![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 hours ago
#19854 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 0x0000000206a0ec40 (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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.dssp._dssp, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 53)
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"procLaunch" : "2026-02-15 13:13:46.4670 -0800",
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"procPath" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
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"crashReporterKey" : "3D03C990-9D81-B6B4-6E53-68C3212D14D9",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["siriAssetIsNotReady","notOptedIn","assetIsNotReady"]},
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"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"sleepWakeUUID" : "06A7E93A-3E02-4ED8-9897-657BEE1BD318",
"sip" : "enabled",
"vmRegionInfo" : "0x8 is not in any region. Bytes before following region: 4308205560
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 100ca0000-100ca4000 [ 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"},
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"vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4308205560
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
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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.
How to cite UCSF ChimeraX
> open
> /Volumes/Rayees_T7/ctPolII_proc/ctPolII_Apo/ctpolII_Apo_DNA_fix_isolde1.pdb
Chain information for ctpolII_Apo_DNA_fix_isolde1.pdb #1
---
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
> set bgColor white
> hide atoms
> show cartoons
> 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
> open
> /Volumes/Rayees_T7/ctPolII_proc/ctPolII_10s/ctpolII_10s_job162_2p9A_DNA_fixed_CTP_isolde1.pdb
Chain information for ctpolII_10s_job162_2p9A_DNA_fixed_CTP_isolde1.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
> open
> /Volumes/Rayees_T7/ctPolII_proc/ctPolII_10s/ctpolII_10s_job162_2p9A_DNA_fixed_RNA12_isolde1.pdb
Chain information for ctpolII_10s_job162_2p9A_DNA_fixed_RNA12_isolde1.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
> open
> /Volumes/Rayees_T7/ctPolII_proc/ctPolII_30s/ctpolii_30s_job063_DNA_fixed_isolde1.pdb
Chain information for ctpolii_30s_job063_DNA_fixed_isolde1.pdb #4
---
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
> open
> /Volumes/Rayees_T7/Rayees_T5_data/ctPolII_proc/ctpolii_maps/ctpolii_apo_maps/CTpol2EC-3p06A.mrc
Opened CTpol2EC-3p06A.mrc as #5, grid size 384,384,384, pixel 0.852, shown at
level 0.00838, step 2, values float32
> open
> /Volumes/Rayees_T7/Rayees_T5_data/ctPolII_proc/ctpolii_maps/ctpolii_10s_maps/CTpol2EC10s_job162_2p9A.mrc
Opened CTpol2EC10s_job162_2p9A.mrc as #6, 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_20s_maps/ctpolii20s_2EM_sessions_comb_data
> /job271_20s_3A.mrc"
Opened job271_20s_3A.mrc as #7, grid size 384,384,384, pixel 0.852, shown at
level 0.00825, step 2, values float32
> ui tool show "Hide Dust"
> surface dust #5 size 5.11
> surface dust #6 size 5.11
> surface dust #7 size 5.11
> ui tool show "Fit in Map"
> fitmap #2 inMap #5
Fit molecule ctpolII_10s_job162_2p9A_DNA_fixed_CTP_isolde1.pdb (#2) to map
CTpol2EC-3p06A.mrc (#5) using 66716 atoms
average map value = 0.02021, steps = 56
shifted from previous position = 0.829
rotated from previous position = 1.02 degrees
atoms outside contour = 25439, contour level = 0.0083837
Position of ctpolII_10s_job162_2p9A_DNA_fixed_CTP_isolde1.pdb (#2) relative to
CTpol2EC-3p06A.mrc (#5) coordinates:
Matrix rotation and translation
0.99986131 -0.01547426 0.00615642 1.89582458
0.01543631 0.99986185 0.00616471 -2.76155326
-0.00625096 -0.00606883 0.99996205 2.22505371
Axis -0.34476888 0.34966793 0.87112959
Axis point 187.27243115 127.94508301 0.00000000
Rotation angle (degrees) 1.01657540
Shift along axis 0.31906218
> fitmap #3 inMap #5
Fit molecule ctpolII_10s_job162_2p9A_DNA_fixed_RNA12_isolde1.pdb (#3) to map
CTpol2EC-3p06A.mrc (#5) using 66702 atoms
average map value = 0.02022, steps = 56
shifted from previous position = 0.828
rotated from previous position = 1.01 degrees
atoms outside contour = 25372, contour level = 0.0083837
Position of ctpolII_10s_job162_2p9A_DNA_fixed_RNA12_isolde1.pdb (#3) relative
to CTpol2EC-3p06A.mrc (#5) coordinates:
Matrix rotation and translation
0.99986429 -0.01533800 0.00601159 1.92306830
0.01530101 0.99986401 0.00615130 -2.75091578
-0.00610512 -0.00605849 0.99996301 2.20639659
Axis -0.34748625 0.34483720 0.87197512
Axis point 187.86821803 130.67379040 0.00000000
Rotation angle (degrees) 1.00666643
