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Opened 90 minutes ago
#19844 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.2-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)
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{
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"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
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"modelCode" : "Mac16,5",
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"pid" : 11827,
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"procLaunch" : "2026-02-12 18:47:51.6260 -0800",
"procStartAbsTime" : 606666183650,
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"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
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"crashReporterKey" : "3D03C990-9D81-B6B4-6E53-68C3212D14D9",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["notOptedIn","siriAssetIsNotReady","assetIsNotReady"]},
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"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. Bytes before following region: 4311318520
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 100f98000-100f9c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":11827},
"vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4311318520
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
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CoreGraphics 96K 6
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page table in kernel 6201K 1
shared memory 4128K 27
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===== Log before crash start =====
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /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
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> 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
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> 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
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> show #!23 models
> show #!22 models
> select add #21
2 models selected
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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
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> show #26 models
> select add #27
2 models selected
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4 models selected
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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
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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
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> show #!32 models
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> select add #32
2 models selected
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4 models selected
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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
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> show #!41 models
> select add #41
2 models selected
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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
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> show #!41 models
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> 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
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> 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
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