id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19844 Crash in QDockWidget::event() in Qt 6.9.2 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.2-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 0x0000000209a06c40 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 414 in event_loop File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1064 in init File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1229 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, PIL._imaging, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, PIL._imagingmath, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.dssp._dssp (total: 57) {""app_name"":""ChimeraX"",""timestamp"":""2026-02-12 19:22:51.00 -0800"",""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 26.2 (25C56)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""FE5F44FC-CBC3-4B06-A305-F2EC259812B2""} { ""uptime"" : 27000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac16,5"", ""coalitionID"" : 1933, ""osVersion"" : { ""train"" : ""macOS 26.2"", ""build"" : ""25C56"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2026-02-12 19:22:31.2217 -0800"", ""codeSigningMonitor"" : 2, ""incident"" : ""FE5F44FC-CBC3-4B06-A305-F2EC259812B2"", ""pid"" : 11827, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""procLaunch"" : ""2026-02-12 18:47:51.6260 -0800"", ""procStartAbsTime"" : 606666183650, ""procExitAbsTime"" : 656576565951, ""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"":""3DB91261-B876-5522-8C0C-C59B6D2AB51A"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""3D03C990-9D81-B6B4-6E53-68C3212D14D9"", ""appleIntelligenceStatus"" : {""state"":""unavailable"",""reasons"":[""notOptedIn"",""siriAssetIsNotReady"",""assetIsNotReady""]}, ""developerMode"" : 1, ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""codeSigningAuxiliaryInfo"" : 0, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""bootSessionUUID"" : ""66D4E9BC-7903-4CE3-85E1-3C4F3A77FFB2"", ""wakeTime"" : 2128, ""sleepWakeUUID"" : ""AFF14696-03CC-4AA5-8C64-CCEE58DC3EC6"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x8 is not in any region. 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,""symbolLocation"":984,""imageIndex"":136}, {""imageOffset"":2299812,""imageIndex"":45}, {""imageOffset"":2299444,""symbol"": ""QWaitCondition::wait(QMutex*, QDeadlineTimer)"" ,""symbolLocation"":108,""imageIndex"":45}, {""imageOffset"":2276332,""imageIndex"":45}, {""imageOffset"":2243220,""imageIndex"":45}, {""imageOffset"":27656,""symbol"": ""_pthread_start"" ,""symbolLocation"":136,""imageIndex"":136}, {""imageOffset"":7080,""symbol"": ""thread_start"" ,""symbolLocation"":8,""imageIndex"":136}]}], ""usedImages"" : [ [deleted to fit within ticket limits] ], ""sharedCache"" : { ""base"" : 6918553600, ""size"" : 5653544960, ""uuid"" : ""acb998b6-263c-3634-b0a8-ae8270a116c2"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=2.1G resident=0K(0%) swapped_out_or_unallocated=2.1G(100%) Writable regions: Total=10.8G written=6201K(0%) resident=6201K(0%) swapped_out=0K(0%) unallocated=10.8G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 128K 1 Activity Tracing 256K 1 AttributeGraph Data 1024K 1 CG image 32K 2 ColorSync 96K 6 CoreAnimation 1632K 101 CoreGraphics 96K 6 CoreUI image data 4016K 36 Foundation 32K 2 Kernel Alloc Once 32K 1 MALLOC 10.0G 343 MALLOC guard page 4112K 4 Mach message 64K 3 OpenGL GLSL 256K 3 PROTECTED_MEMORY 16K 1 STACK GUARD 816K 51 Stack 199.7M 52 Stack Guard 56.0M 1 VM_ALLOCATE 305.7M 286 VM_ALLOCATE (reserved) 352.0M 1 reserved VM address space (unallocated) __AUTH 5935K 652 __AUTH_CONST 89.7M 1042 __CTF 824 1 __DATA 43.5M 1135 __DATA_CONST 59.5M 1182 __DATA_DIRTY 8778K 901 __FONT_DATA 2352 1 __GLSLBUILTINS 5176K 1 __INFO_FILTER 8 1 __LINKEDIT 622.0M 136 __OBJC_RO 78.4M 1 __OBJC_RW 2570K 1 __TEXT 1.5G 1196 __TEXT (graphics) 1280K 8 __TPRO_CONST 128K 2 dyld private memory 1200K 12 mapped file 340.6M 54 page table in kernel 6201K 1 shared memory 4128K 27 =========== ======= ======= TOTAL 13.6G 7256 TOTAL, minus reserved VM space 13.2G 7256 "", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""4e65298835e5161026dfc006f6ac66a1faedce1b"", ""bug_type"" : ""309"", ""roots_installed"" : 0, ""trmStatus"" : 1, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""639124e81d92412bfb4880b3"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000012 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs Opened CTpol2EC-3p06A.mrc as #1, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Opened CTpol2EC-3p06A_tDNA.mrc zone as #4, grid size 384,384,384, pixel 0.852, shown at level 0.0136, step 1, values float32 Opened CTpol2EC-3p06A_RNA.mrc zone as #6, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Opened CTpol2EC-3p06A_BH.mrc zone as #7, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Opened CTpol2EC-3p06A_TL.mrc zone as #8, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Opened CTpol2EC10s_job162_2p9A.mrc as #9, grid size 384,384,384, pixel 0.852, shown at level 0.00992, step 1, values float32 Opened CTpol2EC10s-3p23A.mrc as #10, grid size 384,384,384, pixel 0.852, shown at level 0.0116, step 1, values float32 Opened CTpol2EC10s-active1_3p34A.mrc as #11, grid size 384,384,384, pixel 0.852, shown at level 0.0164, step 1, values float32 Opened CTpol2EC10s-active2_3p24A.mrc as #12, grid size 384,384,384, pixel 0.852, shown at level 0.0125, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite1-3p37A.mrc as #13, grid size 384,384,384, pixel 0.852, shown at level 0.0196, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite3-3p2A.mrc as #14, grid size 384,384,384, pixel 0.852, shown at level 0.00515, step 1, values float32 Opened CTpol2EC10s-trigger1-3p3A.mrc as #15, grid size 384,384,384, pixel 0.852, shown at level 0.00658, step 1, values float32 Opened CTpol2EC10s_job162_2p9A_RNA.mrc zone as #17, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s_job162_2p9A_tDNA.mrc zone as #16, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-3p23A_tDNA.mrc zone as #27, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-3p23A_RNA.mrc zone as #28, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-3p23A_AS.mrc zone as #29, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-3p23A_BH.mrc zone as #30, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-3p23A_TL.mrc zone as #31, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-active2_3p24A_tDNA.mrc zone as #32, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-active2_3p24A_RNA.mrc zone as #33, grid size 384,384,384, pixel 0.852, shown at level 0.00342, step 1, values float32 Opened CTpol2EC10s-active2_3p24A_AS.mrc zone as #34, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-active2_3p24A_BH.mrc zone as #35, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-active2_3p24A_TL.mrc zone as #36, grid size 384,384,384, pixel 0.852, shown at level 0.00637, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite1-3p37A_tDNA.mrc zone as #37, grid size 384,384,384, pixel 0.852, shown at level 0.0105, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite1-3p37A_RNA.mrc zone as #38, grid size 384,384,384, pixel 0.852, shown at level 0.0105, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite1-3p37A_AS.mrc zone as #39, grid size 384,384,384, pixel 0.852, shown at level 0.0105, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite1-3p37A_BH.mrc zone as #40, grid size 384,384,384, pixel 0.852, shown at level 0.0105, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite1-3p37A_TL.mrc zone as #41, grid size 384,384,384, pixel 0.852, shown at level 0.0105, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite3-3p2A_tDNA.mrc zone as #42, grid size 384,384,384, pixel 0.852, shown at level 0.00385, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite3-3p2A_RNA.mrc zone as #43, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite3-3p2A_AS.mrc zone as #44, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite3-3p2A_BH.mrc zone as #45, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite3-3p2A_TL.mrc zone as #46, grid size 384,384,384, pixel 0.852, shown at level 0.00385, step 1, values float32 Opened CTpol2EC10s-trigger1-3p3A_tDNA.mrc zone as #47, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-trigger1-3p3A_RNA.mrc zone as #48, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-trigger1-3p3A_AS.mrc zone as #49, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-trigger1-3p3A_BH.mrc zone as #50, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-trigger1-3p3A_TL.mrc zone as #51, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s_job162_2p9A_AS.mrc zone as #18, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s_job162_2p9A_BH.mrc zone as #19, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s_job162_2p9A_TL.mrc zone as #20, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Log from Thu Feb 12 09:59:51 2026UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs Opened CTpol2EC-3p06A.mrc as #1, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Opened CTpol2EC-3p06A_tDNA.mrc zone as #4, grid size 384,384,384, pixel 0.852, shown at level 0.0136, step 1, values float32 Opened CTpol2EC-3p06A_RNA.mrc zone as #6, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Opened CTpol2EC-3p06A_BH.mrc zone as #7, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Opened CTpol2EC-3p06A_TL.mrc zone as #8, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Opened CTpol2EC10s_job162_2p9A.mrc as #9, grid size 384,384,384, pixel 0.852, shown at level 0.00992, step 1, values float32 Opened CTpol2EC10s-3p23A.mrc as #10, grid size 384,384,384, pixel 0.852, shown at level 0.0116, step 1, values float32 Opened CTpol2EC10s-active1_3p34A.mrc as #11, grid size 384,384,384, pixel 0.852, shown at level 0.0164, step 1, values float32 Opened CTpol2EC10s-active2_3p24A.mrc as #12, grid size 384,384,384, pixel 0.852, shown at level 0.0133, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite1-3p37A.mrc as #13, grid size 384,384,384, pixel 0.852, shown at level 0.0196, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite3-3p2A.mrc as #14, grid size 384,384,384, pixel 0.852, shown at level 0.00515, step 1, values float32 Opened CTpol2EC10s-trigger1-3p3A.mrc as #15, grid size 384,384,384, pixel 0.852, shown at level 0.00658, step 1, values float32 Opened CTpol2EC10s_job162_2p9A_RNA.mrc zone as #17, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s_job162_2p9A_tDNA.mrc zone as #16, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-3p23A_tDNA.mrc zone as #27, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-3p23A_RNA.mrc zone as #28, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-3p23A_AS.mrc zone as #29, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-3p23A_BH.mrc zone as #30, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-3p23A_TL.mrc zone as #31, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-active2_3p24A_tDNA.mrc zone as #32, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-active2_3p24A_RNA.mrc zone as #33, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-active2_3p24A_AS.mrc zone as #34, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-active2_3p24A_BH.mrc zone as #35, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-active2_3p24A_TL.mrc zone as #36, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite1-3p37A_tDNA.mrc zone as #37, grid size 384,384,384, pixel 0.852, shown at level 0.0105, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite1-3p37A_RNA.mrc zone as #38, grid size 384,384,384, pixel 0.852, shown at level 0.0105, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite1-3p37A_AS.mrc zone as #39, grid size 384,384,384, pixel 0.852, shown at level 0.0105, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite1-3p37A_BH.mrc zone as #40, grid size 384,384,384, pixel 0.852, shown at level 0.0105, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite1-3p37A_TL.mrc zone as #41, grid size 384,384,384, pixel 0.852, shown at level 0.0105, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite3-3p2A_tDNA.mrc zone as #42, grid size 384,384,384, pixel 0.852, shown at level 0.00385, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite3-3p2A_RNA.mrc zone as #43, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite3-3p2A_AS.mrc zone as #44, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite3-3p2A_BH.mrc zone as #45, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite3-3p2A_TL.mrc zone as #46, grid size 384,384,384, pixel 0.852, shown at level 0.00385, step 1, values float32 Opened CTpol2EC10s-trigger1-3p3A_tDNA.mrc zone as #47, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-trigger1-3p3A_RNA.mrc zone as #48, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-trigger1-3p3A_AS.mrc zone as #49, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-trigger1-3p3A_BH.mrc zone as #50, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s-trigger1-3p3A_TL.mrc zone as #51, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s_job162_2p9A_AS.mrc zone as #18, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s_job162_2p9A_BH.mrc zone as #19, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Opened CTpol2EC10s_job162_2p9A_TL.mrc zone as #20, grid size 384,384,384, pixel 0.852, shown at level 0.01, step 1, values float32 Log from Thu Feb 12 00:12:03 2026UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs Opened CTpol2EC-3p06A.mrc as #1, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Opened CTpol2EC-3p06A_tDNA.mrc zone as #4, grid size 384,384,384, pixel 0.852, shown at level 0.0136, step 1, values float32 Opened CTpol2EC-3p06A_RNA.mrc zone as #6, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Opened CTpol2EC-3p06A_BH.mrc zone as #7, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Opened CTpol2EC-3p06A_TL.mrc zone as #8, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Opened CTpol2EC10s_job162_2p9A.mrc as #9, grid size 384,384,384, pixel 0.852, shown at level 0.00992, step 1, values float32 Opened CTpol2EC10s-3p23A.mrc as #10, grid size 384,384,384, pixel 0.852, shown at level 0.0106, step 1, values float32 Opened CTpol2EC10s-active1_3p34A.mrc as #11, grid size 384,384,384, pixel 0.852, shown at level 0.0128, step 1, values float32 Opened CTpol2EC10s-active2_3p24A.mrc as #12, grid size 384,384,384, pixel 0.852, shown at level 0.00662, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite1-3p37A.mrc as #13, grid size 384,384,384, pixel 0.852, shown at level 0.0105, step 1, values float32 Opened CTpol2EC10s-Focused-ActiveSite3-3p2A.mrc as #14, grid size 384,384,384, pixel 0.852, shown at level 0.00385, step 1, values float32 Opened CTpol2EC10s-trigger1-3p3A.mrc as #15, grid size 384,384,384, pixel 0.852, shown at level 0.00622, step 1, values float32 Opened CTpol2EC10s_job162_2p9A_BH.mrc zone as #18, grid size 384,384,384, pixel 0.852, shown at level 0.00992, step 1, values float32 Opened CTpol2EC10s_job162_2p9A_TL.mrc zone as #19, grid size 384,384,384, pixel 0.852, shown at level 0.00992, step 1, values float32 Opened CTpol2EC10s_job162_2p9A_AS.mrc zone as #20, grid size 384,384,384, pixel 0.852, shown at level 0.00992, step 1, values float32 Opened CTpol2EC10s_job162_2p9A_RNA.mrc zone as #17, grid size 384,384,384, pixel 0.852, shown at level 0.00992, step 1, values float32 Opened CTpol2EC10s_job162_2p9A_tDNA.mrc zone as #16, grid size 384,384,384, pixel 0.852, shown at level 0.00992, step 1, values float32 Opened CTpol2EC10s-3p23A_tDNA.mrc zone as #21, grid size 384,384,384, pixel 0.852, shown at level 0.0106, step 1, values float32 Opened CTpol2EC10s-3p23A_RNA.mrc zone as #22, grid size 384,384,384, pixel 0.852, shown at level 0.0106, step 1, values float32 Opened CTpol2EC10s-3p23A_AS.mrc zone as #23, grid size 384,384,384, pixel 0.852, shown at level 0.0106, step 1, values float32 Opened CTpol2EC10s-3p23A_BH.mrc zone as #24, grid size 384,384,384, pixel 0.852, shown at level 0.0106, step 