Shift along axis 0.30706504
> fitmap #6 inMap #5
Fit map CTpol2EC10s_job162_2p9A.mrc in map CTpol2EC-3p06A.mrc using 70684
points
correlation = 0.8971, correlation about mean = 0.8337, overlap = 51.68
steps = 56, shift = 0.928, angle = 0.987 degrees
Position of CTpol2EC10s_job162_2p9A.mrc (#6) relative to CTpol2EC-3p06A.mrc
(#5) coordinates:
Matrix rotation and translation
0.99986626 -0.01501576 0.00647951 1.80457066
0.01498051 0.99987291 0.00545466 -2.56359734
-0.00656059 -0.00535686 0.99996413 2.23957619
Axis -0.31384447 0.37853744 0.87075315
Axis point 182.65255824 127.19097287 0.00000000
Rotation angle (degrees) 0.98693015
Shift along axis 0.41334593
> fitmap #7 inMap #5
Fit map job271_20s_3A.mrc in map CTpol2EC-3p06A.mrc using 70685 points
correlation = 0.9359, correlation about mean = 0.8973, overlap = 44.03
steps = 60, shift = 0.657, angle = 0.855 degrees
Position of job271_20s_3A.mrc (#7) relative to CTpol2EC-3p06A.mrc (#5)
coordinates:
Matrix rotation and translation
0.99996307 -0.00857487 -0.00057312 0.98820547
0.00858122 0.99988882 0.01219473 -3.03505590
0.00046849 -0.01219919 0.99992548 1.92257939
Axis -0.81746585 -0.03490543 0.57491842
Axis point 0.00000000 137.06467626 248.97748847
Rotation angle (degrees) 0.85491071
Shift along axis 0.40344200
> fitmap #1 inMap #5
Fit molecule ctpolII_Apo_DNA_fix_isolde1.pdb (#1) to map CTpol2EC-3p06A.mrc
(#5) using 66643 atoms
average map value = 0.02038, steps = 60
shifted from previous position = 0.0242
rotated from previous position = 0.0105 degrees
atoms outside contour = 25101, contour level = 0.0083837
Position of ctpolII_Apo_DNA_fix_isolde1.pdb (#1) relative to
CTpol2EC-3p06A.mrc (#5) coordinates:
Matrix rotation and translation
1.00000000 0.00003529 -0.00009020 0.02577092
-0.00003530 0.99999999 -0.00015559 0.01884098
0.00009020 0.00015560 0.99999998 -0.02905343
Axis 0.84894345 -0.49214361 -0.19258684
Axis point 0.00000000 164.21253901 178.64619962
Rotation angle (degrees) 0.01050128
Shift along axis 0.01820089
> fitmap #2 inMap #6
Fit molecule ctpolII_10s_job162_2p9A_DNA_fixed_CTP_isolde1.pdb (#2) to map
CTpol2EC10s_job162_2p9A.mrc (#6) using 66716 atoms
average map value = 0.0244, steps = 40
shifted from previous position = 0.0499
rotated from previous position = 0.0106 degrees
atoms outside contour = 24742, contour level = 0.010466
Position of ctpolII_10s_job162_2p9A_DNA_fixed_CTP_isolde1.pdb (#2) relative to
CTpol2EC10s_job162_2p9A.mrc (#6) coordinates:
Matrix rotation and translation
0.99999981 -0.00058608 -0.00018800 0.10929979
0.00058620 0.99999960 0.00067820 -0.22563901
0.00018761 -0.00067831 0.99999975 0.04381637
Axis -0.74054039 -0.20505172 0.63996384
Axis point 0.00000000 70.73121231 334.74828781
Rotation angle (degrees) 0.05247701
Shift along axis -0.00663235
> fitmap #2 inMap #7
Fit molecule ctpolII_10s_job162_2p9A_DNA_fixed_CTP_isolde1.pdb (#2) to map
job271_20s_3A.mrc (#7) using 66716 atoms
average map value = 0.0197, steps = 28
shifted from previous position = 0.0401
rotated from previous position = 0.0259 degrees
atoms outside contour = 23737, contour level = 0.0082471
Position of ctpolII_10s_job162_2p9A_DNA_fixed_CTP_isolde1.pdb (#2) relative to
job271_20s_3A.mrc (#7) coordinates:
Matrix rotation and translation
0.99995062 -0.00743215 0.00659750 1.01000832
0.00747256 0.99995334 -0.00612135 0.16001861
-0.00655170 0.00617035 0.99995950 0.29873535
Axis 0.52596970 0.56266274 0.63778250
Axis point 40.20009438 78.17945122 0.00000000
Rotation angle (degrees) 0.66950469
Shift along axis 0.81179846
> fitmap #3 inMap #7
Fit molecule ctpolII_10s_job162_2p9A_DNA_fixed_RNA12_isolde1.pdb (#3) to map
job271_20s_3A.mrc (#7) using 66702 atoms
average map value = 0.0197, steps = 40
shifted from previous position = 0.0308
rotated from previous position = 0.0361 degrees
atoms outside contour = 23772, contour level = 0.0082471
Position of ctpolII_10s_job162_2p9A_DNA_fixed_RNA12_isolde1.pdb (#3) relative
to job271_20s_3A.mrc (#7) coordinates:
Matrix rotation and translation
0.99995114 -0.00738075 0.00657657 1.01733162
0.00742148 0.99995330 -0.00619033 0.16848102
-0.00653057 0.00623883 0.99995921 0.29446777
Axis 0.53221754 0.56124885 0.63383295
Axis point 40.00302882 78.25091969 0.00000000
Rotation angle (degrees) 0.66904463
Shift along axis 0.82264489
> fitmap #3 inMap #6
Fit molecule ctpolII_10s_job162_2p9A_DNA_fixed_RNA12_isolde1.pdb (#3) to map
CTpol2EC10s_job162_2p9A.mrc (#6) using 66702 atoms
average map value = 0.02442, steps = 48
shifted from previous position = 0.0438
rotated from previous position = 0.0364 degrees
atoms outside contour = 24689, contour level = 0.010466
Position of ctpolII_10s_job162_2p9A_DNA_fixed_RNA12_isolde1.pdb (#3) relative
