Users/vatetaud/Desktop/movie5.mp4 > save ""/Users/vatetaud/Desktop/Protein/Deletion > /Lap2/fold_lap2_sp/fold_lap2_sp_cavity.cxs"" > open ""/Users/vatetaud/Desktop/Protein/Deletion > /lap1/fold_lap1x2_sp/fold_lap1x2_sp_model_0.cif"" Chain information for fold_lap1x2_sp_model_0.cif #7 --- Chain | Description A B | . Computing secondary structure > close #6 > ui tool show ""Find Cavities"" > kvfinder #7 17 cavities found for fold_lap1x2_sp_model_0.cif #7 fold_lap1x2_sp_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 7.1.1 | | 221.18 | 231.18 | 1024 | 6.43 | 2.87 7.1.8 | | 47.74 | 54.97 | 221 | 1.9 | 0.54 7.1.17 | | 27.43 | 41.55 | 127 | 1.7 | 0.38 7.1.2 | | 24.41 | 51.37 | 113 | 4.02 | 1.92 7.1.11 | | 20.95 | 26.85 | 97 | 1.34 | 0.41 7.1.16 | | 20.95 | 33.49 | 97 | 2.4 | 0.83 7.1.6 | | 19.01 | 38.34 | 88 | 0 | 0 7.1.10 | | 17.5 | 38.05 | 81 | 0.6 | 0.13 7.1.7 | | 17.28 | 36.68 | 80 | 0 | 0 7.1.4 | | 16.85 | 32.3 | 78 | 0 | 0 7.1.5 | | 16.85 | 32.3 | 78 | 0 | 0 7.1.14 | | 16.85 | 32.3 | 78 | 0 | 0 7.1.9 | | 13.82 | 22.69 | 64 | 1.8 | 0.58 7.1.3 | | 8.64 | 16.79 | 40 | 1.2 | 0.34 7.1.13 | | 7.34 | 15.07 | 34 | 0.85 | 0.28 7.1.15 | | 6.48 | 10.96 | 30 | 0.85 | 0.24 7.1.12 | | 6.05 | 14.22 | 28 | 0.6 | 0.02 > color byattribute a:kvfinder_depth #7.1.1-3,8-13,15-17 1956 atoms, 12 residues, atom kvfinder_depth range 0 to 6.43 > view #7.1.1 @ zoom 0.75 moved plane near -24.761416809315786 [-0.0075937 0.92096027 -0.38958252] moved plane far -24.761416809315786 [-0.0075937 0.92096027 -0.38958252] > surface #7.1.1-17 transparency 50 > color #7.1.1-17 fromatoms transparency 50 > ~surface #7.1 > surface #7.1.1 > select #!7 & (#7.1.1 @ select #7.1.1 1024 atoms, 1 residue, 1 model selected > show #!7/A-B:43-45,67-69,108-113 > view #!7.1.9 @ zoom 0.75 moved plane near -12.070348786215753 [-0.01108152 0.88612304 -0.46331758] moved plane far -12.070348786215753 [-0.01108152 0.88612304 -0.46331758] > ~surface #7.1 > surface #!7.1.9 > select #!7 & (#!7.1.9 @ select #!7.1.9 64 atoms, 1 residue, 1 model selected > show #!7/A:55,80,98,103,106-107/B:41 > view #!7.1.3 @ zoom 0.75 moved plane near -11.208285647160835 [-0.01108152 0.88612304 -0.46331758] moved plane far -11.208285647160835 [-0.01108152 0.88612304 -0.46331758] > ~surface #7.1 > surface #!7.1.3 > select #!7 & (#!7.1.3 @ select #!7.1.3 40 atoms, 1 residue, 1 model selected > show #!7/A:41/B:55,80,98,103,106-107 > view #!7.1.13 @ zoom 0.75 moved plane near -11.86948019332055 [-0.01108152 0.88612304 -0.46331758] moved plane far -11.86948019332055 [-0.01108152 0.88612304 -0.46331758] > ~surface #7.1 > surface #!7.1.13 > select #!7 & (#!7.1.13 @ select #!7.1.13 34 atoms, 1 residue, 1 model selected > show #!7/A:85,87-91/B:121 > view #!7.1.15 @ zoom 0.75 moved plane near -12.811544072106082 [-0.01108152 0.88612304 -0.46331758] moved plane far -12.811544072106082 [-0.01108152 0.88612304 -0.46331758] > ~surface #7.1 > surface #!7.1.15 > select #!7 & (#!7.1.15 @ select #!7.1.15 30 atoms, 1 residue, 1 model selected > show #!7/A:17-18,21-22,51,60 > view #!7.1.12 @ zoom 0.75 moved plane near -14.04005115068538 [-0.01108152 0.88612304 -0.46331758] moved plane far -14.04005115068538 [-0.01108152 0.88612304 -0.46331758] > ~surface #7.1 > surface #!7.1.12 > select #!7 & (#!7.1.12 @ select #!7.1.12 