![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 weeks ago
Closed 2 weeks ago
#19378 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-26.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001fdb62080 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imaging, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 62)
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{
"uptime" : 410000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,3",
"coalitionID" : 50117,
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"build" : "25B78",
"releaseType" : "User"
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"captureTime" : "2025-11-15 19:09:36.8069 -0800",
"codeSigningMonitor" : 1,
"incident" : "8BE34E11-CE5C-44E3-A26B-BC00C7ABDB69",
"pid" : 85493,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-11-14 21:09:48.5563 -0800",
"procStartAbsTime" : 8064850690695,
"procExitAbsTime" : 9965355387797,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.1","CFBundleVersion":"1.10.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"94145AA7-F194-5C87-AA1C-6A08E733EACE","thirdParty":true},
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "A4BBACB1-6F97-89C6-DB33-7689FCB70FA5",
"appleIntelligenceStatus" : {"state":"available"},
"developerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "E08CC5B9-7305-4C59-9AE6-B7A0A087AE2C",
"wakeTime" : 122704,
"sleepWakeUUID" : "25E8C92B-CCF9-4ABD-A54D-E124A4C8E711",
"sip" : "enabled",
"vmRegionInfo" : "0xffffcfc36c5a29a7 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x33dd4fc36c5a29a7","rawCodes":[1,3737230966542444967],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x33dd4fc36c5a29a7 -> 0xffffcfc36c5a29a7 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":85493},
"vmregioninfo" : "0xffffcfc36c5a29a7 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
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> set bgColor white
> lighting soft
> graphics silhouettes true
> ui mousemode right zoom
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/heyao/My Drive/RaiA_2024/NAR_revision/Structural_comparison/Ca-
> raiA_flip2base_isolde_real_space_refine.pdb"
Chain information for Ca-raiA_flip2base_isolde_real_space_refine.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> open "/Users/heyao/My
> Drive/RaiA_2024/NAR_revision/Structural_comparison/Ca_raiA_structural_comparison.cxs"
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256,256,256, pixel 0.856, shown at level 0.56, step 1, values float32
> view name session-start
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> show #!5 models
> close #5
> close #1
> open "/Users/heyao/My Drive/RaiA_2024/NAR_revision/Structural_comparison/Ca-
> raiA_flip2base_isolde_real_space_refine.pdb"
Chain information for Ca-raiA_flip2base_isolde_real_space_refine.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> show #!2 models
> show #!3 models
> show #!4 models
> cartoon style xsection oval width 1.6 thickness 1.6
> select clear
> nucleotides #1#!2-3 atoms
> style nucleic & #1#!2-3 stick
Changed 13010 atom styles
> select clear
> hide #2.1 models
> hide #3.1 models
> hide #3.2 models
> select Mg
22 atoms, 22 residues, 1 model selected
> hide sel atoms
> select clear
> ui tool show Matchmaker
> matchmaker #!2-3#!4.1 to #1
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9ELY_Chiu_Nature.cif, chain A (#2), sequence alignment score = 810.8
RMSD between 185 pruned atom pairs is 0.770 angstroms; (across all 202 pairs:
1.377)
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9CXF_Toor_NatComm.cif, chain A (#3), sequence alignment score = 811.2
RMSD between 180 pruned atom pairs is 0.564 angstroms; (across all 200 pairs:
1.510)
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9G7C_Bujnicki_JMB.cif, chain A (#4.1), sequence alignment score = 562.4