1, values float32 Opened CTpol2EC10s-3p23A.mrc zone as #25, grid size 384,384,384, pixel 0.852, shown at level 0.0106, step 1, values float32 Log from Tue Feb 10 12:24:21 2026UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_apo2.cxs Opened CTpol2EC-3p06A.mrc as #1, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Opened CTpol2EC-3p06A_tDNA.mrc zone as #4, grid size 384,384,384, pixel 0.852, shown at level 0.0136, step 1, values float32 Opened CTpol2EC-3p06A_RNA.mrc zone as #6, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Opened CTpol2EC-3p06A_BH.mrc zone as #7, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Opened CTpol2EC-3p06A_TL.mrc zone as #8, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Log from Mon Feb 9 22:03:27 2026UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_apo.cxs Opened CTpol2EC-3p06A.mrc as #1, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Opened CTpol2EC-3p06A_tDNA.mrc zone as #4, grid size 384,384,384, pixel 0.852, shown at level 0.0136, step 1, values float32 Opened CTpol2EC-3p06A_RNA.mrc zone as #6, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Opened CTpol2EC-3p06A_BH.mrc zone as #7, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Opened CTpol2EC-3p06A_TL.mrc zone as #8, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Log from Mon Feb 9 21:39:56 2026UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_apo.cxs > format session Opened CTpol2EC-3p06A.mrc as #1, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Opened CTpol2EC-3p06A_tDNA.mrc zone as #4, grid size 384,384,384, pixel 0.852, shown at level 0.0136, step 1, values float32 Opened CTpol2EC-3p06A_RNA.mrc zone as #6, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Opened CTpol2EC-3p06A_BH.mrc zone as #7, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Opened CTpol2EC-3p06A_TL.mrc zone as #8, grid size 384,384,384, pixel 0.852, shown at level 0.0152, step 1, values float32 Log from Mon Feb 9 17:07:50 2026UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Volumes/Rayees_T7/Rayees_T5_data/ctPolII_proc/ctpolii_maps/ctpolii_apo_maps/CTpol2EC-3p06A.mrc Opened CTpol2EC-3p06A.mrc as #1, grid size 384,384,384, pixel 0.852, shown at level 0.00838, step 2, values float32 > volume #1 step 1 > volume #1 level 0.016 > set bgColor white > open > /Volumes/Rayees_T7/Rayees_T5_data/ctPolII_proc/ctpolii_maps/ctpolii_apo_maps/CTpol2EC-3p06A.mrc Opened CTpol2EC-3p06A.mrc as #2, grid size 384,384,384, pixel 0.852, shown at level 0.00838, step 2, values float32 > close #2 > open > /Volumes/Rayees_T7/ctPolII_proc/cryosparc_P1_J29_component_001/cryosparc_P1_J29_component_001/Modelling/Frame_000/cry0sparc_P1_J29_component_001_frame000-coot-0.pdb > format pdb Chain information for cry0sparc_P1_J29_component_001_frame000-coot-0.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available N | No description available R | No description available T | No description available > hide atoms > show cartoons > ui tool show ""Fit in Map"" > fitmap #2 inMap #1 Fit molecule cry0sparc_P1_J29_component_001_frame000-coot-0.pdb (#2) to map CTpol2EC-3p06A.mrc (#1) using 33617 atoms average map value = 0.03067, steps = 52 shifted from previous position = 0.0923 rotated from previous position = 0.45 degrees atoms outside contour = 11590, contour level = 0.015996 Position of cry0sparc_P1_J29_component_001_frame000-coot-0.pdb (#2) relative to CTpol2EC-3p06A.mrc (#1) coordinates: Matrix rotation and translation 0.99996966 -0.00649052 0.00430667 0.44194866 0.00649469 0.99997845 -0.00095660 -0.88593760 -0.00430037 0.00098454 0.99999027 0.61230616 Axis 0.12364578 0.54824712 0.82712563 Axis point 142.99212229 65.98695918 0.00000000 Rotation angle (degrees) 0.44975350 Shift along axis 0.07538647 > hide #!1 models > select #2/A:826-861 283 atoms, 288 bonds, 36 residues, 1 model selected > color sel forest green > select #2/A:1083-1123 300 atoms, 304 bonds, 41 residues, 1 model selected > color sel orange > select #2/R1123 Nothing selected > select #2/R 240 atoms, 268 bonds, 11 residues, 1 model selected > color sel red > select #2/T 591 atoms, 662 bonds, 29 residues, 1 model selected > color sel cyan > select #2/N 287 atoms, 320 bonds, 14 residues, 1 model selected > color sel cornflower blue > show #!1 models > ui tool show ""Hide Dust"" > surface dust #1 size 6 > volume #1 level 0.01515 > select clear > select #2/N,T,R 1118 atoms, 1250 bonds, 54 residues, 1 model selected > hide #2 models > show #2 models > hide #!1 models > select #2/N,T,R,A:826-861,1083-1123 583 atoms, 592 bonds, 77 residues, 1 model selected > select #2/A:826-861,1083-1123, N,T,R, Expected an objects specifier or a keyword > select #2/N 287 atoms, 320 bonds, 14 residues, 1 model selected > T;R;A:826-861,1083-1123 Unknown command: T;R;A:826-861,1083-1123 > select #2/N,T,R1 878 atoms, 982 bonds, 43 residues, 1 model selected > select #2/N,T,R 1118 atoms, 1250 bonds, 54 residues, 1 model selected > name #2/N,T,R Scaffold1 ""Scaffold1"": invalid atom specifier > name #2/N ""#2/N"" is not defined > name #2/N:T:R Scaffold1 ""Scaffold1"": invalid atom specifier > name #2/N /T /R Scaffold1 ""/T /R Scaffold1"": contains extra trailing text > select #2/N,T,R 1118 atoms, 1250 bonds, 54 residues, 1 model selected > name selection Scaff1 ""Scaff1"": invalid atom specifier > select #1/N,T,R #1/A:826-861,1083-1123 Nothing selected > select #2/N,T,R #1/A:826-861,1083-1123 1118 atoms, 1250 bonds, 54 residues, 1 model selected > select #2/N,T,R #2/A:826-861,1083-1123 1701 atoms, 1842 bonds, 131 residues, 1 model selected > name Scaff_BH_TL sel > name Scaff ""Scaff"" is not defined > name Scaff sel > select add #2 33617 atoms, 34363 bonds, 4168 residues, 1 model selected > select subtract #2 Nothing selected > select Scaff Nothing selected > name list Scaff sel Scaff_BH_TL sel > select Scaff Nothing selected > select Scaff sel Expected a keyword > select #2/N,T,R #2/A:826-861,1083-1123 1701 atoms, 1842 bonds, 131 residues, 1 model selected > name scaff1 sel > select clear > select scaff1 Nothing selected > select scaff1 Nothing selected > select #2/N,T,R #2/A:826-861,1083-1123 1701 atoms, 1842 bonds, 131 residues, 1 model selected > name scaf1 sel > color blue scaf1 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > show #!1 models > volume zone #1 nearAtoms #2/sel range 4 invert false minimalBounds false > newMap true no atoms specified for zone > volume zone #1 nearAtoms #2/N,T,R #2/A:826-861,1083-1123 range 4 invert > false minimalBounds false newMap true Opened CTpol2EC-3p06A.mrc zone as #3, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > select up 12888 atoms, 13231 bonds, 1545 residues, 1 model selected > select up 12889 atoms, 13231 bonds, 1546 residues, 1 model selected > select up 33617 atoms, 34363 bonds, 4168 residues, 1 model selected > select clear > select ~#2/N,T,R #2/A:826-861,1083-1123 31916 atoms, 32517 bonds, 4037 residues, 5 models selected > cartoon hide (#2 & sel) > select clear > surface dust #1 size 6 [Repeated 1 time(s)] > volume #3 level 0.01179 > surface dust #3 size 5.11 > select ~#2/N,T,R #2/A:837-861,1083-1123 32003 atoms, 32609 bonds, 4048 residues, 5 models selected > cartoon hide (#2 & sel) > show #!3 models > hide #!3 models > close #3 > volume zone #1 nearAtoms #2/N,T,R #2/A:837-861,1083-1123 range 4 invert > false minimalBounds false newMap true Opened CTpol2EC-3p06A.mrc zone as #3, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > surface dust #3 size 5.11 > surface dust #3 size 6 [Repeated 1 time(s)] > volume #3 level 0.01304 > volume zone #1 nearAtoms #2/N,T #2/R:1-5 #2/A:837-861,1083-1123 range 4 > invert false minimalBounds false newMap true Opened CTpol2EC-3p06A.mrc zone as #4, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > close #4 > select ~#2/N,T,#2/R:1-5 #2/A:837-861,1083-1123 Expected an objects specifier or a keyword > select ~#2/T:15-25, #2/R:1-5 #2/A:837-861,1083-1123 Expected an objects specifier or a keyword > select ~#2/T:15-25 #2/R:1-5 #2/A:837-861,1083-1123 32795 atoms, 33494 bonds, 4086 residues, 5 models selected > hide #!3 models > select ~#2/T:15-25 #2/R:5-10 #2/A:837-861,1083-1123 32767 atoms, 33461 bonds, 4085 residues, 5 models selected > cartoon hide (#2 & sel) > select #2/T:15-25 #2/R:5-10 #2/A:837-861,1083-1123 850 atoms, 895 bonds, 83 residues, 1 model selected > select #2/T:15-25 #2/R:5-10 354 atoms, 395 bonds, 17 residues, 1 model selected > style sel ball Changed 354 atom styles > style sel ball Changed 354 atom styles > show sel target ab > select clear > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > close #3 > volume zone #1 nearAtoms #2/T:15-25 #2/R:5-10 #2/A:837-861,1083-1123 range 4 > invert false minimalBounds false newMap true Opened CTpol2EC-3p06A.mrc zone as #3, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > surface dust #3 size 6 > volume zone #1 nearAtoms #2/T:15-25 #2/R:5-10 #2/A:837-861,1083-1123 range 5 > invert false minimalBounds false newMap true Opened CTpol2EC-3p06A.mrc zone as #4, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > hide #!4 models > hide #!3 models > show #!1 models > hide #!1 models > show #!4 models > volume #4 level 0.01244 > volume #3 level 0.01407 > hide #!3 models > show #!3 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > color zone #1 near #2/T:15-25 distance 5 > color zone #1 near #3/T:15-25 distance 5 color zone: No atoms specified. > color zone #3 near #2/T:15-25 distance 5 > color zone #3 near #2/T:15-25 distance 4 > color zone #3 near #2/T:15-25 distance 3 > color zone #3 near #2/T:15-25 distance 2 > color zone #3 near #2/T:15-25 distance 2.5 > color zone #3 near #2/R:5-10 distance 2.5 > color zone #3 near #2/A:837-861,1083-1123 distance 2.5 > color zone #3 near #2/A:837-861,1083-1123 distance 3 > color zone #3 near #2/A:837-861,1083-1123 distance 4 > color zone #3 near #2/A:837-861,1083-1123 distance 3 > select add #3 2 models selected > transparency #3.1 80 > transparency #3.1 70 > select clear > surface dust #3 size 6.02 > surface dust #3 size 6.26 > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > cd /Volumes/Rayees_T7/PolII_Manuscript Current working directory is: /Volumes/Rayees_T7/PolII_Manuscript > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_apo.cxs > includeMaps true > select #2/A:1099-1112 107 atoms, 109 bonds, 14 residues, 1 model selected > hide sel target a > cartoon hide sel > save /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/Apo1.png > width 1136 height 871 supersample 3 transparentBackground true [Repeated 1 time(s)] > select add #3 107 atoms, 109 bonds, 14 residues, 3 models selected > transparency (#2 & sel) 80 > transparency (#2 & sel) 90 > select add #2 33617 atoms, 34363 bonds, 4168 residues, 3 models selected > select subtract #2 2 models selected > select clear > select add #3 2 models selected > transparency #3.1 80 > transparency #3.1 90 > select clear > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > volume #3 level 0.0138 [Repeated 1 time(s)] > hide #!3 models > show #!3 models > color zone #3 near #2/T:15-25 distance 2.5 > color zone #3 near #2/A:837-861,1083-1123 distance 3 > color zone #3 near #2/R:5-10 distance 2.5 > color zone #3 near #2/A:837-861,1083-1123 distance 3 > color zone #3 near #2/R:5-10 distance 2.5 > color zone #3 near #2/A:837-861,1083-1123 distance 3 > color zone #3 near #2/R:5-10 distance 2.5 > select add #3 2 models selected > select clear > close #3 > close #4 > select add #2 33617 atoms, 34363 bonds, 4168 residues, 1 model selected > select subtract #2 Nothing selected > show #!1 models > hide #!1 models > show #!1 models > volume zone #1 nearAtoms #2/T:15-25 range 4 invert false minimalBounds false > newMap true Opened CTpol2EC-3p06A.mrc zone as #3, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #1 nearAtoms #2/T:15-25 range 3 invert false minimalBounds false > newMap true Opened CTpol2EC-3p06A.mrc zone as #4, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume #4 level 0.01554 > volume #4 level 0.01362 > volume zone #1 nearAtoms #2/R:5-10 range 4 invert false minimalBounds false > newMap true Opened CTpol2EC-3p06A.mrc zone as #5, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #1 nearAtoms #2/R:5-10 range 3 invert false minimalBounds false > newMap true Opened CTpol2EC-3p06A.mrc zone as #6, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > hide #!4 models > show #!4 models > show #!3 models > hide #!3 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!4 models > show #!5 models > hide #!5 models > show #!4 models [Repeated 1 time(s)] > volume zone #1 nearAtoms #2/A:837-861 range 3 invert false minimalBounds > false newMap true Opened CTpol2EC-3p06A.mrc zone as #7, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #1 nearAtoms 1083-1123 range 3 invert false minimalBounds false > newMap true Invalid ""nearAtoms"" argument: invalid atoms specifier > volume zone #1 nearAtoms #2/A:1083-1123 range 3 invert false minimalBounds > false newMap true Opened CTpol2EC-3p06A.mrc zone as #8, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > hide #!8 models > show #!8 models > hide #!7 models > show #!7 models > hide #!6 models > show #!6 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > close #5 > close #3 > hide #!4 models > show #!4 models > rename #4 ""CTpol2EC-3p06A_temp.mrc zone"" > hide #!6 models > show #!6 models > rename #6 ""CTpol2EC-3p06A_RNA.mrc zone"" > hide #!7 models > show #!7 models > rename #7 ""CTpol2EC-3p06A_BH.mrc zone"" > hide #!8 models > show #!8 models > rename #8 ""CTpol2EC-3p06A_TL.mrc zone"" > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_apo.cxs > includeMaps true > rename #4 ""CTpol2EC-3p06A_tDNA.mrc zone"" > hide #!6 models > show #!6 models > hide #!7 models > show #!7 models > hide #!8 models > show #!8 models > surface dust #6 size 6 > surface dust #6 size 5 [Repeated 1 time(s)] > surface undust #6 > surface dust #7 size 5.11 > surface dust #8 size 5.11 > surface dust #4 size 5.41 > color zone #6 near #2/R:5-10 distance 2.5 > color zone #3 near #2/A:837-861,1083-1123 distance 3 color zone: No surfaces specified. > color zone #3 near #2/A:837-861 distance 3 color zone: No surfaces specified. > color zone #7 near #2/A:837-861 distance 3 > color zone #8 near #2/A:1083-1123 distance 3 > color zone #4 near #2/T:15-25 distance 2.5 > color zone #6 near #2/R:5-10 distance 3 > select add #8 2 models selected > transparency #8.1 80 > select clear > select add #7 2 models selected > transparency #7.1 80 > select clear > select add #6 2 models selected > transparency #6.1 80 > select subtract #6 Nothing selected > select add #4 2 models selected > transparency #4.1 80 > select clear > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_apo.cxs > includeMaps true ——— End of log from Mon Feb 9 17:07:50 2026 ——— > view name session-start opened ChimeraX session > select #2/A:2000 1 atom, 1 residue, 1 model selected > show sel target ab > size sel atomRadius 2 Changed 1 atom radii > size sel atomRadius 1.5 Changed 1 atom radii > size sel atomRadius 1 Changed 1 atom radii > size sel atomRadius 0.8 Changed 1 atom radii > color sel red > select clear > dssp [Repeated 1 time(s)] > structure #2/A:837-861 helix Unknown command: structure #2/A:837-861 helix > show structure #2/A:837-861 helix Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > structure #2/A:45-60 helix Unknown command: structure #2/A:45-60 helix > cartoon #1 > open > /Volumes/Rayees_T7/ctPolII_proc/cryosparc_P1_J29_component_001/cryosparc_P1_J29_component_001/Modelling/Frame_000/cry0sparc_P1_J29_component_001_frame000-coot-2.pdb Chain information for cry0sparc_P1_J29_component_001_frame000-coot-2.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available N | No description available R | No description available T | No description available > close #3 > open /Volumes/Rayees_T7/ctPolII_proc/ctPolII_Apo/ctPolII_Apo_isolde.pdb Chain information for ctPolII_Apo_isolde.