to CTpol2EC10s_job162_2p9A.mrc (#6) coordinates:
Matrix rotation and translation
0.99999990 -0.00031274 -0.00030372 0.09766814
0.00031293 0.99999976 0.00062599 -0.17241600
0.00030352 -0.00062609 0.99999976 0.02387472
Axis -0.82063412 -0.39799225 0.41007537
Axis point 0.00000000 39.16527983 276.54848584
Rotation angle (degrees) 0.04370955
Shift along axis -0.00173915
> open
> /Volumes/Rayees_T7/Rayees_T5_data/ctPolII_proc/ctpolii_maps/ctpolii_30s_maps/30s_job063_2p75A.mrc
Opened 30s_job063_2p75A.mrc as #8, grid size 384,384,384, pixel 0.852, shown
at level 0.0097, step 2, values float32
> fitmap #8 inMap #5
Fit map 30s_job063_2p75A.mrc in map CTpol2EC-3p06A.mrc using 70718 points
correlation = 0.1967, correlation about mean = 0.06918, overlap = 6.835
steps = 220, shift = 1.38, angle = 5.6 degrees
Position of 30s_job063_2p75A.mrc (#8) relative to CTpol2EC-3p06A.mrc (#5)
coordinates:
Matrix rotation and translation
0.99938720 -0.00948291 -0.03369426 7.18323430
0.01251544 0.99577566 0.09096264 -17.71968653
0.03268933 -0.09132859 0.99528413 10.02756392
Axis -0.93365143 -0.34000063 0.11267024
Axis point 0.00000000 99.03411964 197.72692499
Rotation angle (degrees) 5.60229390
Shift along axis 0.44787576
> fitmap #4 inMap #8
Fit molecule ctpolii_30s_job063_DNA_fixed_isolde1.pdb (#4) to map
30s_job063_2p75A.mrc (#8) using 66609 atoms
average map value = 0.02436, steps = 92
shifted from previous position = 1.7
rotated from previous position = 5.59 degrees
atoms outside contour = 23763, contour level = 0.009695
Position of ctpolii_30s_job063_DNA_fixed_isolde1.pdb (#4) relative to
30s_job063_2p75A.mrc (#8) coordinates:
Matrix rotation and translation
0.99999999 -0.00011596 0.00011784 -0.00740255
0.00011598 0.99999998 -0.00014736 0.01792982
-0.00011783 0.00014737 0.99999998 -0.00318123
Axis 0.66538620 0.53204118 0.52363479
Axis point 0.00000000 32.07406570 111.02517673
Rotation angle (degrees) 0.01268970
Shift along axis 0.00294804
> fitmap #4 inMap #8
Fit molecule ctpolii_30s_job063_DNA_fixed_isolde1.pdb (#4) to map
30s_job063_2p75A.mrc (#8) using 66609 atoms
average map value = 0.02436, steps = 48
shifted from previous position = 0.00943
rotated from previous position = 0.00303 degrees
atoms outside contour = 23771, contour level = 0.009695
Position of ctpolii_30s_job063_DNA_fixed_isolde1.pdb (#4) relative to
30s_job063_2p75A.mrc (#8) coordinates:
Matrix rotation and translation
0.99999998 -0.00016839 0.00011748 -0.00514021
0.00016840 0.99999998 -0.00014062 0.00201391
-0.00011746 0.00014064 0.99999998 -0.00321989
Axis 0.56509324 0.47202106 0.67665777
Axis point -23.54544239 -16.65382247 0.00000000
Rotation angle (degrees) 0.01425871
Shift along axis -0.00413285
> ui tool show "Hide Dust"
> surface dust #8 size 5.11
> volume #5 level 0.01
> volume #6 level 0.01
> volume #7 level 0.01
> volume #8 level 0.01
> select add #8
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.89436,-0.31964,0.31297,22.989,0.31173,0.94709,0.076473,-53.397,-0.32086,0.029168,0.94668,51.552
> fitmap #8 inMap #5
Fit map 30s_job063_2p75A.mrc in map CTpol2EC-3p06A.mrc using 66815 points
correlation = 0.9136, correlation about mean = 0.8532, overlap = 50.1
steps = 180, shift = 3.06, angle = 8.01 degrees
Position of 30s_job063_2p75A.mrc (#8) relative to CTpol2EC-3p06A.mrc (#5)
coordinates:
Matrix rotation and translation
0.89301937 -0.37916200 0.24238931 47.11723403
0.33817191 0.92077843 0.19443980 -73.34180389
-0.29691103 -0.09166925 0.95049492 69.06399216
Axis -0.30374099 0.57253561 0.76154080
Axis point 224.19750968 58.03962552 0.00000000
Rotation angle (degrees) 28.09762834
Shift along axis -3.70718149
> fitmap #4 inMap #8
Fit molecule ctpolii_30s_job063_DNA_fixed_isolde1.pdb (#4) to map
30s_job063_2p75A.mrc (#8) using 66609 atoms
average map value = 0.004249, steps = 160
shifted from previous position = 3.69
rotated from previous position = 6.81 degrees
atoms outside contour = 52860, contour level = 0.01
Position of ctpolii_30s_job063_DNA_fixed_isolde1.pdb (#4) relative to
30s_job063_2p75A.mrc (#8) coordinates:
Matrix rotation and translation
0.92596607 0.24404116 -0.28815057 11.08182215
-0.25957613 0.96558393 -0.01636806 48.40576528
0.27423908 0.08995327 0.95744521 -51.56776457
Axis 0.13946054 -0.73768045 -0.66058937
Axis point 186.80160412 0.00000000 -9.48897099
Rotation angle (degrees) 22.40728031
Shift along axis -0.09739243
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #4 models
> show #4 models
> hide #3 models
> hide #2 models
> hide #1 models
> select clear
> select add #4
66609 atoms, 67346 bonds, 4164 residues, 1 model selected
> view matrix models