RMSD between 130 pruned atom pairs is 1.210 angstroms; (across all 204 pairs:
6.174)
> nucleotides #1#!2-3 tube/slab shape box
> nucleotides #1#!2-3 ladder
> nucleotides #1#!2-3 fill
> style nucleic & #1#!2-3 stick
Changed 13010 atom styles
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> hide #1 models
> show #1 models
> hide #!3 models
> select add #1
4380 atoms, 4907 bonds, 204 residues, 1 model selected
> color sel silver
> select clear
> show #!2 models
> select add #2
4334 atoms, 4856 bonds, 189 pseudobonds, 202 residues, 2 models selected
> color sel cyan
> select clear
> show #!3 models
> hide #!2 models
> select add #3
4318 atoms, 4813 bonds, 200 pseudobonds, 222 residues, 3 models selected
> color #3 #ffb2ffff
> select clear
> show #!4 models
> hide #!3 models
> show #!4.1 models
> select add #4
4826 atoms, 5406 bonds, 167 pseudobonds, 224 residues, 3 models selected
> color sel lime green
> select clear
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #1 models
> select add #4
4826 atoms, 5406 bonds, 167 pseudobonds, 224 residues, 3 models selected
> ui tool show "Color Actions"
> color sel medium spring green
> select clear
> show #!2 models
> hide #!2 models
> select add #4
4826 atoms, 5406 bonds, 167 pseudobonds, 224 residues, 3 models selected
> hide #!4 models
> show #!2 models
> select add #2
9160 atoms, 10262 bonds, 356 pseudobonds, 426 residues, 5 models selected
> select clear
> select add #2
4334 atoms, 4856 bonds, 189 pseudobonds, 202 residues, 2 models selected
> color sel deep sky blue
> select clear
> show #1 models
> show #!4 models
> show #!3 models
> select clear
> save "/Users/heyao/My
> Drive/RaiA_2024/NAR_revision/Structural_comparison/Ca_raiA_structural_comparison.cxs"
> select clear
> view
> select clear
> nucleotides fill
> style nucleic stick
Changed 17836 atom styles
> select clear
> nucleotides atoms
> style nucleic stick
Changed 17836 atom styles
> nucleotides fill
> style nucleic stick
Changed 17836 atom styles
> hide atoms
> select clear
> view
> view name p1
> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true
> view p1
> view name p1
> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true
> turn x 90
> view name p2
> save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3
> transparentBackground true
> nucleotides tube/slab shape box
> nucleotides fill
> style nucleic stick
Changed 17836 atom styles
> nucleotides fill
> style nucleic stick
Changed 17836 atom styles
> show atoms
> select clear
> select Mg
22 atoms, 22 residues, 1 model selected
> delete sel
> select clear
> select add #1
4380 atoms, 4907 bonds, 204 residues, 1 model selected
Alignment identifier is 1/A
> select clear
> select #1/A:23-24
45 atoms, 50 bonds, 2 residues, 1 model selected
> select #1/A:23
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #1/A:23
22 atoms, 24 bonds, 1 residue, 1 model selected
> view sel
> select clear
> view
> ui tool show "Side View"
> select clear
> hide cartoons
> select clear
> select #1/A:23
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #1/A:23-24
45 atoms, 50 bonds, 2 residues, 1 model selected
> select #1/A:28
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #1/A:28
22 atoms, 24 bonds, 1 residue, 1 model selected
> view sel
> select clear
> color byhetero
> select clear
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #1 cartoons
> cartoon style xsection oval width 1.2 thickness 1.2
> cartoon style xsection oval width 1 thickness 1
> cartoon style xsection oval width 0.6 thickness 0.6
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> open /Users/heyao/Desktop/raiA_model_refinement_20251112/Ca-
> raiA/cryosparc_P44_J306_007_volume_map_sharp.mrc
Opened cryosparc_P44_J306_007_volume_map_sharp.mrc as #5, grid size
256,256,256, pixel 0.856, shown at level 0.0348, step 1, values float32