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available N | No description available R | No description available T | No description available > hide atoms > show cartoons > dssp > select ~#3/T:15-25 #3/R:5-10 #3/A:837-861,1083-1123 98754 atoms, 100193 bonds, 8252 residues, 12 models selected > select subtract #2 65137 atoms, 65830 bonds, 4084 residues, 11 models selected > select subtract #1 65137 atoms, 65830 bonds, 4084 residues, 9 models selected > select subtract #4 65137 atoms, 65830 bonds, 4084 residues, 7 models selected > select subtract #6 65137 atoms, 65830 bonds, 4084 residues, 5 models selected > select subtract #7 65137 atoms, 65830 bonds, 4084 residues, 3 models selected > select subtract #8 65137 atoms, 65830 bonds, 4084 residues, 1 model selected > cartoon hide sel > hide #2 models > show #2 models > hide #2 models > hide #3 models > show #3 models > select add #3 66704 atoms, 67449 bonds, 4167 residues, 1 model selected > select clear > select #/A:2000 Expected an objects specifier or a keyword > select #3/A:2000 1 atom, 1 residue, 1 model selected > style sel sphere Changed 1 atom style > hide #!6 models > show #!6 models > show sel target ab > size sel atomRadius 0.8 Changed 1 atom radii > color sel red > select clear > select #3/T:15-25 343 atoms, 367 bonds, 11 residues, 1 model selected > color sel cyan > select #3/R:5-10 202 atoms, 219 bonds, 6 residues, 1 model selected > color sel red > select clear > select #3/A:837-861 409 atoms, 409 bonds, 25 residues, 1 model selected > color sel forest green > select #3/A:1083-1123 613 atoms, 617 bonds, 41 residues, 1 model selected > color sel orange > select clear > cd /Volumes/Rayees_T7/ctPolII_proc Current working directory is: /Volumes/Rayees_T7/ctPolII_proc Cell requested for row 1 is out of bounds for table with 1 rows! Resizing table model. > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_apo.cxs > includeMaps true ——— End of log from Mon Feb 9 21:39:56 2026 ——— > view name session-start opened ChimeraX session > select #3/R:5-10 202 atoms, 219 bonds, 6 residues, 1 model selected > style sel ball Changed 202 atom styles > show sel target ab > select #3/T:15-25 343 atoms, 367 bonds, 11 residues, 1 model selected > style sel ball Changed 343 atom styles > show sel target ab > select clear > cd /Volumes/Rayees_T7/PolII_Manuscript Current working directory is: /Volumes/Rayees_T7/PolII_Manuscript > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_apo.cxs > includeMaps true > dssp [Repeated 1 time(s)] > hide #!8 models > open /Volumes/Rayees_T7/ctPolII_proc/ctPolII_Apo/ctPolII_Apo_isolde2.pdb Chain information for ctPolII_Apo_isolde2.pdb #5 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available N | No description available R | No description available T | No description available > hide #3,5 atoms > show #3,5 cartoons > hide #!6 models > hide #!7 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #5 models > show #5 models > hide #3 models > dssp > select ~#5/T:15-25 #5/R:5-10 #5/A:837-861,1083-1123 165458 atoms, 167642 bonds, 12419 residues, 13 models selected > select subtract #1 165458 atoms, 167642 bonds, 12419 residues, 11 models selected > select subtract #2 131841 atoms, 133279 bonds, 8251 residues, 10 models selected > select subtract #3 65137 atoms, 65830 bonds, 4084 residues, 9 models selected > select subtract #4 65137 atoms, 65830 bonds, 4084 residues, 7 models selected > select subtract #6 65137 atoms, 65830 bonds, 4084 residues, 5 models selected > select subtract #7 65137 atoms, 65830 bonds, 4084 residues, 3 models selected > select subtract #8 65137 atoms, 65830 bonds, 4084 residues, 1 model selected > cartoon hide sel > show #!8 models > select #3/R:5-10 202 atoms, 219 bonds, 6 residues, 1 model selected > select #5/R:5-10 202 atoms, 219 bonds, 6 residues, 1 model selected > color sel red > style sel ball Changed 202 atom styles > show sel target ab > select clear > select #5/T:15-25 343 atoms, 367 bonds, 11 residues, 1 model selected > style sel ball Changed 343 atom styles > show sel target ab > color sel cyan > select #3/A:837-861 409 atoms, 409 bonds, 25 residues, 1 model selected > select #5/A:837-861 409 atoms, 409 bonds, 25 residues, 1 model selected > color sel forest green > select #3/A:1083-1123 613 atoms, 617 bonds, 41 residues, 1 model selected > select #5/A:1083-1123 613 atoms, 617 bonds, 41 residues, 1 model selected > color sel orange > select clear > select #5/A:2000 1 atom, 1 residue, 1 model selected > style sel sphere Changed 1 atom style > show sel target ab > color sel red > color sel orange red > show #!6 models > size sel atomRadius 0.8 Changed 1 atom radii > select clear > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_apo.cxs > includeMaps true > show #!7 models > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_apo.cxs > includeMaps true > select #5/A:1098-1113 242 atoms, 244 bonds, 16 residues, 1 model selected > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_apo.cxs > includeMaps true > delete atoms sel > delete bonds sel > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_apo2.cxs > includeMaps true ——— End of log from Mon Feb 9 22:03:27 2026 ——— > view name session-start opened ChimeraX session > open > /Volumes/Rayees_T7/Rayees_T5_data/ctPolII_proc/ctpolii_maps/ctpolii_10s_maps/CTpol2EC10s_job162_2p9A.mrc Opened CTpol2EC10s_job162_2p9A.mrc as #9, grid size 384,384,384, pixel 0.852, shown at level 0.0105, step 2, values float32 > open > /Volumes/Rayees_T7/Rayees_T5_data/ctPolII_proc/ctpolii_maps/ctpolii_10s_maps/CTpol2EC10s-3p23A.mrc Opened CTpol2EC10s-3p23A.mrc as #10, grid size 384,384,384, pixel 0.852, shown at level 0.00761, step 2, values float32 > open > /Volumes/Rayees_T7/Rayees_T5_data/ctPolII_proc/ctpolii_maps/ctpolii_10s_maps/CTpol2EC10s-active1_3p34A.mrc Opened CTpol2EC10s-active1_3p34A.mrc as #11, grid size 384,384,384, pixel 0.852, shown at level 0.00717, step 2, values float32 > open > /Volumes/Rayees_T7/Rayees_T5_data/ctPolII_proc/ctpolii_maps/ctpolii_10s_maps/CTpol2EC10s-active2_3p24A.mrc Opened CTpol2EC10s-active2_3p24A.mrc as #12, grid size 384,384,384, pixel 0.852, shown at level 0.00821, step 2, values float32 > open > /Volumes/Rayees_T7/Rayees_T5_data/ctPolII_proc/ctpolii_maps/ctpolii_10s_maps/CTpol2EC10s-Focused- > ActiveSite1-3p37A.mrc Opened CTpol2EC10s-Focused-ActiveSite1-3p37A.mrc as #13, grid size 384,384,384, pixel 0.852, shown at level 0.00812, step 2, values float32 > open > /Volumes/Rayees_T7/Rayees_T5_data/ctPolII_proc/ctpolii_maps/ctpolii_10s_maps/CTpol2EC10s-Focused- > ActiveSite3-3p2A.mrc Opened CTpol2EC10s-Focused-ActiveSite3-3p2A.mrc as #14, grid size 384,384,384, pixel 0.852, shown at level 0.00817, step 2, values float32 > open > /Volumes/Rayees_T7/Rayees_T5_data/ctPolII_proc/ctpolii_maps/ctpolii_10s_maps/CTpol2EC10s-trigger1-3p3A.mrc Opened CTpol2EC10s-trigger1-3p3A.mrc as #15, grid size 384,384,384, pixel 0.852, shown at level 0.00788, step 2, values float32 > hide #!15 models > hide #!14 models > hide #!13 models > hide #!12 models > hide #!11 models > hide #!10 models > hide #!8 models > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > volume #9 step 1 > volume #9 level 0.03237 > ui tool show ""Side View"" > show #!5 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > volume #9 level 0.009919 > ui tool show ""Hide Dust"" > surface dust #9 size 5.11 > hide #!9 models > show #!10 models > volume #10 step 1 > volume #10 level 0.01065 > volume #11 step 1 > surface dust #11 size 5.11 > volume #11 level 0.01815 > hide #!11 models > show #!12 models > volume #12 step 1 > surface dust #12 size 5.11 > hide #!12 models > show #!13 models > volume #13 step 1 > surface dust #13 size 5.11 > volume #13 level 0.01051 > volume #14 step 1 > surface dust #14 size 5.11 > volume #15 step 1 > volume #15 level 0.008068 > volume #15 level 0.01066 > surface dust #14 size 5.11 > surface dust #15 size 5.11 > volume #15 level 0.007329 > volume #15 level 0.01029 > volume #15 level 0.007699 > hide #!15 models > show #!11 models > volume #11 level 0.01285 > hide #!11 models > show #!12 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > volume #12 level 0.007417 > volume #12 level 0.002239 > volume #12 level 0.003833 > volume #12 level 0.006621 > hide #!12 models > show #!13 models > hide #!13 models > show #!11 models > hide #!11 models > show #!12 models > hide #!12 models > show #!13 models > hide #!13 models > show #!14 models > hide #!14 models > show #!15 models > show #!14 models > hide #!14 models > show #!14 models > hide #!15 models > hide #!14 models > show #!13 models > hide #!13 models > show #!12 models > hide #!12 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!12 models > hide #!12 models > show #!13 models > hide #!13 models > show #!12 models > show #!11 models > hide #!11 models > show #!11 models > show #!13 models > hide #!13 models > show #!14 models > hide #!14 models > show #!14 models > hide #!14 models > hide #!12 models > hide #!11 models > show #!11 models > show #!12 models > show #!13 models > hide #!13 models > hide #!12 models > hide #!11 models > show #!11 models > show #!12 models > hide #!11 models > show #!13 models > hide #!13 models > show #!14 models > show #!15 models > hide #!14 models > volume #15 level 0.004741 > volume #15 level 0.00622 > hide #!15 models > show #!14 models > hide #!14 models > show #!13 models > hide #!13 models > show #!12 models > hide #!12 models > show #!11 models > hide #!11 models > show #!15 models > show #!14 models > hide #!15 models > volume #14 level 0.0009649 > volume #14 level 0.003847 > hide #!5 models > hide #!14 models > show #!14 models > show #!5 models > hide #!14 models > show #2 models > hide #!5 models > show #!9 models > hide #!9 models > show #!9 models > volume zone #9 nearAtoms #2/T:5-22 range 4 invert false minimalBounds false > newMap true Opened CTpol2EC10s_job162_2p9A.mrc zone as #16, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > rename #16 ""CTpol2EC10s_job162_2p9A_tDNA.mrc zone"" > surface dust #16 size 5.11 > volume zone #9 nearAtoms #2/R:7-10 range 4 invert false minimalBounds false > newMap true Opened CTpol2EC10s_job162_2p9A.mrc zone as #17, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > rename #17 ""CTpol2EC10s_job162_2p9A_RNA.mrc zone"" > hide #!17 models > hide #!16 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > volume zone #9 nearAtoms #2/A:837-861 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s_job162_2p9A.mrc zone as #18, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > rename #18 ""CTpol2EC10s_job162_2p9A_BH.mrc zone"" > surface dust #18 size 5.19 > show #!17 models > show #!16 models > volume zone #9 nearAtoms #2/A:1083-1123 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s_job162_2p9A.mrc zone as #19, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > surface dust #19 size 5.11 > rename #19 ""CTpol2EC10s_job162_2p9A_TL.mrc zone"" > volume zone #9 nearAtoms #2/A:493-501 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s_job162_2p9A.mrc zone as #20, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > rename #20 ""CTpol2EC10s_job162_2p9A_AS.mrc zone"" > surface dust #20 size 5.11 > volume zone #9 nearAtoms #2/R:11 range 4 invert false minimalBounds false > newMap true Opened CTpol2EC10s_job162_2p9A.mrc zone as #21, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #9 nearAtoms #2/R:5-11 range 4 invert false minimalBounds false > newMap true Opened CTpol2EC10s_job162_2p9A.mrc zone as #22, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > hide #!21 models > hide #!20 models > hide #!19 models > hide #!18 models > hide #!17 models > hide #!16 models > hide #!22 models > show #!22 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > hide #!22 models > show #!22 models > show #!21 models > hide #!22 models > show #!20 models > hide #!20 models > hide #!21 models > show #!21 models > close #21 > rename #22 ""CTpol2EC10s_job162_2p9A_RNA.mrc zone"" > show #!17 models > hide #!17 models > close #17 > rename #22 id #17 > cd /Volumes/Rayees_T7/PolII_Manuscript Current working directory is: /Volumes/Rayees_T7/PolII_Manuscript > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true > show #!20 models > show #!19 models > show #!18 models > show #!17 models > show #!16 models > select add #16 2 models selected > color #16.1 forest green > color #16.1 cyan > select subtract #16 Nothing selected > select add #17 3 models selected > color #17.1 red > select subtract #17 Nothing selected > select add #18 3 models selected > color #18.1 forest green > select subtract #18 Nothing selected > select add #19 3 models selected > color #19.1 orange > select subtract #19 Nothing selected > select add #20 3 models selected > color #20.1 blue > transparency #20.1 80 > select subtract #20 Nothing selected > surface dust #17 size 5.11 > hide #!16 models > show #!16 models > hide #!16 models > show #!16 models > select add #16 2 models selected > transparency #16.1 80 > select #20 3 models selected > select clear > select add #20 3 models selected > color #20.1 purple > select clear > select ~#2/T:15-22 #2/R:5-11 #2/A:493-501, 837-861,1083-1123 165898 atoms, 168080 bonds, 1 pseudobond, 12396 residues, 43 models selected > select subtract #3 99194 atoms, 100631 bonds, 1 pseudobond, 8229 residues, 42 models selected > select subtract #4 99194 atoms, 100631 bonds, 1 pseudobond, 8229 residues, 40 models selected > select subtract #5 32732 atoms, 33428 bonds, 4078 residues, 38 models selected > select subtract #6 32732 atoms, 33428 bonds, 4078 residues, 36 models selected > select subtract #7 32732 atoms, 33428 bonds, 4078 residues, 34 models selected > select subtract #8 32732 atoms, 33428 bonds, 4078 residues, 32 models selected > select subtract #9 32732 atoms, 33428 bonds, 4078 residues, 30 models selected > select subtract #10 32732 atoms, 33428 bonds, 4078 residues, 28 models selected > select subtract #11 32732 atoms, 33428 bonds, 4078 residues, 26 models selected > select subtract #12 32732 atoms, 33428 bonds, 4078 residues, 24 models selected > select subtract #13 32732 atoms, 33428 bonds, 4078 residues, 22 models selected > select subtract #14 32732 atoms, 33428 bonds, 4078 residues, 20 models selected > select subtract #15 32732 atoms, 33428 bonds, 4078 residues, 18 models selected > select subtract #16 32732 atoms, 33428 bonds, 4078 residues, 15 models selected > select subtract #17 32732 atoms, 33428 bonds, 4078 residues, 12 models selected > select subtract #18 32732 atoms, 33428 bonds, 4078 residues, 9 models selected > select subtract #19 32732 atoms, 33428 bonds, 4078 residues, 6 models selected > select subtract #20 32732 atoms, 33428 bonds, 4078 residues, 3 models selected > select subtract #1 32732 atoms, 33428 bonds, 4078 residues, 1 model selected > cartoon hide sel > select add #2 33617 atoms, 34363 bonds, 4168 residues, 1 model selected > select subtract #2 Nothing selected > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true > hide #!17 models > hide #!18 models > hide #!19 models > hide #!20 models > hide #!16 models > show #!16 models > hide #!16 models > volume zone #9 nearAtoms #2/T:15-22 range 4 invert false minimalBounds false > newMap true Opened CTpol2EC10s_job162_2p9A.mrc zone as #21, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > surface dust #21 size 5.11 > surface undust #21 [Repeated 1 time(s)] > surface dust #21 size 5.11 > rename #21 ""CTpol2EC10s_job162_2p9A_tDNA.mrc zone"" > close #16 > rename #21 id #16 > show #!17 models > show #!18 models > show #!19 models > select add #16 3 models selected > color #16.1 cyan > select clear > select add #16 3 models selected > select add #17 6 models selected > select add #18 9 models selected > select add #19 12 models selected > transparency #16.1#17.1#18.1#19.1 70 > select clear > show #!20 models > select #2/A:493-501 73 atoms, 74 bonds, 9 residues, 1 model selected > color sel purple > select clear > hide #!20 models > select #2/R:11 20 atoms, 21 bonds, 1 residue, 1 model selected > show sel target ab > select clear > select #2/R:5-11 #2/T:15-22 316 atoms, 352 bonds, 15 residues, 1 model selected > show sel target ab > select clear [Repeated 1 time(s)] > hide #!16 models > hide #!17 models > hide #!18 models > hide #!19 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!10 models > hide #2 models > show #2 models > hide #!10 models > show #3 models > hide #3 models > show #3 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > hide #3 models > show #3 models > show #2 models > hide #3 models > select #2/R:5-11 #2/T:15-22 316 atoms, 352 bonds, 15 residues, 1 model selected > cartoon hide sel > select clear > show #!16 models > show #!17 models > show #!18 models > show #!19 models > hide #!19 models > hide #!18 models > hide #!17 models > hide #!16 models > show #!9 models > hide #!9 models > show #!10 models > volume zone #10 nearAtoms #2/T:15-22 range 4 invert false minimalBounds > false newMap truetrue Invalid ""newMap"" argument: Expected true or false (or 1 or 0) > volume zone #10 nearAtoms #2/T:15-22 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-3p23A.mrc zone as #21, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > rename #21 ""CTpol2EC10s-3p23A_tDNA.mrc zone"" > select add #21 3 models selected > surface dust #21 size 5.11 > color #21.1 cyan > select clear > volume zone #10 nearAtoms #2/R:7-11 range 4 invert false minimalBounds false > newMap true Opened CTpol2EC10s-3p23A.mrc zone as #22, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > rename #22 ""CTpol2EC10s-3p23A_RNA.mrc zone"" > volume zone #map nearAtoms #2/A:493-501 range 4 invert false minimalBounds > false newMap true Missing or invalid ""volumes"" argument: invalid density maps specifier > volume zone #10 nearAtoms #2/A:493-501 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-3p23A.mrc zone as #23, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #10 nearAtoms #2/A:837-861 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-3p23A.mrc zone as #24, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > hide #!22 models > hide #!21 models > show #!22 models > surface dust #22 size 5.11 > surface dust #23 size 5.11 > surface dust #24 size 5.11 > surface undust #24 > surface dust #24 size 5.11 > hide #!23 models > show #!23 models > rename #23 ""CTpol2EC10s-3p23A_AS.mrc zone"" > hide #!24 models > show #!24 models > rename #24 ""CTpol2EC10s-3p23A_BH.mrc zone"" > hide #!24 models > show #!24 models > volume zone #10 nearAtoms #2/A:1083-1123 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-3p23A.mrc zone as #25, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > hide #!24 models > hide #!23 models > hide #!22 models > surface dust #25 size 5.11 > show #!23 models > hide #!23 models > show #!24 models > show #!22 models > hide #!22 models > hide #!24 models > hide #!25 models > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true > show #!25 models > show #!24 models > hide #!24 models > show #!24 models > select add #24 3 models selected > color #24.1 forest green > select subtract #24 Nothing selected > select add #24 3 models selected > select subtract #24 Nothing selected > select add #24 3 models selected > select subtract #24 Nothing selected > select add #24 3 models selected > select subtract #24 Nothing selected > hide #!24 models > show #!24 models > show #!21 models > hide #!21 models > show #!10 models > show #!11 models > hide #!11 models > show #!9 models > hide #!9 models > show #!9 models > ui tool show ""Fit in Map"" > fitmap #10 inMap #9 Fit map CTpol2EC10s-3p23A.mrc in map CTpol2EC10s_job162_2p9A.mrc using 382573 points correlation = 0.9459, correlation about mean = 0.8509, overlap = 352 steps = 60, shift = 2.07, angle = 1.16 degrees Position of CTpol2EC10s-3p23A.mrc (#10) relative to CTpol2EC10s_job162_2p9A.mrc (#9) coordinates: Matrix rotation and translation 0.99985678 -0.00328772 0.01660182 -1.91582149 0.00347210 0.99993248 -0.01108923 3.18599111 -0.01656424 0.01114529 0.99980068 0.20641471 Axis 0.54903296 0.81896330 0.16691892 Axis point -5.60079238 0.00000000 167.99236517 Rotation angle (degrees) 1.16025023 Shift along axis 1.59181517 > fitmap #10 inMap #9 Fit map CTpol2EC10s-3p23A.mrc in map CTpol2EC10s_job162_2p9A.mrc using 382573 points correlation = 0.9459, correlation about mean = 0.8509, overlap = 352 steps = 24, shift = 0.00204, angle = 0.00228 degrees Position of CTpol2EC10s-3p23A.mrc (#10) relative to CTpol2EC10s_job162_2p9A.mrc (#9) coordinates: Matrix rotation and translation 0.99985677 -0.00332258 0.01659537 -1.90957858 0.00350658 0.99993257 -0.01107066 3.17534497 -0.01655747 0.01112727 0.99980100 0.20883209 Axis 0.54839039 0.81902652 0.16871142 Axis point -5.58909564 0.00000000 167.51795368 Rotation angle (degrees) 1.15969819 Shift along axis 1.58872955 > show #!11 models > fitmap #11 inMap #9 Fit map CTpol2EC10s-active1_3p34A.mrc in map CTpol2EC10s_job162_2p9A.mrc using 282891 points correlation = 0.9395, correlation about mean = 0.7958, overlap = 290.8 steps = 72, shift = 0.936, angle = 2.48 degrees Position of CTpol2EC10s-active1_3p34A.mrc (#11) relative to CTpol2EC10s_job162_2p9A.mrc (#9) coordinates: Matrix rotation and translation 0.99975226 0.01775789 -0.01341894 -0.57597249 -0.01824285 0.99915146 -0.03692648 9.54850466 0.01275182 0.03716213 0.99922789 -7.11140414 Axis 0.85721287 -0.30279846 -0.41653233 Axis point 0.00000000 201.30575062 250.48808599 Rotation angle (degrees) 2.47679830 Shift along axis -0.42287375 > show #!12 models > fitmap #12 inMap #9 Fit map CTpol2EC10s-active2_3p24A.mrc in map CTpol2EC10s_job162_2p9A.mrc using 848901 points correlation = 0.8924, correlation about mean = 0.8671, overlap = 354.7 steps = 84, shift = 1.11, angle = 2.53 degrees Position of CTpol2EC10s-active2_3p24A.mrc (#12) relative to CTpol2EC10s_job162_2p9A.mrc (#9) coordinates: Matrix rotation and translation 0.99980385 0.01801100 -0.00823814 -1.44794679 -0.01832249 0.99905382 -0.03944312 10.05172895 0.00751994 0.03958632 0.99918786 -6.55520018 Axis 0.89402499 -0.17826417 -0.41102458 Axis point 0.00000000 174.76873579 248.87696109 Rotation angle (degrees) 2.53322285 Shift along axis -0.39201533 > show #!13 models > fitmap #12 inMap #9 Fit map CTpol2EC10s-active2_3p24A.mrc in map CTpol2EC10s_job162_2p9A.mrc using 848901 points correlation = 0.8924, correlation about mean = 0.867, overlap = 354.7 steps = 28, shift = 0.0172, angle = 0.00274 degrees Position of CTpol2EC10s-active2_3p24A.mrc (#12) relative to CTpol2EC10s_job162_2p9A.mrc (#9) coordinates: Matrix rotation and translation 0.99980348 0.01801112 -0.00828252 -1.42662924 -0.01832423 0.99905449 -0.03942517 10.03944523 0.00756460 0.03956919 0.99918820 -6.55677906 Axis 0.89377650 -0.17930118 -0.41111391 Axis point -0.00000000 174.75087785 248.72830834 Rotation angle (degrees) 2.53280220 Shift along axis -0.37958903 > fitmap #13 inMap #9 Fit map CTpol2EC10s-Focused-ActiveSite1-3p37A.mrc in map CTpol2EC10s_job162_2p9A.mrc using 378579 points correlation = 0.9208, correlation about mean = 0.8012, overlap = 300.3 steps = 72, shift = 1.51, angle = 1.87 degrees Position of CTpol2EC10s-Focused-ActiveSite1-3p37A.mrc (#13) relative to CTpol2EC10s_job162_2p9A.mrc (#9) coordinates: Matrix rotation and translation 0.99961613 -0.00453843 -0.02733116 5.39018312 0.00406205 0.99983931 -0.01746022 3.04894611 0.02740601 0.01734250 0.99947394 -6.00501275 Axis 0.53189085 -0.83654965 0.13144126 Axis point 220.74766258 0.00000000 203.32042892 Rotation angle (degrees) 1.87482494 Shift along axis -0.47291218 > show #!14 models > fitmap #14 inMap #9 Fit map CTpol2EC10s-Focused-ActiveSite3-3p2A.mrc in map CTpol2EC10s_job162_2p9A.mrc using 2896526 points correlation = 0.8106, correlation about mean = 0.8676, overlap = 358.6 steps = 72, shift = 1.56, angle = 1.83 degrees Position of CTpol2EC10s-Focused-ActiveSite3-3p2A.mrc (#14) relative to CTpol2EC10s_job162_2p9A.mrc (#9) coordinates: Matrix rotation and translation 0.99964031 -0.00136929 -0.02678394 4.76355683 0.00090037 0.99984626 -0.01751148 3.60856301 0.02680380 0.01748106 0.99948785 -5.90485451 Axis 0.54640673 -0.83676977 0.03544061 Axis point 223.05648525 0.00000000 187.62580922 Rotation angle (degrees) 1.83495898 Shift along axis -0.62596856 > show #!15 models > fitmap #15 inMap #9 Fit map CTpol2EC10s-trigger1-3p3A.mrc in map CTpol2EC10s_job162_2p9A.mrc using 874818 points correlation = 0.8921, correlation about mean = 0.8673, overlap = 348.6 steps = 72, shift = 1.06, angle = 2.18 degrees Position of CTpol2EC10s-trigger1-3p3A.mrc (#15) relative to CTpol2EC10s_job162_2p9A.mrc (#9) coordinates: Matrix rotation and translation 0.99984597 0.01440712 -0.01002387 -0.60065264 -0.01473768 0.99932252 -0.03372405 8.54391220 0.00953121 0.03386658 0.99938091 -6.05665636 Axis 0.88748444 -0.25676380 -0.38267966 Axis point -0.00000000 187.96643976 246.45712546 Rotation angle (degrees) 2.18234481 Shift along axis -0.40907803 > hide #!15 models > hide #!14 models > hide #!13 models > hide #!12 models > hide #!11 models > hide #!10 models > hide #!9 models > show #!16 models > show #!9 models > show #!17 models > hide #!17 models > hide #!16 models > show #!21 models > fitmap #21 inMap #9 Fit map CTpol2EC10s-3p23A_tDNA.mrc zone in map CTpol2EC10s_job162_2p9A.mrc using 2587 points correlation = 0.9483, correlation about mean = 0.8142, overlap = 1.736 steps = 56, shift = 1.93, angle = 1.49 degrees Position of CTpol2EC10s-3p23A_tDNA.mrc zone (#21) relative to CTpol2EC10s_job162_2p9A.mrc (#9) coordinates: Matrix rotation and translation 0.99967331 -0.00116975 0.02553244 -3.83007613 0.00128983 0.99998818 -0.00468689 2.46262312 -0.02552665 0.00471829 0.99966301 3.16784239 Axis 0.18095128 0.98235296 0.04732122 Axis point 118.44577447 0.00000000 164.81929847 Rotation angle (degrees) 1.48917949 Shift along axis 1.87601410 > show #!22 models > show #!23 models > hide #!25 models > hide #!24 models > hide #!23 models > show #!10 models > show #!23 models > show #!24 models > show #!25 models > fitmap #21 inMap #10 Fit map CTpol2EC10s-3p23A_tDNA.mrc zone in map CTpol2EC10s-3p23A.mrc using 2587 points correlation = 0.9993, correlation about mean = 0.9964, overlap = 1.61 steps = 44, shift = 0.281, angle = 0.653 degrees Position of CTpol2EC10s-3p23A_tDNA.mrc zone (#21) relative to CTpol2EC10s-3p23A.mrc (#10) coordinates: Matrix rotation and translation 0.99999857 0.00092193 0.00141672 -0.39878633 -0.00091897 0.99999740 -0.00208679 0.52492878 -0.00141864 0.00208549 0.99999682 -0.04778598 Axis 0.77697196 0.52800732 -0.34281604 Axis point 0.00000000 25.98252166 255.63923995 Rotation angle (degrees) 0.15383732 Shift along axis -0.01629776 > fitmap #22 inMap #10 Fit map CTpol2EC10s-3p23A_RNA.mrc zone in map CTpol2EC10s-3p23A.mrc using 2085 points correlation = 0.9979, correlation about mean = 0.9896, overlap = 1.599 steps = 56, shift = 2.2, angle = 1.08 degrees Position of CTpol2EC10s-3p23A_RNA.mrc zone (#22) relative to CTpol2EC10s-3p23A.mrc (#10) coordinates: Matrix rotation and translation 0.99995029 0.00958760 -0.00273872 -1.16270176 -0.00958805 0.99995402 -0.00015189 1.79477958 0.00273714 0.00017814 0.99999624 -0.41023531 Axis 0.01654695 -0.27454926 -0.96143065 Axis point 183.23715317 122.01857152 0.00000000 Rotation angle (degrees) 0.57138921 Shift along axis -0.11758177 > fitmap #23 inMap #10 Fit map CTpol2EC10s-3p23A_AS.mrc zone in map CTpol2EC10s-3p23A.mrc using 1906 points correlation = 0.9948, correlation about mean = 0.9787, overlap = 2.542 steps = 56, shift = 2.09, angle = 1.57 degrees Position of CTpol2EC10s-3p23A_AS.mrc zone (#23) relative to CTpol2EC10s-3p23A.mrc (#10) coordinates: Matrix rotation and translation 0.99992810 0.00821628 -0.00873409 0.24106390 -0.00834404 0.99985724 -0.01469283 4.14900667 0.00861212 0.01476465 0.99985391 -3.73856538 Axis 0.77549816 -0.45665661 -0.43596714 Axis point 0.00000000 258.25417627 277.45464571 Rotation angle (degrees) 1.08826235 Shift along axis -0.07783506 > fitmap #24 inMap #10 Fit map CTpol2EC10s-3p23A_BH.mrc zone in map CTpol2EC10s-3p23A.mrc using 3192 points correlation = 0.9996, correlation about mean = 0.998, overlap = 2.462 steps = 72, shift = 2.06, angle = 1.39 degrees Position of CTpol2EC10s-3p23A_BH.mrc zone (#24) relative to CTpol2EC10s-3p23A.mrc (#10) coordinates: Matrix rotation and translation 0.99998170 -0.00424394 0.00431114 0.00326623 0.00423767 0.99998995 0.00146388 -0.86936656 -0.00431731 -0.00144558 0.99998964 0.90876728 Axis -0.23380507 0.69338286 0.68158301 Axis point 207.99625003 0.00000000 -0.73344392 Rotation angle (degrees) 0.35649610 Shift along axis 0.01583281 > fitmap #25 inMap #10 Fit map CTpol2EC10s-3p23A.mrc zone in map CTpol2EC10s-3p23A.mrc using 3838 points correlation = 0.9977, correlation about mean = 0.9904, overlap = 3.388 steps = 80, shift = 2.05, angle = 1.22 degrees Position of CTpol2EC10s-3p23A.mrc zone (#25) relative to CTpol2EC10s-3p23A.mrc (#10) coordinates: Matrix rotation and translation 0.99999399 -0.00346202 -0.00020103 0.63222700 0.00346189 0.99999378 -0.00067589 -0.28320827 0.00020337 0.00067519 0.99999975 -0.12031541 Axis 0.19120771 -0.05723134 0.97987968 Axis point 81.81603974 181.41518080 0.00000000 Rotation angle (degrees) 0.20242881 Shift along axis 0.01920044 > hide #!25 models > hide #!24 models > hide #!23 models > hide #!22 models > hide #!21 models > hide #!9 models > hide #!10 models > show #!25 models > show #!24 models > show #!23 models > show #!22 models > show #!21 models > show #!20 models > show #!19 models > hide #!25 models > hide #!24 models > hide #!23 models > hide #!22 models > hide #!21 models > hide #!20 models > hide #!19 models > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true ——— End of log from Tue Feb 10 12:24:21 2026 ——— > view name session-start opened ChimeraX session > hide #2 models > show #!10 models > open > /Volumes/Rayees_T7/ctPolII_proc/ctPolII_10s/ctpolii_10s_job162_2p9A_RNA11_isolde1.pdb Chain information for ctpolii_10s_job162_2p9A_RNA11_isolde1.pdb #26 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available N | No description available R | No description available T | No description available > hide #26 atoms > show #26 cartoons > volume zone #10 nearAtoms #26/T:15-22 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-3p23A.mrc zone as #27, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume #27 level 0.003877 > volume #27 level 0.008231 > volume zone #10 nearAtoms #26/R:7-11 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-3p23A.mrc zone as #28, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #10 nearAtoms #26/A:493-501 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-3p23A.mrc zone as #29, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #10 nearAtoms #26/A:837-861 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-3p23A.mrc zone as #30, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #10 nearAtoms #26/A:1083-1123 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-3p23A.mrc zone as #31, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > select add #27 3 models selected > hide #!31 models > hide #!30 models > hide #!29 models > hide #!28 models > hide #!27 models > show #!27 models > rename #27 ""CTpol2EC10s-3p23A_tDNA.mrc zone"" > show #!28 models > hide #!28 models > rename #28 ""CTpol2EC10s-3p23A_RNA.mrc zone"" > show #!28 models > hide #!28 models > show #!29 models > rename #29 ""CTpol2EC10s-3p23A_AS.mrc zone"" > hide #!29 models > show #!29 models > hide #!29 models > show #!30 models > rename #30 ""CTpol2EC10s-3p23A_BH.mrc zone"" > hide #!30 models > show #!30 models > rename #31 ""CTpol2EC10s-3p23A_TL.mrc zone"" > hide #!30 models > hide #!27 models > show #!27 models > color #!27.1 cyan > select clear > hide #!27 models > show #!28 models > color #26,28 red > undo > select clear > hide #!28 models > show #!28 models > hide #!28 models > show #!28 models > show #!27 models > hide #!27 models > select add #28 3 models selected > color #28.1 red > select clear > hide #!28 models > show #!29 models > select