> #4,0.92961,-0.33513,0.15335,45.859,0.30893,0.93547,0.17163,-69.35,-0.20098,-0.11217,0.97315,55.565
> view matrix models
> #4,0.92794,-0.32835,0.1764,41.201,0.30667,0.94156,0.13937,-64.923,-0.21185,-0.075225,0.9744,50.396
> fitmap #4 inMap #8
Fit molecule ctpolii_30s_job063_DNA_fixed_isolde1.pdb (#4) to map
30s_job063_2p75A.mrc (#8) using 66609 atoms
average map value = 0.02436, steps = 112
shifted from previous position = 3.87
rotated from previous position = 5.83 degrees
atoms outside contour = 24534, contour level = 0.01
Position of ctpolii_30s_job063_DNA_fixed_isolde1.pdb (#4) relative to
30s_job063_2p75A.mrc (#8) coordinates:
Matrix rotation and translation
1.00000000 -0.00005134 0.00006600 -0.00639488
0.00005135 0.99999999 -0.00013776 0.02829433
-0.00006599 0.00013776 0.99999999 -0.01188972
Axis 0.85486196 0.40951528 0.31860361
Axis point 0.00000000 91.71488336 198.44717971
Rotation angle (degrees) 0.00923333
Shift along axis 0.00233212
> fitmap #4 inMap #8
Fit molecule ctpolii_30s_job063_DNA_fixed_isolde1.pdb (#4) to map
30s_job063_2p75A.mrc (#8) using 66609 atoms
average map value = 0.02436, steps = 48
shifted from previous position = 0.00333
rotated from previous position = 0.00413 degrees
atoms outside contour = 24538, contour level = 0.01
Position of ctpolii_30s_job063_DNA_fixed_isolde1.pdb (#4) relative to
30s_job063_2p75A.mrc (#8) coordinates:
Matrix rotation and translation
0.99999999 -0.00011244 0.00009957 -0.00073965
0.00011246 0.99999998 -0.00015613 0.02189135
-0.00009956 0.00015614 0.99999998 -0.00652214
Axis 0.72069292 0.45957287 0.51903227
Axis point 0.00000000 62.20177250 122.12353066
Rotation angle (degrees) 0.01241304
Shift along axis 0.00614241
> show #!5 models
> hide #!5 models
> hide #!8 models
> select clear
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> hide #4 models
> show #1 models
> select #1/R
297 atoms, 321 bonds, 9 residues, 1 model selected
> color sel red
> style sel ball
Changed 297 atom styles
> show sel target ab
> select #1/A:51
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/T:15-28
440 atoms, 472 bonds, 14 residues, 1 model selected
> color sel cyan
> style sel ball
Changed 440 atom styles
> show sel target ab
> select clear
> show #!5 models
> volume #5 step 1
> volume #6 step 1
> volume #7 step 1
> volume #8 step 1
> hide #!5 models
> show #!6 models
> volume #5 level 0.03
> show #4 models
> hide #!6 models
> show #!5 models
> volume #5 level 0.02
> volume #5 level 0.015
> volume #5 level 0.013
> volume #5 level 0.014
> show #!6 models
> select #1/T:15-28
440 atoms, 472 bonds, 14 residues, 1 model selected
> volume #6 level 0.014
> show #!7 models
> hide #!6 models
> hide #!5 models
> volume #7 level 0.014
> show #!8 models
> volume #8 level 0.014
> hide #!8 models
> hide #!7 models
> hide #4 models
> select clear
> dssp
> volume zone #5 nearAtoms #1/T:16-22 range 4 invert false minimalBounds false
> newMap true
Opened CTpol2EC-3p06A.mrc zone as #9, grid size 384,384,384, pixel 0.852,
shown at step 1, values float32
> volume zone #5 nearAtoms #1/R:7-9 range 4 invert false minimalBounds false
> newMap true
Opened CTpol2EC-3p06A.mrc zone as #10, grid size 384,384,384, pixel 0.852,
shown at step 1, values float32
> volume zone #5 nearAtoms #1/A:493-501 range 4 invert false minimalBounds
> false newMap true
Opened CTpol2EC-3p06A.mrc zone as #11, grid size 384,384,384, pixel 0.852,
shown at step 1, values float32
> volume zone #5 nearAtoms #1/A:837-861 range 4 invert false minimalBounds
> false newMap true
Opened CTpol2EC-3p06A.mrc zone as #12, grid size 384,384,384, pixel 0.852,
shown at step 1, values float32
> volume zone #5 nearAtoms #1/A:1083-1123 range 4 invert false minimalBounds
> false newMap true
Opened CTpol2EC-3p06A.mrc zone as #13, grid size 384,384,384, pixel 0.852,
shown at step 1, values float32
> select ~#1/R:7-9 #1/T:16-22 #1/A:838-860 #1/A:1083-1123 #1/A:493-501
265247 atoms, 268172 bonds, 16580 residues, 22 models selected
> select subtract #13
265247 atoms, 268172 bonds, 16580 residues, 20 models selected
> select subtract #12
265247 atoms, 268172 bonds, 16580 residues, 18 models selected
> select subtract #11
265247 atoms, 268172 bonds, 16580 residues, 16 models selected
> select subtract #10
265247 atoms, 268172 bonds, 16580 residues, 14 models selected
> select subtract #9
265247 atoms, 268172 bonds, 16580 residues, 12 models selected
> select subtract #8
265247 atoms, 268172 bonds, 16580 residues, 10 models selected
> select subtract #7
265247 atoms, 268172 bonds, 16580 residues, 8 models selected
> select subtract #6
265247 atoms, 268172 bonds, 16580 residues, 6 models selected
> select subtract #5