> volume #5 level 0.2898
> volume #5 color #b2b2b281
> volume #5 level 0.4
> volume #5 level 0.3
> select clear
> select add #1
4380 atoms, 4907 bonds, 204 residues, 1 model selected
> show #!2 models
> hide #!2 models
> color #1 #d6d6d6ff
> color #1 #76d6ffff
> color sel byhetero
> select clear
> show #2.1 models
> hide #1 models
> show #1 models
> hide #!2 models
> select add #1
4380 atoms, 4907 bonds, 204 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dodger blue
> color sel deep sky blue
> color sel byhetero
> select add #2
8714 atoms, 9763 bonds, 189 pseudobonds, 406 residues, 3 models selected
> show #!2 models
> select clear
> select add #2
4334 atoms, 4856 bonds, 189 pseudobonds, 202 residues, 2 models selected
> color sel silver
> color sel byhetero
> select clear
> hide #2.1 models
> show #2.1 models
> hide #!2 models
> select clear
> surface dust #5 size 5
> select clear
> hide #1 cartoons
> select clear
> show #!4 models
> hide #!5 models
> hide #2.1 models
> show #2.1 models
> hide #1 models
> show #1 models
> hide #2.1 models
> hide #!2 models
> hide #!4 models
> show #!5 models
> view name p3
> save "/Users/heyao/My
> Drive/RaiA_2024/NAR_revision/Structural_comparison/Ca_raiA_structural_comparison.cxs"
> save /Users/heyao/Desktop/11.png width 2000 height 2000 supersample 3
> transparentBackground true
> hide #1 models
> show #!2 models
> hide #!5 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!2 models
> show #!5 models
> save /Users/heyao/Desktop/11.png width 2000 height 2000 supersample 3
> transparentBackground true
> view name p3
> hide #!5 models
> hide #1 models
> show #!2 models
> save /Users/heyao/Desktop/12.png width 2000 height 2000 supersample 3
> transparentBackground true
> hide #!2 models
> show #!3 models
> save /Users/heyao/Desktop/13.png width 2000 height 2000 supersample 3
> transparentBackground true
> hide #!3 models
> show #!4 models
> hide #4.1.1 models
> save /Users/heyao/Desktop/14.png width 2000 height 2000 supersample 3
> transparentBackground true
> show #1 models
> hide #!4 models
> show #!5 models
> fitmap #1 inMap #5
Fit molecule Ca-raiA_flip2base_isolde_real_space_refine.pdb (#1) to map
cryosparc_P44_J306_007_volume_map_sharp.mrc (#5) using 4380 atoms
average map value = 0.3516, steps = 44
shifted from previous position = 0.00487
rotated from previous position = 0.0222 degrees
atoms outside contour = 2228, contour level = 0.3
Position of Ca-raiA_flip2base_isolde_real_space_refine.pdb (#1) relative to
cryosparc_P44_J306_007_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99999994 0.00013628 -0.00032600 0.02175851
-0.00013623 0.99999998 0.00015937 -0.00309180
0.00032602 -0.00015933 0.99999993 -0.01345924
Axis -0.41111243 -0.84108259 -0.35152047
Axis point 43.03571144 0.00000000 64.70033062
Rotation angle (degrees) 0.02220852
Shift along axis -0.00161353
> fitmap #1 inMap #5
Fit molecule Ca-raiA_flip2base_isolde_real_space_refine.pdb (#1) to map
cryosparc_P44_J306_007_volume_map_sharp.mrc (#5) using 4380 atoms
average map value = 0.3516, steps = 28
shifted from previous position = 0.0083
rotated from previous position = 0.00946 degrees
atoms outside contour = 2226, contour level = 0.3
Position of Ca-raiA_flip2base_isolde_real_space_refine.pdb (#1) relative to
cryosparc_P44_J306_007_volume_map_sharp.mrc (#5) coordinates:
Matrix rotation and translation
0.99999998 0.00008865 -0.00020163 0.00844154
-0.00008864 0.99999999 0.00006177 -0.00169879
0.00020164 -0.00006175 0.99999998 -0.01585479
Axis -0.26996742 -0.88144339 -0.38752437
Axis point 68.32965835 0.00000000 49.03806337
Rotation angle (degrees) 0.01310664
Shift along axis 0.00536256
> hide #!5 models
> view list
Named views: p1, p2, p3, session-start
> select #1/A:23
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #1/A:23