add #29 3 models selected > color #29.1 purple > select clear > hide #!29 models > show #!30 models > select add #30 3 models selected > color #30.1 forest green > select #26/A:258 16 atoms, 15 bonds, 1 residue, 1 model selected > hide #!30 models > show #!31 models > color sel red > select add #31 16 atoms, 15 bonds, 1 residue, 4 models selected > color (#26 & sel) orange > select subtract #31 16 atoms, 15 bonds, 1 residue, 1 model selected > select add #31 16 atoms, 15 bonds, 1 residue, 4 models selected > color (#26 & sel) orange > select clear > select add #31 3 models selected > color #31.1 orange > select clear > hide #26 models > show #26 models > hide #26 models > show #26 models > hide #!31 models > volume zone #11 nearAtoms #26/T:15-22 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-active1_3p34A.mrc zone as #32, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #11 nearAtoms #2/R:7-11 range 4 invert false minimalBounds false > newMap true Opened CTpol2EC10s-active1_3p34A.mrc zone as #33, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > hide #!32 models > show #!32 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > hide #!33 models > hide #!32 models > show #!27 models > show #!28 models > show #!29 models > show #!30 models > show #!31 models > color cyan #27 ; color red #28 ; color purple #29 ; color forestgreen #30 ; > color orange #31 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > volume #27 color forestgreen > undo [Repeated 1 time(s)] > show #!30 models > volume #27 color forestgreen > volume #28 color blue > show #!31 models > volume #27 color cyan > volume #28 color red > volume #29 color purple > volume #30 color forestgreen > volume #31 color orange > show #!32 models > hide #!32 models > show #!32 models > hide #!32 models > close #32 > close #33 > hide #26 models > hide #!27 models > hide #!28 models > hide #!29 models > hide #!30 models > hide #!31 models > show #!12 models > show #!13 models > show #!14 models > hide #!14 models > hide #!13 models > hide #!12 models > show #26 models > show #!9 models > ui tool show ""Fit in Map"" > fitmap #26 inMap #9 Fit molecule ctpolii_10s_job162_2p9A_RNA11_isolde1.pdb (#26) to map CTpol2EC10s_job162_2p9A.mrc (#9) using 66734 atoms average map value = 0.0243, steps = 48 shifted from previous position = 0.02 rotated from previous position = 0.0227 degrees atoms outside contour = 21248, contour level = 0.0099185 Position of ctpolii_10s_job162_2p9A_RNA11_isolde1.pdb (#26) relative to CTpol2EC10s_job162_2p9A.mrc (#9) coordinates: Matrix rotation and translation 0.99999994 -0.00008453 0.00032191 -0.03777553 0.00008460 0.99999997 -0.00021585 0.03059149 -0.00032190 0.00021587 0.99999992 0.03427256 Axis 0.54414206 0.81146122 0.21316686 Axis point 98.77448105 0.00000000 136.92842069 Rotation angle (degrees) 0.02272906 Shift along axis 0.01157433 > fitmap #26 inMap #9 Fit molecule ctpolii_10s_job162_2p9A_RNA11_isolde1.pdb (#26) to map CTpol2EC10s_job162_2p9A.mrc (#9) using 66734 atoms average map value = 0.0243, steps = 60 shifted from previous position = 0.00143 rotated from previous position = 0.00131 degrees atoms outside contour = 21245, contour level = 0.0099185 Position of ctpolii_10s_job162_2p9A_RNA11_isolde1.pdb (#26) relative to CTpol2EC10s_job162_2p9A.mrc (#9) coordinates: Matrix rotation and translation 0.99999995 -0.00007840 0.00030806 -0.03659993 0.00007846 0.99999998 -0.00019865 0.02865286 -0.00030805 0.00019867 0.99999993 0.03346811 Axis 0.52996945 0.82180220 0.20922124 Axis point 101.04102584 0.00000000 138.00855452 Rotation angle (degrees) 0.02147757 Shift along axis 0.01115238 > fitmap #26 inMap #9 Fit molecule ctpolii_10s_job162_2p9A_RNA11_isolde1.pdb (#26) to map CTpol2EC10s_job162_2p9A.mrc (#9) using 66734 atoms average map value = 0.0243, steps = 48 shifted from previous position = 0.00127 rotated from previous position = 0.00553 degrees atoms outside contour = 21248, contour level = 0.0099185 Position of ctpolii_10s_job162_2p9A_RNA11_isolde1.pdb (#26) relative to CTpol2EC10s_job162_2p9A.mrc (#9) coordinates: Matrix rotation and translation 0.99999993 -0.00017226 0.00031960 -0.02170508 0.00017233 0.99999996 -0.00021827 0.01646143 -0.00031956 0.00021833 0.99999993 0.03133695 Axis 0.51529315 0.75436319 0.40670523 Axis point 80.25171287 0.00000000 90.46823221 Rotation angle (degrees) 0.02427270 Shift along axis 0.01397832 > hide #!9 models > show #!12 models > volume zone #12 nearAtoms #26/T:15-22 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-active2_3p24A.mrc zone as #32, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #12 nearAtoms #26/R:7-11 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-active2_3p24A.mrc zone as #33, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #12 nearAtoms #26/A:493-501 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-active2_3p24A.mrc zone as #34, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #12 nearAtoms #26/A:837-861 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-active2_3p24A.mrc zone as #35, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #12 nearAtoms #26/A:1083-1123 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-active2_3p24A.mrc zone as #36, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > hide #!32 models > show #!32 models > hide #!32 models > show #!32 models > hide #!32 models > hide #!33 models > show #!33 models > hide #!33 models > show #!33 models > hide #!34 models > show #!34 models > hide #!34 models > show #!34 models > hide #!35 models > show #!35 models > hide #!36 models > show #!36 models > show #!32 models > hide #!32 models > show #!32 models > volume #32 color cyan > volume #33 color red > volume #34 color purple > volume #35 color forestgreen > volume #36 color orange > cd /Volumes/Rayees_T7/PolII_Manuscript Current working directory is: /Volumes/Rayees_T7/PolII_Manuscript > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true > rename #32 ""CTpol2EC10s-active2_3p24A_tDNA.mrc zone"" > rename #33 ""CTpol2EC10s-active2_3p24A_RNA.mrc zone"" > rename #34 ""CTpol2EC10s-active2_3p24A_AS.mrc zone"" > rename #35 ""CTpol2EC10s-active2_3p24A_BH.mrc zone"" > rename #36 ""CTpol2EC10s-active2_3p24A_TL.mrc zone"" > hide #!32 models > show #!32 models > hide #!33 models > show #!33 models > hide #!34 models > show #!34 models > hide #!35 models > show #!35 models > hide #!36 models > show #!36 models > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true > hide #!32 models > hide #!33 models > hide #!34 models > hide #!35 models > hide #!36 models > show #!13 models > volume zone #13 nearAtoms #26/T:15-22 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-Focused-ActiveSite1-3p37A.mrc zone as #37, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #13 nearAtoms #26/R:7-11 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-Focused-ActiveSite1-3p37A.mrc zone as #38, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #13 nearAtoms #26/A:493-501 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-Focused-ActiveSite1-3p37A.mrc zone as #39, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #13 nearAtoms #26/A:837-861 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-Focused-ActiveSite1-3p37A.mrc zone as #40, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #13 nearAtoms #26/A:1083-1123 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-Focused-ActiveSite1-3p37A.mrc zone as #41, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume #37 color cyan > volume #38 color red > volume #39 color purple > volume #40 color forestgreen > volume #41 color orange > rename #37 ""CTpol2EC10s-Focused-ActiveSite1-3p37A_tDNA.mrc zone"" > rename #38 ""CTpol2EC10s-Focused-ActiveSite1-3p37A_RNA.mrc zone"" > rename #39 ""CTpol2EC10s-Focused-ActiveSite1-3p37A_AS.mrc zone"" > rename #40 ""CTpol2EC10s-Focused-ActiveSite1-3p37A_BH.mrc zone"" > rename #41 ""CTpol2EC10s-Focused-ActiveSite1-3p37A_TL.mrc zone"" > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > hide #!37 models > show #!37 models > hide #!38 models > show #!38 models > hide #!41 models > hide #!40 models > hide #!39 models > hide #!38 models > hide #!37 models > hide #26 models > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true > show #26 models > show #!14 models > hide #!14 models > volume zone #14 nearAtoms #26/T:15-22 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-Focused-ActiveSite3-3p2A.mrc zone as #42, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #14 nearAtoms #26/R:7-11 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-Focused-ActiveSite3-3p2A.mrc zone as #43, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #14 nearAtoms #26/A:493-501 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-Focused-ActiveSite3-3p2A.mrc zone as #44, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #14 nearAtoms #26/A:837-861 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-Focused-ActiveSite3-3p2A.mrc zone as #45, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #14 nearAtoms #26/A:1083-1123 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-Focused-ActiveSite3-3p2A.mrc zone as #46, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #14 nearAtoms #26/A:1083-1123 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-Focused-ActiveSite3-3p2A.mrc zone as #47, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > close #42-47 > volume zone #14 nearAtoms #26/T:15-22 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-Focused-ActiveSite3-3p2A.mrc zone as #42, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #14 nearAtoms #26/R:7-11 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-Focused-ActiveSite3-3p2A.mrc zone as #43, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #14 nearAtoms #26/A:493-501 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-Focused-ActiveSite3-3p2A.mrc zone as #44, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #14 nearAtoms #26/A:837-861 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-Focused-ActiveSite3-3p2A.mrc zone as #45, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #14 nearAtoms #26/A:1083-1123 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-Focused-ActiveSite3-3p2A.mrc zone as #46, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > rename #42 ""CTpol2EC10s-Focused-ActiveSite3-3p2A_tDNA.mrc zone"" > hide #!42 models > show #!42 models > hide #!43 models > show #!43 models > rename #43 ""CTpol2EC10s-Focused-ActiveSite3-3p2A_RNA.mrc zone"" > rename #44 ""CTpol2EC10s-Focused-ActiveSite3-3p2A_AS.mrc zone"" > rename #45 ""CTpol2EC10s-Focused-ActiveSite3-3p2A_BH.mrc zone"" > rename #46 ""CTpol2EC10s-Focused-ActiveSite3-3p2A_TL.mrc zone"" > volume #42 color cyan > volume #43 color red > volume #44 color purple > volume #45 color forestgreen > volume #46 color orange > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true > hide #!42 models > hide #!43 models > hide #!44 models > hide #!45 models > hide #!46 models > show #!15 models > hide #!15 models > show #!15 models > volume zone #15 nearAtoms #26/T:15-22 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-trigger1-3p3A.mrc zone as #47, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #15 nearAtoms #26/R:7-11 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-trigger1-3p3A.mrc zone as #48, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #15 nearAtoms #26/A:493-501 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-trigger1-3p3A.mrc zone as #49, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #15 nearAtoms #26/A:837-861 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-trigger1-3p3A.mrc zone as #50, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > volume zone #15 nearAtoms #26/A:1083-1123 range 4 invert false minimalBounds > false newMap true Opened CTpol2EC10s-trigger1-3p3A.mrc zone as #51, grid size 384,384,384, pixel 0.852, shown at step 1, values float32 > rename #47 ""CTpol2EC10s-trigger1-3p3A_tDNA.mrc zone"" > rename #48 ""CTpol2EC10s-trigger1-3p3A_RNA.mrc zone"" > rename #49 ""CTpol2EC10s-trigger1-3p3A_AS.mrc zone"" > rename #50 ""CTpol2EC10s-trigger1-3p3A_BH.mrc zone"" > rename #51 ""CTpol2EC10s-trigger1-3p3A_TL.mrc zone"" > volume #47 color cyan > volume #48 color red > volume #49 color purple > volume #50 color forestgreen > volume #51 color orange > ui tool show ""Side View"" > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true [Repeated 1 time(s)] > hide #!51 models > hide #!50 models > hide #!49 models > hide #!48 models > hide #26 models > ui tool show ""Hide Dust"" > show #!48 models > show #!49 models > show #!50 models > show #!51 models > surface dust #47 size 5.11 > surface dust #48 size 5.11 > surface dust #49 size 5.11 > surface dust #50 size 5.11 > surface dust #51 size 5.11 > volume #51 level 0.00199 > hide #!51 models > hide #!50 models > hide #!49 models > hide #!48 models > hide #!47 models > show #!46 models > show #!45 models > show #!44 models > show #!43 models > show #!42 models > surface dust #42 size 5.11 > surface dust #43 size 5.11 [Repeated 1 time(s)] > surface dust #44 size 5.11 > surface dust #45 size 5.11 > surface dust #46 size 5.11 > volume #45 level 0.01097 > volume #44 level 0.01 > volume #45 level 0.01 > volume #47 level 0.01 > volume #48 level 0.01 > volume #49 level 0.01 > volume #50 level 0.01 > volume #51 level 0.01 > volume #43 level 0.01 > hide #!46 models > show #!46 models > hide #!46 models > hide #!45 models > hide #!44 models > hide #!43 models > hide #!42 models > show #!43 models > show #!42 models > show #!41 models > show #!40 models > show #!39 models > show #!38 models > show #!37 models > surface dust #37 size 5.11 > surface dust #38 size 5.11 > surface dust #39 size 5.11 > surface dust #40 size 5.11 > surface dust #41 size 5.11 > surface dust #42 size 5.11 > hide #!43 models > hide #!42 models > hide #!41 models > hide #!40 models > hide #!39 models > hide #!38 models > hide #!37 models > show #!36 models > show #!35 models > show #!34 models > show #!33 models > show #!32 models > surface dust #32 size 5.11 > surface dust #33 size 5.11 > surface dust #34 size 5.11 > surface dust #35 size 5.11 > surface dust #36 size 5.11 > volume #36 level 0.01 > volume #35 level 0.01 > volume #34 level 0.01 > volume #33 level 0.01 > volume #32 level 0.01 > volume #31 level 0.01 > volume #29 level 0.01 > volume #30 level 0.01 > hide #!36 models > hide #!35 models > hide #!34 models > hide #!33 models > hide #!32 models > show #!31 models > show #!29 models > show #!28 models > show #!27 models > surface dust #27 size 5.11 > surface dust #28 size 5.11 > surface dust #29 size 5.11 > surface dust #30 size 5.11 > surface dust #31 size 5.11 > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true > hide #!27 models > hide #!28 models > hide #!29 models > hide #!30 models > hide #!31 models > show #!25 models > show #!24 models > show #!23 models > show #!22 models > show #!21 models > hide #!25 models > show #!25 models > rename #25 ""CTpol2EC10s-3p23A_TL.mrc zone"" > volume #21 color cyan > volume #22 color red > volume #23 color purple > volume #24 color forestgreen > volume #25 color orange > volume #28 level 0.01 > volume #27 level 0.01 > volume #25 level 0.01 > volume #24 level 0.01 > volume #23 level 0.01 > volume #22 level 0.01 > volume #21 level 0.01 > volume #16 level 0.001 > volume #16 level 0.01 > volume #17 level 0.01 > volume #20 level 0.01 > volume #19 level 0.01 > volume #18 level 0.01 > volume #15 level 0.01 > volume #14 level 0.01 > hide #!25 models > hide #!24 models > hide #!23 models > hide #!22 models > hide #!21 models > show #!21 models > hide #!21 models > show #!20 models > rename #20 id #52 > rename #19 id #53 > rename #18 id #54 > rename #52 id #18 > rename #54 id #19 > rename #53 id #20 > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true > show #!13 models > hide #!13 models > show #!15 models > hide #!15 models > show #!16 models > show #!17 models > show #!19 models > show #!20 models > show #2 models > show #26 models > select ~#26/T:15-22 #26/R:5-11 #26/A:493-501, 837-861,1083-1123 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 99 models selected > cartoon hide (#2,26 & sel) > select subtract #51 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 97 models selected > select add #51 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 99 models selected > select clear > show #!25 models > hide #!25 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #!51 models > hide #!51 models > show #!50 models > hide #!50 models > show #!49 models > show #!48 models > hide #!49 models > hide #!48 models > hide #26 models > show #26 models > select #26/T:15-22 251 atoms, 269 bonds, 8 residues, 1 model selected > show sel target ab > style sel ball Changed 251 atom styles > select #26/R:5-11 232 atoms, 251 bonds, 7 residues, 1 model selected > color sel red > style sel ball Changed 232 atom styles > show sel target ab > select clear > select #26/A:493-501 123 atoms, 124 bonds, 9 residues, 1 model selected > color sel purple > select clear > select #26/A:837-861 409 atoms, 409 bonds, 25 residues, 1 model selected > color sel forest green > select clear > select #26/A:1083-1123 613 atoms, 617 bonds, 41 residues, 1 model selected > color sel orange > select clear > hide #26 models > show #26 models > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true > open > /Volumes/Rayees_T7/ctPolII_proc/ctPolII_10s/ctpolII_10s_job162_2p9A_UTP_isolde1.pdb Chain information for ctpolII_10s_job162_2p9A_UTP_isolde1.pdb #52 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available N | No description available R | No description available T | No description available > hide #26,52 atoms > show #26,52 cartoons > hide #26 models > hide #!20 models > hide #!19 models > hide #!18 models > hide #!17 models > hide #!16 models > fitmap #26 inMap #9 Fit molecule ctpolii_10s_job162_2p9A_RNA11_isolde1.pdb (#26) to map CTpol2EC10s_job162_2p9A.mrc (#9) using 66734 atoms average map value = 0.0243, steps = 44 shifted from previous position = 0.00897 rotated from previous position = 0.00858 degrees atoms outside contour = 21264, contour level = 0.0099185 Position of ctpolii_10s_job162_2p9A_RNA11_isolde1.pdb (#26) relative to CTpol2EC10s_job162_2p9A.mrc (#9) coordinates: Matrix rotation and translation 0.99999995 -0.00002286 0.00031627 -0.04542463 0.00002292 0.99999998 -0.00020944 0.04744955 -0.00031626 0.00020945 0.99999993 0.02842244 Axis 0.55114484 0.83223297 0.06022998 Axis point 86.75203289 0.00000000 171.81176249 Rotation angle (degrees) 0.02177354 Shift along axis 0.01616541 > fitmap #52 inMap #9 Fit molecule ctpolII_10s_job162_2p9A_UTP_isolde1.pdb (#52) to map CTpol2EC10s_job162_2p9A.mrc (#9) using 66748 atoms average map value = 0.02428, steps = 48 shifted from previous position = 0.0129 rotated from previous position = 0.013 degrees atoms outside contour = 21273, contour level = 0.0099185 Position of ctpolII_10s_job162_2p9A_UTP_isolde1.pdb (#52) relative to CTpol2EC10s_job162_2p9A.mrc (#9) coordinates: Matrix rotation and translation 0.99999998 -0.00007088 0.00020699 -0.03498578 0.00007089 1.00000000 -0.00006216 0.00028270 -0.00020699 0.00006218 0.99999998 0.02530639 Axis 0.27334208 0.91002828 0.31166110 Axis point 124.37926645 0.00000000 167.16266492 Rotation angle (degrees) 0.01303202 Shift along axis -0.00141881 > select #52/U 44 atoms, 45 bonds, 1 residue, 1 model selected > show sel target ab > select #52/A:855 24 atoms, 23 bonds, 1 residue, 1 model selected > select #52/R:11 Nothing selected > select ~#52/T:15-22 #52/R:5-10 #52/A:493-501, 837-861,1083-1123 #52/U/1 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 100 models selected > select subtract #51 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 98 models selected > select subtract #50 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 96 models selected > select subtract #49 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 94 models selected > select subtract #48 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 92 models selected > select subtract #47 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 90 models selected > select subtract #46 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 88 models selected > select subtract #45 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 86 models selected > select subtract #44 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 84 models selected > select subtract #43 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 82 models selected > select subtract #42 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 80 models selected > select subtract #41 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 78 models selected > select subtract #40 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 76 models selected > select subtract #39 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 74 models selected > select subtract #38 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 72 models selected > select subtract #37 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 70 models selected > select subtract #36 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 68 models selected > select subtract #35 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 66 models selected > select subtract #34 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 64 models selected > select subtract #33 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 62 models selected > select subtract #32 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 60 models selected > select subtract #31 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 58 models selected > select subtract #30 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 56 models selected > select subtract #29 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 54 models selected > select subtract #28 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 52 models selected > select subtract #27 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 50 models selected > select subtract #26 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 49 models selected > select subtract #25 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 47 models selected > select subtract #24 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 45 models selected > select subtract #23 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 43 models selected > select subtract #22 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 41 models selected > select subtract #21 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 39 models selected > select subtract #20 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 37 models selected > select subtract #19 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 35 models selected > select subtract #18 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 33 models selected > select subtract #17 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 31 models selected > select subtract #16 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 29 models selected > select subtract #15 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 27 models selected > select subtract #14 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 25 models selected > select subtract #13 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 23 models selected > select subtract #12 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 21 models selected > select subtract #11 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 19 models selected > select subtract #10 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 17 models selected > select subtract #9 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 15 models selected > select subtract #8 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 13 models selected > select subtract #7 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 11 models selected > select subtract #6 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 9 models selected > select subtract #5 165427 atoms, 167614 bonds, 12413 residues, 7 models selected > select subtract #4 165427 atoms, 167614 bonds, 12413 residues, 5 models selected > select subtract #3 98723 atoms, 100165 bonds, 8246 residues, 4 models selected > select subtract #2 65106 atoms, 65802 bonds, 4078 residues, 3 models selected > select subtract #1 65106 atoms, 65802 bonds, 4078 residues, 1 model selected > cartoon hide sel > select #52/T:15-22 251 atoms, 269 bonds, 8 residues, 1 model selected > color sel cyan > style sel ball Changed 251 atom styles > show sel target ab > select clear > select #52/R:5-10 #52/U/1 246 atoms, 264 bonds, 7 residues, 1 model selected > color sel red > style sel ball Changed 246 atom styles > show sel target ab > select clear > select #52/A:493-501 123 atoms, 124 bonds, 9 residues, 1 model selected > color sel purple > select clear > select #52/A: 837-861 409 atoms, 409 bonds, 25 residues, 1 model selected > color sel forest green > select clear > select #52/A: 1083-1123 613 atoms, 617 bonds, 41 residues, 1 model selected > color sel orange > select clear > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true > hide #52 models > show #52 models > show #!16 models > show #!17 models > show #!18 models > show #!19 models > show #!20 models > show #26 models > hide #26 models > show #26 models > hide #26 models > show #26 models > show #2 models > hide #2 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > hide #26 models > hide #52 models > show #26 models > hide #26 models > show #26 models > select ~#26/T:15-22 #26/R:5-11 #26/A:493-501, 837-861,1083-1123 298637 atoms, 302311 bonds, 1 pseudobond, 20732 residues, 100 models selected > select subtract #27 298637 atoms, 302311 bonds, 1 pseudobond, 20732 residues, 98 models selected > select subtract #28 298637 atoms, 302311 bonds, 1 pseudobond, 20732 residues, 96 models selected > select subtract #29 298637 atoms, 302311 bonds, 1 pseudobond, 20732 residues, 94 models selected > select subtract #30 298637 atoms, 302311 bonds, 1 pseudobond, 20732 residues, 92 models selected > select subtract #31 298637 atoms, 302311 bonds, 1 pseudobond, 20732 residues, 90 models selected > select subtract #32 298637 atoms, 302311 bonds, 1 pseudobond, 20732 residues, 88 models selected > select subtract #33 298637 atoms, 302311 bonds, 1 pseudobond, 20732 residues, 86 models selected > select subtract #34 298637 atoms, 302311 bonds, 1 pseudobond, 20732 residues, 84 models selected > select subtract #35 298637 atoms, 302311 bonds, 1 pseudobond, 20732 residues, 82 models selected > select subtract #36 298637 atoms, 302311 bonds, 1 pseudobond, 20732 residues, 80 models selected > select subtract #37 298637 atoms, 302311 bonds, 1 pseudobond, 20732 residues, 78 models selected > select subtract #38 298637 atoms, 302311 bonds, 1 pseudobond, 20732 residues, 76 models selected > select subtract #39 298637 atoms, 302311 bonds, 1 pseudobond, 20732 residues, 74 models selected > select clear > select #26 66734 atoms, 67481 bonds, 4168 residues, 1 model selected > select clear > select ~#26/T:15-22 #26/R:5-11 #26/A:493-501, 837-861,1083-1123 298637 atoms, 302311 bonds, 1 pseudobond, 20732 residues, 100 models selected > select subtract #1 298637 atoms, 302311 bonds, 1 pseudobond, 20732 residues, 98 models selected > select subtract #2 265020 atoms, 267948 bonds, 1 pseudobond, 16564 residues, 97 models selected > select subtract #3 198316 atoms, 200499 bonds, 1 pseudobond, 12397 residues, 96 models selected > select subtract #4 198316 atoms, 200499 bonds, 1 pseudobond, 12397 residues, 94 models selected > select subtract #5 131854 atoms, 133296 bonds, 8246 residues, 92 models selected > select subtract #6 131854 atoms, 133296 bonds, 8246 residues, 90 models selected > select subtract #7 131854 atoms, 133296 bonds, 8246 residues, 88 models selected > select subtract #8 131854 atoms, 133296 bonds, 8246 residues, 86 models selected > select subtract #9 131854 atoms, 133296 bonds, 8246 residues, 84 models selected > select subtract #10 131854 atoms, 133296 bonds, 8246 residues, 82 models selected > select subtract #11 131854 atoms, 133296 bonds, 8246 residues, 80 models selected > select subtract #12 131854 atoms, 133296 bonds, 8246 residues, 78 models selected > select subtract #13 131854 atoms, 133296 bonds, 8246 residues, 76 models selected > select subtract #14 131854 atoms, 133296 bonds, 8246 residues, 74 models selected > select subtract #15 131854 atoms, 133296 bonds, 8246 residues, 72 models selected > select subtract #16 131854 atoms, 133296 bonds, 8246 residues, 70 models selected > select subtract #18 131854 atoms, 133296 bonds, 8246 residues, 68 models selected > select subtract #17 131854 atoms, 133296 bonds, 8246 residues, 66 models selected > select subtract #19 131854 atoms, 133296 bonds, 8246 residues, 64 models selected > select subtract #20 131854 atoms, 133296 bonds, 8246 residues, 62 models selected > select subtract #21 131854 atoms, 133296 bonds, 8246 residues, 60 models selected > select subtract #22 131854 atoms, 133296 bonds, 8246 residues, 58 models selected > select subtract #23 131854 atoms, 133296 bonds, 8246 residues, 56 models selected > select subtract #24 131854 atoms, 133296 bonds, 8246 residues, 54 models selected > select subtract #25 131854 atoms, 133296 bonds, 8246 residues, 52 models selected > select subtract #27 131854 atoms, 133296 bonds, 8246 residues, 50 models selected > select subtract #28 131854 atoms, 133296 bonds, 8246 residues, 48 models selected > select subtract #29 131854 atoms, 133296 bonds, 8246 residues, 46 models selected > select subtract #30 131854 atoms, 133296 bonds, 8246 residues, 44 models selected > select subtract #31 131854 atoms, 133296 bonds, 8246 residues, 42 models selected > select subtract #32 131854 atoms, 133296 bonds, 8246 residues, 40 models selected > select subtract #33 131854 atoms, 133296 bonds, 8246 residues, 38 models selected > select subtract #34 131854 atoms, 133296 bonds, 8246 residues, 36 models selected > select subtract #35 131854 atoms, 133296 bonds, 8246 residues, 34 models selected > select subtract #36 131854 atoms, 133296 bonds, 8246 residues, 32 models selected > select subtract #37 131854 atoms, 133296 bonds, 8246 residues, 30 models selected > select subtract #38 131854 atoms, 133296 bonds, 8246 residues, 28 models selected > select subtract #39 131854 atoms, 133296 bonds, 8246 residues, 26 models selected > select subtract #40 131854 atoms, 133296 bonds, 8246 residues, 24 models selected > select subtract #41 131854 atoms, 133296 bonds, 8246 residues, 22 models selected > select subtract #42 131854 atoms, 133296 bonds, 8246 residues, 20 models selected > select subtract #43 131854 atoms, 133296 bonds, 8246 residues, 18 models selected > select subtract #44 131854 atoms, 133296 bonds, 8246 residues, 16 models selected > select subtract #45 131854 atoms, 133296 bonds, 8246 residues, 14 models selected > select subtract #46 131854 atoms, 133296 bonds, 8246 residues, 12 models selected > select subtract #47 131854 atoms, 133296 bonds, 8246 residues, 10 models selected > select subtract #48 131854 atoms, 133296 bonds, 8246 residues, 8 models selected > select subtract #49 131854 atoms, 133296 bonds, 8246 residues, 6 models selected > select subtract #50 131854 atoms, 133296 bonds, 8246 residues, 4 models selected > select subtract #51 131854 atoms, 133296 bonds, 8246 residues, 2 models selected > select subtract #52 65106 atoms, 65802 bonds, 4078 residues, 1 model selected > cartoon hide sel > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true > open > /Volumes/Rayees_T7/ctPolII_proc/ctPolII_10s/ctpolII_10s_job162_2p9A_UMP_isolde1.pdb Chain information for ctpolII_10s_job162_2p9A_UMP_isolde1.pdb #53 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available N | No description available R | No description available T | No description available > hide sel atoms [Repeated 1 