265247 atoms, 268172 bonds, 16580 residues, 4 models selected
> select subtract #4
198638 atoms, 200826 bonds, 12416 residues, 3 models selected
> select subtract #3
131936 atoms, 133381 bonds, 8249 residues, 2 models selected
> select subtract #2
65220 atoms, 65923 bonds, 4082 residues, 1 model selected
> cartoon hide sel
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> select #1/R:1-5
161 atoms, 173 bonds, 5 residues, 1 model selected
> hide sel target a
> select #1/T:23-28
189 atoms, 202 bonds, 6 residues, 1 model selected
> hide sel target a
> hide #!13 models
> show #!13 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> rename #9 "CTpol2EC-3p06A_tDNA.mrc zone"
> select add #10
189 atoms, 202 bonds, 6 residues, 3 models selected
> select subtract #10
189 atoms, 202 bonds, 6 residues, 1 model selected
> hide #!10 models
> show #!10 models
> rename #10 "CTpol2EC-3p06A_RNA.mrc zone"
> volume zone #5 nearAtoms #1/T:16-22 range 3 invert false minimalBounds false
> newMap true
Opened CTpol2EC-3p06A.mrc zone as #14, grid size 384,384,384, pixel 0.852,
shown at step 1, values float32
> volume zone #5 nearAtoms #1/R:7-9 range 3 invert false minimalBounds false
> newMap true
Opened CTpol2EC-3p06A.mrc zone as #15, grid size 384,384,384, pixel 0.852,
shown at step 1, values float32
> volume zone #5 nearAtoms #1/A:493-501 range 3 invert false minimalBounds
> false newMap true
Opened CTpol2EC-3p06A.mrc zone as #16, grid size 384,384,384, pixel 0.852,
shown at step 1, values float32
> volume zone #5 nearAtoms #1/A:837-861 range 3 invert false minimalBounds
> false newMap true
Opened CTpol2EC-3p06A.mrc zone as #17, grid size 384,384,384, pixel 0.852,
shown at step 1, values float32
> volume zone #5 nearAtoms #1/A:1083-1123 range 3 invert false minimalBounds
> false newMap true
Opened CTpol2EC-3p06A.mrc zone as #18, grid size 384,384,384, pixel 0.852,
shown at step 1, values float32
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!17 models
> hide #!17 models
> show #!16 models
> hide #!16 models
> show #!15 models
> hide #!15 models
> show #!14 models
> hide #!14 models
> show #!13 models
> hide #!13 models
> show #!9 models
> close #9-13
> show #!14 models
> rename #14 "CTpol2EC-3p06A_tDNA.mrc zone"
> hide #!14 models
> show #!15 models
> rename #15 "CTpol2EC-3p06A_RNA.mrc zone"
> hide #!15 models
> show #!16 models
> rename #16 "CTpol2EC-3p06A_AS.mrc zone"
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!17 models
> rename #17 "CTpol2EC-3p06A_BH.mrc zone"
> hide #!17 models
> show #!18 models
> rename #18 "CTpol2EC-3p06A_TL.mrc zone"
> select #1/R:6
34 atoms, 36 bonds, 1 residue, 1 model selected
> hide sel target a
> show #!17 models
> show #!16 models
> show #!15 models
> show #!14 models
> surface dust #14 size 5.11
> surface dust #15 size 5.11
> surface dust #16 size 5.11
> surface dust #17 size 5.11
> surface dust #18 size 5.11
> select add #14
34 atoms, 36 bonds, 1 residue, 3 models selected
> color (#1 & sel) cyan
> select clear
> select add #14
2 models selected
> color #14.1 cyan
> select subtract #14
Nothing selected
> select add #15
2 models selected
> color #15.1 red
> select subtract #15
Nothing selected
> select add #16
2 models selected
> color #16.1 purple
> select subtract #16
Nothing selected
> select add #17
2 models selected
> color #17.1 forest green
> select subtract #17
Nothing selected
> select add #18
2 models selected
> color #18.1 orange
> select clear
> select #1/T:15
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide sel target a
> cartoon hide sel
> select #1/T:15
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> show #!17 models
> select #1/A:2000
1 atom, 1 residue, 1 model selected
> style sel sphere
Changed 1 atom style
> show sel target ab
> color sel magenta
> select clear
> select #1/A:493-501
123 atoms, 124 bonds, 9 residues, 1 model selected
> cartoon hide sel
> select add #14
123 atoms, 124 bonds, 9 residues, 3 models selected
> select add #15
123 atoms, 124 bonds, 9 residues, 5 models selected
> select add #16
123 atoms, 124 bonds, 9 residues, 7 models selected
> select add #17
123 atoms, 124 bonds, 9 residues, 9 models selected
> select add #18
123 atoms, 124 bonds, 9 residues, 11 models selected
> show #!16 models
> show #!15 models
> show #!14 models
> transparency (#1 & sel) 80
> select clear
> select add #14
2 models selected
> transparency #14.1 80
> transparency #14.1 70
> select clear
> select add #15
2 models selected
> transparency #15.1 70
> select clear
> select add #17
2 models selected
> transparency #17.1 70
> select subtract #17
Nothing selected
> select add #18
2 models selected
> transparency #18.1 70
> select clear
> select #1/A:838-860