28 atoms, 1 residue, 1 model selected > show #!7/B:13,16-17,120,122 > view #!7.1.10 @ zoom 0.75 moved plane near -16.502304700748184 [-0.01108152 0.88612304 -0.46331758] moved plane far -16.502304700748184 [-0.01108152 0.88612304 -0.46331758] > ~surface #7.1 > surface #!7.1.10 > select #!7 & (#!7.1.10 @ select #!7.1.10 81 atoms, 1 residue, 1 model selected > show #!7/A:117/B:52,61-63,81,93,95,117 > view #!7.1.5 @ zoom 0.75 moved plane near -14.865165761270987 [-0.54731525 0.06725025 -0.83422026] moved plane far -14.865165761270987 [-0.54731525 0.06725025 -0.83422026] > ~surface #7.1 > surface #!7.1.5 > select #!7 & (#!7.1.5 @ select #!7.1.5 78 atoms, 1 residue, 1 model selected > show #!7/A:95-97,108,112-114/B:67,114-115 > view #!7.1.10 @ zoom 0.75 moved plane near -18.960531008187672 [-0.54731525 0.06725025 -0.83422026] moved plane far -18.960531008187672 [-0.54731525 0.06725025 -0.83422026] > ~surface #7.1 > surface #!7.1.10 > select #!7 & (#!7.1.10 @ select #!7.1.10 81 atoms, 1 residue, 1 model selected > show #!7/A:117/B:52,61-63,81,93,95,117 > view #!7.1.9 @ zoom 0.75 moved plane near -15.443774410483902 [-0.35703425 -0.2843109 -0.88977181] moved plane far -15.443774410483902 [-0.35703425 -0.2843109 -0.88977181] > ~surface #7.1 > surface #!7.1.9 > select #!7 & (#!7.1.9 @ select #!7.1.9 64 atoms, 1 residue, 1 model selected > show #!7/A:55,80,98,103,106-107/B:41 > view #!7.1.4 @ zoom 0.75 moved plane near -15.771343658739555 [-0.6258038 -0.40665492 -0.66558351] moved plane far -15.771343658739555 [-0.6258038 -0.40665492 -0.66558351] > ~surface #7.1 > surface #!7.1.4 > select #!7 & (#!7.1.4 @ select #!7.1.4 78 atoms, 1 residue, 1 model selected > show #!7/A:67,114-115/B:95-97,108,112-114 > view #!7.1.3 @ zoom 0.75 moved plane near -14.32925308289731 [-0.6258038 -0.40665492 -0.66558351] moved plane far -14.32925308289731 [-0.6258038 -0.40665492 -0.66558351] > ~surface #7.1 > surface #!7.1.3 > select #!7 & (#!7.1.3 @ select #!7.1.3 40 atoms, 1 residue, 1 model selected > show #!7/A:41/B:55,80,98,103,106-107 > view #!7.1.13 @ zoom 0.75 moved plane near -14.157257716450507 [-0.6258038 -0.40665492 -0.66558351] moved plane far -14.157257716450507 [-0.6258038 -0.40665492 -0.66558351] > ~surface #7.1 > surface #!7.1.13 > select #!7 & (#!7.1.13 @ select #!7.1.13 34 atoms, 1 residue, 1 model selected > show #!7/A:85,87-91/B:121 > view #!7.1.5 @ zoom 0.75 moved plane near -15.17863281739283 [-0.6258038 -0.40665492 -0.66558351] moved plane far -15.17863281739283 [-0.6258038 -0.40665492 -0.66558351] > ~surface #7.1 > surface #!7.1.5 > select #!7 & (#!7.1.5 @ select #!7.1.5 78 atoms, 1 residue, 1 model selected > show #!7/A:95-97,108,112-114/B:67,114-115 > view #!7.1.14 @ zoom 0.75 moved plane near -11.06245230975077 [-0.6258038 -0.40665492 -0.66558351] moved plane far -11.06245230975077 [-0.6258038 -0.40665492 -0.66558351] > ~surface #7.1 > surface #!7.1.14 > select #!7 & (#!7.1.14 @ select #!7.1.14 78 atoms, 1 residue, 1 model selected > show #!7/A:20-21,28,49,63,118,120 > view #!7.1.7 @ zoom 0.75 moved plane near -13.137150701372148 [-0.6258038 -0.40665492 -0.66558351] moved plane far -13.137150701372148 [-0.6258038 -0.40665492 -0.66558351] > ~surface #7.1 > surface #!7.1.7 > select #!7 & (#!7.1.7 @ select #!7.1.7 80 atoms, 1 