time(s)] > select add #53 131842 atoms, 133284 bonds, 8246 residues, 2 models selected > hide sel atoms > show sel cartoons > select clear > fitmap #53 inMap #9 Fit molecule ctpolII_10s_job162_2p9A_UMP_isolde1.pdb (#53) to map CTpol2EC10s_job162_2p9A.mrc (#9) using 66736 atoms average map value = 0.02429, steps = 44 shifted from previous position = 0.0208 rotated from previous position = 0.0186 degrees atoms outside contour = 21263, contour level = 0.0099185 Position of ctpolII_10s_job162_2p9A_UMP_isolde1.pdb (#53) relative to CTpol2EC10s_job162_2p9A.mrc (#9) coordinates: Matrix rotation and translation 0.99999997 0.00003774 0.00025337 -0.04387764 -0.00003769 0.99999998 -0.00020040 0.05589235 -0.00025337 0.00020039 0.99999995 0.01940746 Axis 0.61616465 0.77903482 -0.11595630 Axis point 83.07731363 0.00000000 207.85785297 Rotation angle (degrees) 0.01863469 Shift along axis 0.01425582 > hide #53 models > hide #26 models > show #26 models > hide #26 models > show #53 models > hide #!20 models > hide #!19 models > hide #!18 models > hide #!17 models > hide #!16 models > select #53/U 32 atoms, 33 bonds, 1 residue, 1 model selected > style sel ball Changed 32 atom styles > show sel target ab > select clear > hide #53 models > show #53 models > select ~#53/T:15-22 #53/R:5-10 #53/A:493-501, 837-861,1083-1123 #53/U/11 365371 atoms, 369792 bonds, 1 pseudobond, 24900 residues, 101 models selected > select subtract #52 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 100 models selected > select subtract #51 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 98 models selected > select subtract #50 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 96 models selected > select subtract #49 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 94 models selected > select subtract #48 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 92 models selected > select subtract #47 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 90 models selected > select subtract #46 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 88 models selected > select subtract #45 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 86 models selected > select subtract #44 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 84 models selected > select subtract #43 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 82 models selected > select subtract #42 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 80 models selected > select subtract #41 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 78 models selected > select subtract #40 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 76 models selected > select subtract #39 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 74 models selected > select subtract #38 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 72 models selected > select subtract #37 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 70 models selected > select subtract #36 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 68 models selected > select subtract #35 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 66 models selected > select subtract #34 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 64 models selected > select subtract #33 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 62 models selected > select subtract #32 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 60 models selected > select subtract #31 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 58 models selected > select subtract #30 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 56 models selected > select subtract #29 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 54 models selected > select subtract #28 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 52 models selected > select subtract #27 298623 atoms, 302298 bonds, 1 pseudobond, 20732 residues, 50 models selected > select subtract #26 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 49 models selected > select subtract #25 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 47 models selected > select subtract #24 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 45 models selected > select subtract #23 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 43 models selected > select subtract #22 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 41 models selected > select subtract #21 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 39 models selected > select subtract #20 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 37 models selected > select subtract #19 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 35 models selected > select subtract #18 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 33 models selected > select subtract #17 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 31 models selected > select subtract #16 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 29 models selected > select subtract #15 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 27 models selected > select subtract #14 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 25 models selected > select subtract #13 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 23 models selected > select subtract #12 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 21 models selected > select subtract #11 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 19 models selected > select subtract #10 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 17 models selected > select subtract #9 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 15 models selected > select subtract #8 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 13 models selected > select subtract #7 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 11 models selected > select subtract #6 231889 atoms, 234817 bonds, 1 pseudobond, 16564 residues, 9 models selected > select subtract #5 165427 atoms, 167614 bonds, 12413 residues, 7 models selected > select subtract #4 165427 atoms, 167614 bonds, 12413 residues, 5 models selected > select subtract #3 98723 atoms, 100165 bonds, 8246 residues, 4 models selected > select subtract #2 65106 atoms, 65802 bonds, 4078 residues, 3 models selected > select subtract #1 65106 atoms, 65802 bonds, 4078 residues, 1 model selected > cartoon hide sel > select #53/T:15-22 251 atoms, 269 bonds, 8 residues, 1 model selected > color sel cyan > style sel ball Changed 251 atom styles > show sel target ab > select #53/R:5-10 #53/U/11 234 atoms, 252 bonds, 7 residues, 1 model selected > style sel ball Changed 234 atom styles > show sel target ab > color sel red > select clear > select #53/A:493-501 123 atoms, 124 bonds, 9 residues, 1 model selected > color sel purple > select #53/A:837-861 409 atoms, 409 bonds, 25 residues, 1 model selected > color sel forest green > select #53/A:1083-1123 613 atoms, 617 bonds, 41 residues, 1 model selected > color sel orange > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true > select clear > show #52 models > hide #52 models > show #52 models > hide #52 models > show #52 models > hide #52 models > show #52 models > hide #52 models > show #52 models > hide #52 models > show #52 models > hide #52 models > show #52 models > show #3 models > hide #3 models > show #26 models > select ~#26/T:15-22 #26/R:5-11 #26/A:493-501, 837-861,1083-1123 365373 atoms, 369793 bonds, 1 pseudobond, 24900 residues, 101 models selected > select subtract #25 365373 atoms, 369793 bonds, 1 pseudobond, 24900 residues, 99 models selected > select subtract #24 365373 atoms, 369793 bonds, 1 pseudobond, 24900 residues, 97 models selected > select subtract #23 365373 atoms, 369793 bonds, 1 pseudobond, 24900 residues, 95 models selected > select subtract #22 365373 atoms, 369793 bonds, 1 pseudobond, 24900 residues, 93 models selected > select subtract #21 365373 atoms, 369793 bonds, 1 pseudobond, 24900 residues, 91 models selected > select subtract #20 365373 atoms, 369793 bonds, 1 pseudobond, 24900 residues, 89 models selected > select subtract #19 365373 atoms, 369793 bonds, 1 pseudobond, 24900 residues, 87 models selected > select subtract #18 365373 atoms, 369793 bonds, 1 pseudobond, 24900 residues, 85 models selected > select subtract #17 365373 atoms, 369793 bonds, 1 pseudobond, 24900 residues, 83 models selected > select subtract #16 365373 atoms, 369793 bonds, 1 pseudobond, 24900 residues, 81 models selected > select subtract #15 365373 atoms, 369793 bonds, 1 pseudobond, 24900 residues, 79 models selected > select subtract #14 365373 atoms, 369793 bonds, 1 pseudobond, 24900 residues, 77 models selected > select subtract #13 365373 atoms, 369793 bonds, 1 pseudobond, 24900 residues, 75 models selected > select subtract #12 365373 atoms, 369793 bonds, 1 pseudobond, 24900 residues, 73 models selected > select subtract #11 365373 atoms, 369793 bonds, 1 pseudobond, 24900 residues, 71 models selected > select subtract #10 365373 atoms, 369793 bonds, 1 pseudobond, 24900 residues, 69 models selected > select subtract #9 365373 atoms, 369793 bonds, 1 pseudobond, 24900 residues, 67 models selected > select subtract #8 365373 atoms, 369793 bonds, 1 pseudobond, 24900 residues, 65 models selected > select subtract #7 365373 atoms, 369793 bonds, 1 pseudobond, 24900 residues, 63 models selected > select subtract #6 365373 atoms, 369793 bonds, 1 pseudobond, 24900 residues, 61 models selected > select subtract #5 298911 atoms, 302590 bonds, 20749 residues, 59 models selected > select subtract #4 298911 atoms, 302590 bonds, 20749 residues, 57 models selected > select subtract #3 232207 atoms, 235141 bonds, 16582 residues, 56 models selected > select subtract #2 198590 atoms, 200778 bonds, 12414 residues, 55 models selected > select subtract #1 198590 atoms, 200778 bonds, 12414 residues, 53 models selected > select subtract #27 198590 atoms, 200778 bonds, 12414 residues, 51 models selected > select subtract #28 198590 atoms, 200778 bonds, 12414 residues, 49 models selected > select subtract #29 198590 atoms, 200778 bonds, 12414 residues, 47 models selected > select subtract #30 198590 atoms, 200778 bonds, 12414 residues, 45 models selected > select subtract #31 198590 atoms, 200778 bonds, 12414 residues, 43 models selected > select subtract #32 198590 atoms, 200778 bonds, 12414 residues, 41 models selected > select subtract #33 198590 atoms, 200778 bonds, 12414 residues, 39 models selected > select subtract #34 198590 atoms, 200778 bonds, 12414 residues, 37 models selected > select subtract #35 198590 atoms, 200778 bonds, 12414 residues, 35 models selected > select subtract #36 198590 atoms, 200778 bonds, 12414 residues, 33 models selected > select subtract #37 198590 atoms, 200778 bonds, 12414 residues, 31 models selected > select subtract #38 198590 atoms, 200778 bonds, 12414 residues, 29 models selected > select subtract #39 198590 atoms, 200778 bonds, 12414 residues, 27 models selected > select subtract #40 198590 atoms, 200778 bonds, 12414 residues, 25 models selected > select subtract #41 198590 atoms, 200778 bonds, 12414 residues, 23 models selected > select subtract #42 198590 atoms, 200778 bonds, 12414 residues, 21 models selected > select subtract #43 198590 atoms, 200778 bonds, 12414 residues, 19 models selected > select subtract #44 198590 atoms, 200778 bonds, 12414 residues, 17 models selected > select subtract #45 198590 atoms, 200778 bonds, 12414 residues, 15 models selected > select subtract #46 198590 atoms, 200778 bonds, 12414 residues, 13 models selected > select subtract #47 198590 atoms, 200778 bonds, 12414 residues, 11 models selected > select subtract #48 198590 atoms, 200778 bonds, 12414 residues, 9 models selected > select subtract #49 198590 atoms, 200778 bonds, 12414 residues, 7 models selected > select subtract #50 198590 atoms, 200778 bonds, 12414 residues, 5 models selected > select subtract #51 198590 atoms, 200778 bonds, 12414 residues, 3 models selected > select subtract #52 131842 atoms, 133284 bonds, 8246 residues, 2 models selected > select subtract #53 65106 atoms, 65802 bonds, 4078 residues, 1 model selected > cartoon hide sel > hide #52 models > hide #53 models > hide #26 models > show #26 models > select #26/T:15-22 251 atoms, 269 bonds, 8 residues, 1 model selected > color sel cyan > style sel ball Changed 251 atom styles > show sel target ab > select #26/R:5-11 232 atoms, 251 bonds, 7 residues, 1 model selected > color sel red > style sel ball Changed 232 atom styles > show sel target ab > select clear > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true > show #!16 models > show #!17 models > show #!18 models > show #!19 models > show #!20 models > show #!21 models > hide #!20 models > hide #!19 models > hide #!18 models > hide #!17 models > hide #!16 models > show #!25 models > show #!24 models > show #!23 models > show #!22 models > select add #21 2 models selected > select add #22 4 models selected > select add #23 6 models selected > select add #24 8 models selected > select add #25 10 models selected > select add #26 66734 atoms, 67481 bonds, 4168 residues, 11 models selected > transparency (#26 & sel) 80 > select subtract #26 10 models selected > select add #26 66734 atoms, 67481 bonds, 4168 residues, 11 models selected > select subtract #26 10 models selected > select clear > select add #21 2 models selected > select add #22 4 models selected > select add #23 6 models selected > select add #24 8 models selected > select add #25 10 models selected > transparency #21.1#22.1#23.1#24.1#25.1 80 > select clear > hide #26 models > hide #!25 models > hide #!24 models > hide #!23 models > hide #!22 models > hide #!21 models > show #!27 models > show #!28 models > show #!29 models > show #!30 models > show #!31 models > show #26 models > select add #27 2 models selected > select add #28 4 models selected > select add #29 6 models selected > select add #30 8 models selected > select add #31 10 models selected > transparency #27.1#28.1#29.1#30.1#31.1 80 > select clear > select add #27 2 models selected > select add #28 4 models selected > select add #29 6 models selected > select add #30 8 models selected > select add #31 10 models selected > transparency #27.1#28.1#29.1#30.1#31.1 90 > select clear > hide #!31 models > hide #!30 models > hide #!29 models > hide #!28 models > hide #!27 models > show #!32 models > show #!33 models > show #!34 models > show #!35 models > show #!36 models > select add #32 2 models selected > select add #33 4 models selected > select add #34 6 models selected > select add #35 8 models selected > select add #36 10 models selected > transparency #32.1#33.1#34.1#35.1#36.1 90 > select clear > hide #!32 models > hide #!33 models > hide #!34 models > hide #!35 models > hide #!36 models > show #!37 models > show #!38 models > show #!39 models > show #!40 models > show #!41 models > select add #41 2 models selected > select add #40 4 models selected > select add #39 6 models selected > select add #38 8 models selected > select add #37 10 models selected > transparency #37.1#38.1#39.1#40.1#41.1 90 > select clear > select add #41 2 models selected > select add #40 4 models selected > select add #39 6 models selected > select add #38 8 models selected > select add #37 10 models selected > transparency #37.1#38.1#39.1#40.1#41.1 80 > select clear > hide #!41 models > hide #!40 models > hide #!39 models > hide #!38 models > hide #!37 models > show #!41 models > hide #!41 models > show #!42 models > show #!43 models > show #!44 models > show #!45 models > show #!46 models > select add #46 2 models selected > select add #45 4 models selected > select add #44 6 models selected > select add #43 8 models selected > select add #42 10 models selected > transparency #42.1#43.1#44.1#45.1#46.1 80 > select clear > hide #!46 models > show #!46 models > show #!47 models > hide #!46 models > hide #!45 models > hide #!44 models > hide #!43 models > hide #!42 models > show #!48 models > show #!49 models > show #!50 models > show #!51 models > select add #51 