366 atoms, 366 bonds, 23 residues, 1 model selected
> color sel forest green
> select clear
> select #1/A:1083-1123
613 atoms, 617 bonds, 41 residues, 1 model selected
> color sel orange
> select clear
> hide #!18 models
> show #!18 models
> hide #!17 models
> show #!17 models
> hide #!15 models
> show #!15 models
> hide #!16 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/Fig3/Apo_10s_20s_30s_initial_maps_vol_zones.cxs
> includeMaps true
> rename #2 id #19
> rename #3 id #20
> rename #4 id #21
> rename #5 id #22
> rename #6 id #23
> rename #7 id #24
> rename #8 id #25
> rename #22 id #2
> rename #14 id #3
> rename #15 id #4
> rename #16 id #5
> rename #17 id #6
> rename #18 id #7
> show #!5 models
> hide #!5 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!6 models
> save
> /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig3/Apo_10s_20s_30s_initial_maps_vol_zones.cxs
> includeMaps true
> hide #1 models
> hide #!7 models
> show #19 models
> hide #19 models
> show #20 models
> hide #20 models
> show #20 models
> hide #20 models
> show #1 models
> hide #1 models
> show #20 models
> select #20/R
358 atoms, 386 bonds, 11 residues, 1 model selected
> color sel red
> select clear
> show #1 models
> hide #1 models
> select #20/R:9-12
129 atoms, 138 bonds, 4 residues, 1 model selected
> style sel ball
Changed 129 atom styles
> show sel target ab
> select clear
> select #20/T:13-20
254 atoms, 274 bonds, 8 residues, 1 model selected
> color sel cyan
> style sel ball
Changed 254 atom styles
> show sel target ab
> select clear
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> select #20/T:13
32 atoms, 34 bonds, 1 residue, 1 model selected
> hide sel target a
> select clear
> hide #1 models
> select ~#20/R:9-12 #20/T:14-20 #20/A:493-501 #20/A:838-860 #20/A:1083-1123
265217 atoms, 268139 bonds, 16579 residues, 22 models selected
> select subtract #19
198501 atoms, 200681 bonds, 12412 residues, 21 models selected
> select subtract #7
198501 atoms, 200681 bonds, 12412 residues, 19 models selected
> select subtract #6
198501 atoms, 200681 bonds, 12412 residues, 17 models selected
> select subtract #5
198501 atoms, 200681 bonds, 12412 residues, 15 models selected
> select subtract #4
198501 atoms, 200681 bonds, 12412 residues, 13 models selected
> select subtract #3
198501 atoms, 200681 bonds, 12412 residues, 11 models selected
> select subtract #2
198501 atoms, 200681 bonds, 12412 residues, 9 models selected
> select subtract #1
131858 atoms, 133298 bonds, 8247 residues, 8 models selected
> select subtract #21
65249 atoms, 65952 bonds, 4083 residues, 7 models selected
> select subtract #23
65249 atoms, 65952 bonds, 4083 residues, 5 models selected
> select subtract #24
65249 atoms, 65952 bonds, 4083 residues, 3 models selected
> select subtract #25
65249 atoms, 65952 bonds, 4083 residues, 1 model selected
> cartoon hide sel
> select clear
> select #20/A:493-501
123 atoms, 124 bonds, 9 residues, 1 model selected
> color sel purple
> select clear
> select #20/A:838-860
366 atoms, 366 bonds, 23 residues, 1 model selected
> color sel forest green
> select #20/A:1083-1123
613 atoms, 617 bonds, 41 residues, 1 model selected
> color sel orange
> select clear
> volume zone #23 nearAtoms #20/T:14-20 range 3 invert false minimalBounds
> false newMap true
Opened CTpol2EC10s_job162_2p9A.mrc zone as #8, grid size 384,384,384, pixel
0.852, shown at step 1, values float32
> volume zone #23 nearAtoms #20/R:9-12 range 3 invert false minimalBounds
> false newMap true
Opened CTpol2EC10s_job162_2p9A.mrc zone as #9, grid size 384,384,384, pixel
0.852, shown at step 1, values float32
> volume zone #23 nearAtoms #20/A:493-501 range 3 invert false minimalBounds
> false newMap true
Opened CTpol2EC10s_job162_2p9A.mrc zone as #10, grid size 384,384,384, pixel
0.852, shown at step 1, values float32
> volume zone #23 nearAtoms #20/A:837-861 range 3 invert false minimalBounds
> false newMap true
Opened CTpol2EC10s_job162_2p9A.mrc zone as #11, grid size 384,384,384, pixel
0.852, shown at step 1, values float32
> volume zone #23 nearAtoms #20/A:1083-1123 range 3 invert false minimalBounds
> false newMap true
Opened CTpol2EC10s_job162_2p9A.mrc zone as #12, grid size 384,384,384, pixel
0.852, shown at step 1, values float32
> hide #!8 models
> show #!8 models
> rename #8 "CTpol2EC10s_job162_2p9A_tDNA.mrc zone"
> rename #9 "CTpol2EC10s_job162_2p9A_RNA.mrc zone"
> hide #!9 models
> show #!9 models
> hide #!10 models
> show #!10 models
> rename #10 "CTpol2EC10s_job162_2p9A_AS.mrc zone"
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> rename #11 "CTpol2EC10s_job162_2p9A_BH.mrc zone"
> hide #!12 models
> show #!12 models