residue, 1 model selected > show #!7/B:20-21,28,49,63,118,120 > view #!7.1.10 @ zoom 0.75 moved plane near -18.768455649065714 [-0.6258038 -0.40665492 -0.66558351] moved plane far -18.768455649065714 [-0.6258038 -0.40665492 -0.66558351] > ~surface #7.1 > surface #!7.1.10 > select #!7 & (#!7.1.10 @ select #!7.1.10 81 atoms, 1 residue, 1 model selected > show #!7/A:117/B:52,61-63,81,93,95,117 > view #!7.1.11 @ zoom 0.75 moved plane near -14.877634976073429 [-0.6258038 -0.40665492 -0.66558351] moved plane far -14.877634976073429 [-0.6258038 -0.40665492 -0.66558351] > ~surface #7.1 > surface #!7.1.11 > select #!7 & (#!7.1.11 @ select #!7.1.11 97 atoms, 1 residue, 1 model selected > show #!7/A:52,81,93,95,117/B:117 > view #!7.1.6,10-11 @ zoom 0.75 moved plane near -27.641652114120756 [-0.67579906 -0.37858377 -0.6324318 ] moved plane far -27.641652114120756 [-0.67579906 -0.37858377 -0.6324318 ] > ~surface #7.1 > surface #!7.1.6,10-11 > select #!7 & (#!7.1.6,10-11 @ select #!7.1.6,10-11 266 atoms, 3 residues, 3 models selected > show #!7/A:33,36,43,47,52,65,81,93,95,115,117/B:52,61-63,81,93,95,108,117 > view #!7.1.10-11 @ zoom 0.75 moved plane near -22.019034983401387 [-0.67579906 -0.37858377 -0.6324318 ] moved plane far -22.019034983401387 [-0.67579906 -0.37858377 -0.6324318 ] > ~surface #7.1 > surface #!7.1.10-11 > select #!7 & (#!7.1.10-11 @ select #!7.1.10-11 178 atoms, 2 residues, 2 models selected > show #!7/A:52,81,93,95,117/B:52,61-63,81,93,95,117 > view #!7.1.1,10-11 @ zoom 0.75 moved plane near -32.68024535019525 [-0.67579906 -0.37858377 -0.6324318 ] moved plane far -32.68024535019525 [-0.67579906 -0.37858377 -0.6324318 ] > ~surface #7.1 > surface #!7.1.1,10-11 > select #!7 & (#!7.1.1,10-11 @ select #!7.1.1,10-11 1202 atoms, 3 residues, 3 models selected > show > #!7/A:43-45,52,67-69,81,93,95,108-113,117/B:43-45,52,61-63,67-69,81,93,95,108-113,117 > view > movie record > turn y 2 180 > wait 180 > movie encode /Users/vatetaud/Desktop/movie6.mp4 Movie saved to /Users/vatetaud/Desktop/movie6.mp4 > mlp sel mlp: no amino acids specified > mlp sel mlp: no amino acids specified > select #7 4092 atoms, 1752 bonds, 261 residues, 19 models selected > mlp sel Map values for surface ""fold_lap1x2_sp_model_0.cif_A SES surface"": minimum -28.33, mean -3.789, maximum 23.03 Map values for surface ""fold_lap1x2_sp_model_0.cif_B SES surface"": minimum -28.26, mean -3.676, maximum 23.02 To also show corresponding color key, enter the above mlp command and add key true > movie record > turn y 2 180 > wait 180 > movie encode /Users/vatetaud/Desktop/movie7.mp4 Movie saved to /Users/vatetaud/Desktop/movie7.mp4 > select #7 4092 atoms, 1752 bonds, 261 residues, 19 models selected > close #7 > open ""/Users/vatetaud/Desktop/Protein/Deletion > /RuvC/Initial/fold_ruvc_omc_vp/fold_ruvc_omc_vp_model_0.cif"" Chain information for fold_ruvc_omc_vp_model_0.cif #6 --- Chain | Description A | . Computing secondary structure > select #6 1394 atoms, 1423 bonds, 175 residues, 1 model selected > color sel blue > color sel #7aec7dff > color sel #7bec7dff > color sel #7bec7eff > color sel #7dec80ff > color sel #83ec89ff > color sel #8fec9cff > color sel #9becb0ff > color sel #a6ecc5ff > color sel #afecdaff > color sel #b1e9ecff > color sel #add6ecff > color