2 models selected > select add #50 4 models selected > select add #49 6 models selected > select add #48 8 models selected > select add #47 10 models selected > transparency #47.1#48.1#49.1#50.1#51.1 80 > select clear > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true > hide #!51 models > hide #!50 models > hide #!49 models > hide #!48 models > hide #!47 models > show #52 models > show #53 models > hide #26 models > show #26 models > rename #26 id #54 > rename #52 id #55 > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true > hide #55 models > hide #54 models > hide #53 models > show #53 models > show #!16 models > show #!17 models > show #!18 models > show #!19 models > show #!20 models > hide #53 models > show #53 models > hide #53 models > show #54 models > hide #54 models > show #54 models > hide #54 models > show #55 models > hide #55 models > hide #!20 models > hide #!19 models > hide #!18 models > hide #!17 models > hide #!16 models > show #!21 models > show #!22 models > show #!23 models > show #!24 models > show #!25 models > show #53 models > hide #53 models > show #54 models > hide #54 models > show #55 models > hide #55 models > hide #!25 models > hide #!24 models > hide #!23 models > hide #!22 models > hide #!21 models > show #!27 models > show #!28 models > show #!29 models > show #!30 models > show #!31 models > show #!25 models > hide #!25 models > show #!25 models > hide #!25 models > show #!25 models > show #!24 models > show #!23 models > hide #!23 models > hide #!24 models > hide #!25 models > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > close #23-25 > show #!21 models > hide #!21 models > show #!22 models > hide #!22 models > close #21-22 > hide #!27 models > hide #!28 models > hide #!29 models > hide #!30 models > hide #!31 models > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true > show #!16 models > show #!17 models > show #!18 models > show #!19 models > show #!20 models > show #!27 models > hide #!27 models > hide #!20 models > hide #!19 models > hide #!18 models > hide #!17 models > hide #!16 models > show #!27 models > show #!28 models > show #!29 models > show #!30 models > show #!31 models > show #!10 models > hide #!10 models > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true > show #!10 models > surface dust #10 size 5.11 > volume #10 level 0.006168 > volume #10 level 0.01161 > hide #!10 models > show #!11 models > volume #11 level 0.01635 > show #!12 models > surface dust #12 size 5.11 > surface dust #11 size 5.11 > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true > volume #12 level 0.002264 > hide #!12 models > hide #!31 models > hide #!30 models > hide #!29 models > hide #!28 models > hide #!27 models > show #!32 models > show #!33 models > show #!34 models > show #!35 models > show #55 models > volume #12 level 0.001594 > volume #12 level 0.004945 > hide #!35 models > hide #!34 models > hide #!33 models > hide #!32 models > hide #!12 models > show #!12 models > volume #12 level 0.007626 > volume #12 level 0.01332 > show #2 models > hide #2 models > show #3 models > hide #3 models > show #3 models > open > /Volumes/Rayees_T7/ctPolII_proc/ctPolII_10s/ctpolII_10s_job162_2p9A_UTP_isolde2.pdb Chain information for ctpolII_10s_job162_2p9A_UTP_isolde2.pdb #21 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available N | No description available R | No description available T | No description available > hide #55 models > show #55 models > hide #55 models > show #55 models > hide #55 models > hide #21 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > hide #!12 models > show #!12 models > show #!13 models > volume #13 level 0.01957 > hide #!13 models > show #!14 models > hide #!12 models > volume #14 level 0.00515 > hide #!14 models > show #!15 models > volume #15 level 0.006578 > hide #!15 models > show #55 models > hide #55 models > show #55 models > hide #55 models > show #54 models > hide #54 models > show #53 models > hide #53 models > open > /Volumes/Rayees_T7/ctPolII_proc/ctPolII_10s/ctpolII_10s_job162_2p9A_UMP_isolde1.pdb Chain information for ctpolII_10s_job162_2p9A_UMP_isolde1.pdb #22 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available N | No description available R | No description available T | No description available > hide #3 models > show #3 models > hide #22 models > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true ——— End of log from Thu Feb 12 00:12:03 2026 ——— > view name session-start opened ChimeraX session > ui tool show ""Side View"" > hide #3 models > show #!41 models > hide #!41 models > show #53 models > show #!16 models > show #!17 models > show #!18 models > show #!19 models > show #!20 models > hide #!20 models > hide #!19 models > hide #!18 models > hide #!17 models > hide #!16 models > show #21 models > hide #21 models > show #!27 models > show #!28 models > show #54 models > hide #54 models > show #54 models > hide #53 models > hide #54 models > show #53 models > show #55 models > hide #53 models > show #21 models > hide #21 models > hide #!28 models > hide #!27 models > hide #55 models > show #21 models > hide #21 atoms > show #21 cartoons > show #22 models > hide #21-22 atoms > show #21-22 cartoons > select clear > hide #22 models > hide #21 models > show #21 models > select ~#21/T:15-22 #21/R:5-11 #21/A:493-501, 837-861,1083-1123 498887 atoms, 504801 bonds, 1 pseudobond, 33237 residues, 93 models selected > select subtract #22 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 92 models selected > select subtract #27 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 90 models selected > select subtract #28 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 88 models selected > select subtract #29 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 86 models selected > select subtract #30 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 84 models selected > select subtract #31 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 82 models selected > select subtract #32 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 80 models selected > select subtract #33 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 78 models selected > select subtract #34 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 76 models selected > select subtract #35 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 74 models selected > select subtract #36 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 72 models selected > select subtract #37 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 70 models selected > select subtract #38 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 68 models selected > select subtract #39 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 66 models selected > select subtract #40 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 64 models selected > select subtract #41 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 62 models selected > select subtract #42 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 60 models selected > select subtract #43 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 58 models selected > select subtract #44 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 56 models selected > select subtract #45 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 54 models selected > select subtract #46 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 52 models selected > select subtract #47 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 50 models selected > select subtract #48 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 48 models selected > select subtract #49 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 46 models selected > select subtract #50 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 44 models selected > select subtract #51 432151 atoms, 437319 bonds, 1 pseudobond, 29069 residues, 42 models selected > select subtract #53 365415 atoms, 369837 bonds, 1 pseudobond, 24901 residues, 41 models selected > select subtract #54 298681 atoms, 302356 bonds, 1 pseudobond, 20733 residues, 40 models selected > select subtract #55 231933 atoms, 234862 bonds, 1 pseudobond, 16565 residues, 39 models selected > select subtract #20 231933 atoms, 234862 bonds, 1 pseudobond, 16565 residues, 37 models selected > select subtract #19 231933 atoms, 234862 bonds, 1 pseudobond, 16565 residues, 35 models selected > select subtract #18 231933 atoms, 234862 bonds, 1 pseudobond, 16565 residues, 33 models selected > select subtract #17 231933 atoms, 234862 bonds, 1 pseudobond, 16565 residues, 31 models selected > select subtract #16 231933 atoms, 234862 bonds, 1 pseudobond, 16565 residues, 29 models selected > select subtract #15 231933 atoms, 234862 bonds, 1 pseudobond, 16565 residues, 27 models selected > select subtract #14 231933 atoms, 234862 bonds, 1 pseudobond, 16565 residues, 25 models selected > select subtract #13 231933 atoms, 234862 bonds, 1 pseudobond, 16565 residues, 23 models selected > select subtract #12 231933 atoms, 234862 bonds, 1 pseudobond, 16565 residues, 21 models selected > select subtract #11 231933 atoms, 234862 bonds, 1 pseudobond, 16565 residues, 19 models selected > select subtract #10 231933 atoms, 234862 bonds, 1 pseudobond, 16565 residues, 17 models selected > select subtract #9 231933 atoms, 234862 bonds, 1 pseudobond, 16565 residues, 15 models selected > select subtract #8 231933 atoms, 234862 bonds, 1 pseudobond, 16565 residues, 13 models selected > select subtract #7 231933 atoms, 234862 bonds, 1 pseudobond, 16565 residues, 11 models selected > select subtract #6 231933 atoms, 234862 bonds, 1 pseudobond, 16565 residues, 9 models selected > select subtract #5 165471 atoms, 167659 bonds, 12414 residues, 7 models selected > select subtract #4 165471 atoms, 167659 bonds, 12414 residues, 5 models selected > select subtract #3 98767 atoms, 100210 bonds, 8247 residues, 4 models selected > select subtract #2 65150 atoms, 65847 bonds, 4079 residues, 3 models selected > select subtract #1 65150 atoms, 65847 bonds, 4079 residues, 1 model selected > cartoon hide sel > select #21/T:15-22 251 atoms, 269 bonds, 8 residues, 1 model selected > color sel cyan > select #21/U 44 atoms, 45 bonds, 1 residue, 1 model selected > style sel ball Changed 44 atom styles > show sel target ab > select clear > select #21/R:5-10 #21/U 246 atoms, 264 bonds, 7 residues, 1 model selected > color sel red > select clear > select #21/R:5-10 #21/U 246 atoms, 264 bonds, 7 residues, 1 model selected > style sel ball Changed 246 atom styles > show sel target ab > select clear > select #21/A:493-501 123 atoms, 124 bonds, 9 residues, 1 model selected > color sel purple > select #21/A:837-861 409 atoms, 409 bonds, 25 residues, 1 model selected > color sel forest green > select #21/A:1083-1123 613 atoms, 617 bonds, 41 residues, 1 model selected > color sel orange > select clear > show #!32 models > show #!33 models > show #!34 models > show #!35 models > show #!36 models > select #21/T:15-22 251 atoms, 269 bonds, 8 residues, 1 model selected > style sel ball Changed 251 atom styles > show sel target ab > select clear > hide #!34 models > show #!34 models > hide #!33 models > show #!33 models > volume #36 level 0.006372 > hide #!34 models > show #!34 models > hide #!34 models > show #!34 models > volume #33 level 0.003423 > show #!12 models > volume #12 level 0.01253 > hide #!12 models > hide #!36 models > hide #!35 models > hide #!34 models > hide #!33 models > show #!31 models > hide #!32 models > hide #!31 models > cd /Volumes/Rayees_T7/PolII_Manuscript Current working directory is: /Volumes/Rayees_T7/PolII_Manuscript > save > /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig1/ctPolii_10s.cxs > includeMaps true ——— End of log from Thu Feb 12 09:59:51 2026 ——— > view name session-start opened ChimeraX session > show #!37 models > show #!38 models > show #!39 models > hide #!39 models > show #!39 models > hide #!39 models > show #!39 models > show #!40 models > show #!41 models > show #!42 models > show #!43 models > show #!44 models > show #!45 models > hide #!37 models > hide #!38 models > hide #!39 models > hide #!40 models > hide #!41 models > show #!46 models > volume #46 level 0.006067 > show #!47 models > show #!48 models > show #!49 models > show #!50 models > show #!51 models > hide #!42 models > hide #!43 models > hide #!44 models > hide #!45 models > hide #!46 models > hide #!51 models > hide #!50 models > hide #!49 models > hide #!48 models > hide #!47 models > show #!16 models > show #!17 models > show #54 models > hide #21 models > show #!18 models > hide #!18 models > show #!18 models > show #!19 models > show #!20 models > volume #20 level 0.003713 > volume #20 level 0.008821 > volume #20 level 0.01 > hide #!20 models > hide #!19 models > hide #!18 models > hide #!17 models > hide #!16 models > show #22 models > hide #22 models > show #!27 models > show #!28 models > show #!29 models > show #!30 models > show #!31 models > volume #31 level 0.003381 > hide #54 models > hide #!31 models > hide #!30 models > hide #!29 models > hide #!28 models > hide #!27 models > show #!32 models > show #!33 models > show #!34 models > show #!35 models > show #54 models > show #!36 models > volume #36 level 0.006093 > hide #!36 models > hide #!35 models > hide #!34 models > hide #!33 models > hide #!32 models > show #!37 models > show #!38 models > show #!39 models > show #!40 models > show #!41 models > volume #41 level 0.007047 > hide #!39 models > hide #!41 models > hide #!40 models > hide #!38 models > hide #!37 models > show #!42 models > show #!43 models > show #!44 models > show #!45 models > show #!46 models > volume #46 level 0.004217 > show #!41 models > hide #54 models > show #54 models > hide #!46 models > show #!46 models > hide #!46 models > hide #!41 models > show #!41 models > hide #!41 models > show #!46 models > hide #!46 models > hide #!45 models > hide #!44 models > hide #!43 models > hide #!42 models > show #!32 models > show #!33 models > show #!34 models > show #!35 models > show #!36 models > volume #36 level 0.005256 > show #!31 models > hide #!31 models > show #!31 models > hide #!31 models > show #!31 models > hide #!31 models > hide #!35 models > hide #!34 models > hide #!33 models > hide #!32 models > show #!31 models > hide #!31 models > show #!31 models > hide #!31 models > show #!31 models > hide #!31 models > show #!31 models > show #!20 models > hide #!31 models > hide #!36 models > show #!19 models > show #!18 models > show #!17 models > show #!16 models > hide #54 models > show #54 models > select #54/R 360 atoms, 389 bonds, 11 residues, 1 model selected > cartoon hide sel > select clear > hide #!18 models > select #54/T 917 atoms, 988 bonds, 29 residues, 1 model selected > cartoon hide sel > select clear > dssp > select #54/A:493-501 123 atoms, 124 bonds, 9 residues, 1 model selected > cartoon hide sel > select clear ===== 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 M4 Max 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: Mac16,5 Model Number: Z1FW00077LL/A Chip: Apple M4 Max Total Number of Cores: 16 (12 performance and 4 efficiency) Memory: 64 GB System Firmware Version: 13822.61.10 OS Loader Version: 13822.61.10 Software: System Software Overview: System Version: macOS 26.2 (25C56) Kernel Version: Darwin 25.2.0 Time since boot: 10 hours, 15 minutes Graphics/Displays: Apple M4 Max: Chipset Model: Apple M4 Max Type: GPU Bus: Built-In Total Number of Cores: 40 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal SyncMaster: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 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 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: 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 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 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 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 assigned normal Window Toolkit all ChimeraX