> rename #12 "CTpol2EC10s_job162_2p9A_TL.mrc zone"
> surface dust #8 size 5.11
> surface dust #9 size 5.11
> surface dust #10 size 5.11
> surface dust #11 size 5.11
> surface dust #12 size 5.11
> hide #!8 models
> show #!8 models
> select add #8
2 models selected
> color #8.1 cyan
> select subtract #8
Nothing selected
> select add #9
2 models selected
> color #9.1 red
> hide #20 models
> show #21 models
> hide #21 models
> select subtract #9
Nothing selected
> select add #10
2 models selected
> color #10.1 purple
> select subtract #10
Nothing selected
> select add #11
2 models selected
> color #11.1 forest green
> select subtract #11
Nothing selected
> select add #12
2 models selected
> color #12.1 orange
> select #8
2 models selected
> hide #!12 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> show #20 models
> show #!8 models
> show #!9 models
> show #!10 models
> hide #!10 models
> show #!11 models
> show #!12 models
> show #19 models
> hide #19 models
> select clear
> select add #8
2 models selected
> select add #9
4 models selected
> select add #10
6 models selected
> select add #11
8 models selected
> select add #12
10 models selected
> transparency #8.1#9.1#11.1#12.1 70
> select clear
> select #20/A:493-501
123 atoms, 124 bonds, 9 residues, 1 model selected
> cartoon hide sel
> select clear
> select #20/A:2000
1 atom, 1 residue, 1 model selected
> style sel sphere
Changed 1 atom style
> show sel target ab
> color sel magenta
> select clear
> rename #8 id #26
> rename #10 id #27
> rename #12 id #28
> rename #9 id #29
> rename #11 id #30
> rename #19 id #31
> rename #20 id #8
> rename #23 id #9
> rename #26 id #10
> rename #27 id #11
> rename #28 id #12
> rename #10 id #32
> rename #11 id #33
> rename #32 id #10
> rename #29 id #11
> rename #12 id #34
> rename #33 id #12
> rename #30 id #13
> rename #34 id #14
> save
> /Volumes/Rayees_T7/PolII_Manuscript/Data/PolII_Figures/Fig3/Apo_10s_20s_30s_initial_maps_vol_zones.cxs
> includeMaps true
> show #!12 models
> hide #!12 models
> show #31 models
> hide #31 models
> hide #!14 models
> hide #!13 models
> hide #!11 models
> hide #!10 models
> hide #8 models
> show #8 models
> show #31 models
> hide #31 models
> show #31 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> select #31/T:14-20 #31/R:911 #31/A:493-501 #31/A:838-860 #31/A:1083-1123
1324 atoms, 1346 bonds, 80 residues, 1 model selected
> select ~#31/T:14-20 #31/R:911 #31/A:493-501 #31/A:838-860 #31/A:1083-1123
265346 atoms, 268278 bonds, 16583 residues, 32 models selected
> select subtract #25
265346 atoms, 268278 bonds, 16583 residues, 30 models selected
> select subtract #24
265346 atoms, 268278 bonds, 16583 residues, 28 models selected
> select subtract #21
198737 atoms, 200932 bonds, 12419 residues, 27 models selected
> select subtract #14
198737 atoms, 200932 bonds, 12419 residues, 25 models selected
> select subtract #13
198737 atoms, 200932 bonds, 12419 residues, 23 models selected
> select subtract #12
198737 atoms, 200932 bonds, 12419 residues, 21 models selected
> select subtract #11
198737 atoms, 200932 bonds, 12419 residues, 19 models selected
> select subtract #10
198737 atoms, 200932 bonds, 12419 residues, 17 models selected
> select subtract #9
198737 atoms, 200932 bonds, 12419 residues, 15 models selected
> select subtract #8
132035 atoms, 133487 bonds, 8252 residues, 14 models selected
> select subtract #7
132035 atoms, 133487 bonds, 8252 residues, 12 models selected
> select subtract #6
132035 atoms, 133487 bonds, 8252 residues, 10 models selected
> select subtract #5
132035 atoms, 133487 bonds, 8252 residues, 8 models selected
> select subtract #4
132035 atoms, 133487 bonds, 8252 residues, 6 models selected
> select subtract #3
132035 atoms, 133487 bonds, 8252 residues, 4 models selected
> select subtract #2
132035 atoms, 133487 bonds, 8252 residues, 2 models selected
> select subtract #1
65392 atoms, 66104 bonds, 4087 residues, 1 model selected
> cartoon hide sel
> select clear
> hide #8 models
> select #31/R:9-11
98 atoms, 105 bonds, 3 residues, 1 model selected
> cartoon sel
> select #31/A:2000
Nothing selected
> style #31 sphere
Changed 66716 atom styles
> show #31 target ab
> undo
> style #31 sphere
Changed 66716 atom styles
> show #31 target ab
> undo
> select #31/A:2000
Nothing selected
> show metals
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show ions
> select #31/M
1 atom, 1 residue, 1 model selected
> changechains #32/M A
No residues specified
> changechains #32/M:2000 A:2000
No residues specified
> changechains #32/M:2000 #32/A:2000
Missing or invalid "fromIds" argument: Expected a text string
> changechains #31/M:2000 #31/A:2000