sel #a7c7ecff > color sel #a1bbecff > color sel #9cb2ecff > color sel #98acecff > color sel #96a9ecff > color sel #94a5ecff > color sel #93a3ecff > color sel #91a0ecff > color sel #8f9cecff > color sel #8c98ecff > color sel #8a94ecff > color sel #888eecff > color sel #8588ecff > color sel #8385ecff > color sel #8282ecff > color sel #8382ecff > color sel #8483ecff > color sel #8684ecff > color sel #8886ecff > color sel #8b88ecff > color sel #8f8aecff > color sel #938cecff > color sel #968eecff > color sel #988fecff > color sel #9a91ecff > color sel #9d94ecff > color sel #a197ecff > color sel #a59aecff > color sel #a99cecff > color sel #ad9fecff > color sel #b0a1ecff > color sel #b3a4ecff > color sel #b5a6ecff > color sel #b8a8ecff > color sel #baaaecff > color sel #bbabecff > color sel #bcabecff > color sel #bbabecff > color sel #baabecff > color sel #b9aaecff > color sel #b8aaecff > color sel #b8a9ecff > color sel #b7a8ecff > color sel #b6a7ecff > color sel #b5a6ecff > color sel #b3a5ecff > color sel #b2a4ecff > color sel #b1a4ecff > color sel #b0a3ecff > color sel #afa3ecff > color sel #aea2ecff > color sel #aca1ecff > color sel #aba0ecff > color sel #aaa0ecff > color sel #aa9fecff > color sel #a99fecff > color sel #a89eecff > color sel #a79decff > color sel #a59cecff > color sel #a39aecff > color sel #a098ecff > color sel #9c95ecff > color sel #9791ecff > color sel #938eecff > color sel #908cecff > color sel #8d8aecff > color sel #8b88ecff > color sel #8887ecff > color sel #8785ecff > color sel #8584ecff > color sel #8484ecff > color sel #8383ecff > color sel #8183ecff > color sel #7f83ecff > color sel #7e83ecff > color sel #7d83ecff > color sel #7d84ecff > color sel #7d85ecff > color sel #7e85ecff > color sel #7e86ecff > color sel #7f87ecff > color sel #8088ecff > color sel #8089ecff > color sel #8189ecff > color sel #8289ecff > color sel #8389ecff > color sel #848aecff > color sel #858aecff > color sel #868aecff > color sel #878becff > color sel #878cecff > color sel #888decff > color sel #898eecff > color sel #8a8fecff > color sel #8a90ecff > color sel #8b91ecff > color sel #8b92ecff > color sel #8c93ecff > color sel #8d94ecff > color sel #8d95ecff > color sel #8c96ecff > color sel #8c97ecff > color sel #8b98ecff > color sel #8a98ecff > color sel #8a99ecff > color sel #8a9aecff > color sel #899aecff > color sel #8a9becff > color sel #8a9cecff > color sel #8b9decff > color sel #8c9decff > color sel #8c9eecff > color sel #8ea0ecff > color sel #90a2ecff > color sel #91a3ecff > color sel #93a5ecff > color sel #94a5ecff > color sel #95a6ecff > color sel #94a5ecff > color sel #94a4ecff > color sel #93a3ecff > color sel #92a1ecff > color sel #919fecff > color sel #909decff > color sel #8f9cecff > color sel #8e9aecff > color sel #8d99ecff > color sel #8c98ecff > color sel #8c96ecff > color sel #8b95ecff > color sel #8a95ecff > color sel #8993ecff > color sel #8892ecff > color sel #8791ecff > color sel #8691ecff > select clear > ui tool show ""Find Cavities"" > kvfinder #6 2 cavities found for fold_ruvc_omc_vp_model_0.cif #6 fold_ruvc_omc_vp_model_0.cif Cavities --- ID | | Volume | Area | Points | Maximum Depth | Average Depth 6.1.2 | | 30.67 | 50.76 | 142 | 3 | 1.54 6.1.1 | | 19.87 | 25.09 | 92 | 1.34 | 0.32 > color byattribute a:kvfinder_depth #6.1.1-2 234 atoms, 2 residues, atom kvfinder_depth range 0 to 3 > close #6 > open ""/Users/vatetaud/Desktop/Protein/Deletion > /LpxA/alignement_LpxA_Ec_LpxA_VP/4d45f96aa4adc4a6.A.cif"" Chain information for 4d45f96aa4adc4a6.A.cif #6 --- Chain | Description A | . Computing secondary structure > close #6 > open /Users/vatetaud/Desktop/Protein/TIM/Bam/Bam_complex_E.coli.cif Summary of feedback from opening /Users/vatetaud/Desktop/Protein/TIM/Bam/Bam_complex_E.coli.cif --- warnings | Atom H is not in the residue template for LEU /B:22 Atom H is not in the residue template for CYS /C:25 Atom H is not in the residue template for GLU /D:26 Atom H is not in the residue template for GLU /E:24 Atom H is not in the residue template for PHE /A:24 Bam_complex_E.coli.cif title: E. coli BAM complex (BamABCDE) by cryoEM [more info...] Chain information for Bam_complex_E.coli.cif #6 --- Chain | Description | UniProt A | Outer membrane protein assembly factor BamA | BAMA_ECO45 24-806 B | Outer membrane protein assembly factor BamB | BAMB_ECOLI 22-392 C | Outer membrane protein assembly factor BamC | BAMC_ECOLI 25-189 D | Outer membrane protein assembly factor BamD | BAMD_ECO57 26-243 E | Outer membrane protein assembly factor BamE | BAME_ECOL6 24-110 > view > hide #6 surfaces > select #6 24947 atoms, 25220 bonds, 1624 residues, 1 model selected > hide sel surfaces > show sel cartoons > hide sel atoms > select clear > show #6 surfaces > save /Users/vatetaud/Desktop/image12.png supersample 3 > open > /Users/vatetaud/Desktop/Protein/OM_biogenesis/BamA_Vp/fold_bama_model_0.cif Chain information for fold_bama_model_0.cif #7 --- Chain | Description A | . Computing secondary structure > hide #5.1 models > show #5.1 models > hide #5.1 models > hide #!5 models > hide #!6 models > view > show #7 surfaces > show #!6 models > select #7 5404 atoms, 5515 bonds, 695 residues, 1 model selected > color (#!7 & sel) #ffff9dff > color (#!7 & sel) #b4bf6cff > color (#!7 & sel) #f8fd96ff > hide #!6 models > select clear > save /Users/vatetaud/Desktop/image13.png supersample 3 > hide #!7 surfaces > select #7/A:353 9 atoms, 8 bonds, 1 residue, 1 model selected ===== 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 M5 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: MacBook Pro Model Identifier: Mac17,2 Model Number: Z1KK000ABFN/A Chip: Apple M5 Total Number of Cores: 10 (4 Super and 6 Efficiency) Memory: 24 GB System Firmware Version: 18000.101.7 OS Loader Version: 18000.101.7 Software: System Software Overview: System Version: macOS 26.4.1 (25E253) Kernel Version: Darwin 25.4.0 Time since boot: 21 jours, 13 heures et 50 minutes Graphics/Displays: Apple M5: Chipset Model: Apple M5 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 4 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 DELL P2719H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported 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: 2.21.2 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: 2.4.6 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: 6.7.0 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: 0.9.2 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: 0.15.0 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 new normal Unassigned