Missing or invalid "fromIds" argument: Expected a text string
> changechains #31/M:2000 A:2000
Chain IDs of 1 residues changed
> hide ions
> select 31/A:2000
Expected an objects specifier or a keyword
> select #31/A:2000
Nothing selected
> style #31 sphere
Changed 66716 atom styles
> show #31 target ab
> undo
> show ions #31
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show ions
> select #31/A:2000
Nothing selected
> sequence chain A #31
Missing or invalid "chains" argument: invalid chains specifier
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #1/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> sequence chain #1/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> select clear
> select #31//chain_id='A:2000':2000@MG
Nothing selected
> select clear
Drag select of 1 atoms
> color sel magenta
> select clear
> select #31/A:2000
Nothing selected
> select #31/A:2000
Nothing selected
> select #31/3
4 atoms, 4 residues, 1 model selected
> hide sel target a
> select #31/T:14-20
222 atoms, 239 bonds, 7 residues, 1 model selected
> color sel cyan
> style sel ball
Changed 222 atom styles
> show sel target ab
> select #31/R:9-11
98 atoms, 105 bonds, 3 residues, 1 model selected
> color sel red
> style sel ball
Changed 98 atom styles
> show sel target ab
> select #31/U:1
45 atoms, 46 bonds, 1 residue, 1 model selected
> style sel ball
Changed 45 atom styles
> show sel target ab
> select clear
> select #31/U:1
45 atoms, 46 bonds, 1 residue, 1 model selected
> color sel orange red
> select clear
> select #31/A:493-501
123 atoms, 124 bonds, 9 residues, 1 model selected
> color sel purple
> select clear
> select #31/A:838-860
366 atoms, 366 bonds, 23 residues, 1 model selected
> color sel forest green
> select #31/A:1083-1123
613 atoms, 617 bonds, 41 residues, 1 model selected
> color sel orange
> select clear
> show #!10 models
> show #!11 models
> show #!12 models
> hide #!12 models
> show #!13 models
> show #!14 models
> show #!24 models
> hide #!14 models
> hide #!13 models
> hide #!11 models
> hide #!10 models
> hide #!24 models
> show #!24 models
> ui tool show "Volume Viewer"
> volume #24 level 0.01789
> volume #24 level 0.01322
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> hide #!24 models
> hide #31 models
> show #31 models
> show #8 models
> hide #31 models
> hide ions
> show #8/A:2000
> select clear
> show #!24 models
> volume zone #24 nearAtoms #8/T:14-20 range 3 invert false minimalBounds
> false newMap true
Opened job271_20s_3A.mrc zone as #15, grid size 384,384,384, pixel 0.852,
shown at step 1, values float32
> volume zone #24 nearAtoms #8/R:9-12 range 3 invert false minimalBounds false
> newMap true
Opened job271_20s_3A.mrc zone as #16, grid size 384,384,384, pixel 0.852,
shown at step 1, values float32
> volume zone #24 nearAtoms #8/A:493-501 range 3 invert false minimalBounds
> false newMap true
Opened job271_20s_3A.mrc zone as #17, grid size 384,384,384, pixel 0.852,
shown at step 1, values float32
> volume zone #24 nearAtoms #8/A:837-861 range 3 invert false minimalBounds
> false newMap true
Opened job271_20s_3A.mrc zone as #18, grid size 384,384,384, pixel 0.852,
shown at step 1, values float32
> volume zone #24 nearAtoms #8/A:1083-1123 range 3 invert false minimalBounds
> false newMap true
Opened job271_20s_3A.mrc zone as #19, grid size 384,384,384, pixel 0.852,
shown at step 1, values float32
> surface dust #15 size 5.11
> surface dust #16 size 5.11
> surface dust #17 size 5.11
> surface dust #18 size 5.11
> surface dust #19 size 5.11
> select add #15
2 models selected
> color #15.1 cyan
> select subtract #15
Nothing selected
> select add #16
2 models selected
> rename #15 "job271_20s_3A_tDNA.mrc zone"
> hide #!16 models
> show #!16 models
> rename #16 "job271_20s_3A_RNA.mrc zone"
> select add #17
4 models selected
> rename #17 "job271_20s_3A_AS.mrc zone"
> select subtract #17
2 models selected
> select subtract #16
Nothing selected
> select add #18
2 models selected
> select subtract #18
Nothing selected
> rename #18 "job271_20s_3A_BH.mrc zone"
> select add #18
2 models selected
> color #18.1 forest green
> select clear
> select add #16
2 models selected
> color #16.1 red
> select add #19
4 models selected
> select subtract #19
2 models selected
> rename #19 "job271_20s_3A_TL.mrc zone"
> select add #19
4 models selected
> color #16.1#19.1 orange
> undo
> select subtract #16
2 models selected
> color #19.1 orange
> select clear
> ui tool show "Volume Viewer"
===== 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: 1 day, 2 hours, 19 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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