22 atoms, 24 bonds, 1 residue, 1 model selected
> view sel
> select clear
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> view list
Named views: p1, p2, p3, session-start
> view name p4
> save /Users/heyao/Desktop/11.png width 2000 height 2000 supersample 3
> transparentBackground true
> hide #1 models
> hide #!5 models
> show #!2 models
> save /Users/heyao/Desktop/12.png width 2000 height 2000 supersample 3
> transparentBackground true
> hide #!2 models
> show #!3 models
> save /Users/heyao/Desktop/13.png width 2000 height 2000 supersample 3
> transparentBackground true
> hide #!3 models
> show #!4 models
> save /Users/heyao/Desktop/14.png width 2000 height 2000 supersample 3
> transparentBackground true
> show #!5 models
> hide #!5 models
> save /Users/heyao/Desktop/14.png width 1000 height 1000 supersample 3
> transparentBackground true
> show #1 models
> hide #!4.1 models
> hide #!4 models
> show #!5 models
> save /Users/heyao/Desktop/11.png width 1000 height 1000 supersample 3
> transparentBackground true
> hide #1 models
> hide #!5 models
> show #!2 models
> save /Users/heyao/Desktop/12.png width 1000 height 1000 supersample 3
> transparentBackground true
> hide #!2 models
> show #!3 models
> save /Users/heyao/Desktop/13.png width 1000 height 1000 supersample 3
> transparentBackground true
> hide #!3 models
> show #!4 models
> show #!4.1 models
> save /Users/heyao/Desktop/14.png width 1000 height 1000 supersample 3
> transparentBackground true
> hide #!4 models
> show #1 models
> select #1/A:80
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:80-81
42 atoms, 46 bonds, 2 residues, 1 model selected
> view sel
> select #1/A80,81,192,183,184
Nothing selected
> select #1/A:80,81,192,183,184
106 atoms, 116 bonds, 5 residues, 1 model selected
> view sel
> select #1/A:80,81,182,183,184
108 atoms, 120 bonds, 5 residues, 1 model selected
> view sel
> show #!5 models
> select clear
> hide #!5 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #4.1.1 models
> hide #4.1.1 models
> show #4.1.1 models
> hide #4.1.1 models
> hide #!4.1 models
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #4.1.1 models
> hide #4.1.1 models
> show #3.2 models
> hide #3.2 models
> show #3.2 models
> hide #3.2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!5 models
> view list
Named views: p1, p2, p3, p4, session-start
> view name p5
> save /Users/heyao/Desktop/11.png width 1000 height 1000 supersample 3
> transparentBackground true
> hide #1 models
> hide #!5 models
> show #!2 models
> save /Users/heyao/Desktop/12.png width 1000 height 1000 supersample 3
> transparentBackground true
> hide #!2 models
> show #!3 models
> save /Users/heyao/Desktop/13.png width 1000 height 1000 supersample 3
> transparentBackground true
> hide #!3 models
> show #!4 models
> save /Users/heyao/Desktop/14.png width 1000 height 1000 supersample 3
> transparentBackground true
> hide #!4 models
> show #1 models
> show #!5 models
> save /Users/heyao/Desktop/14.png width 2000 height 2000 supersample 3
> transparentBackground true
> save /Users/heyao/Desktop/11.png width 2000 height 2000 supersample 3
> transparentBackground true
> hide #1 models
> hide #!5 models
> show #!2 models
> save /Users/heyao/Desktop/12.png width 2000 height 2000 supersample 3
> transparentBackground true
> hide #!2 models
> show #!3 models
> save /Users/heyao/Desktop/13.png width 2000 height 2000 supersample 3
> transparentBackground true
> hide #!3 models
> show #!4 models
> save /Users/heyao/Desktop/14.png width 2000 height 2000 supersample 3
> transparentBackground true
> show #1 models
> hide #!4 models
> view p5
> show #!4 models
> hide #1 models
> view
> hide #!4.1 models
> show #1 models
> select #1/A:23
22 atoms, 24 bonds, 1 residue, 1 model selected
> view sel
> show #!2 models
> show #!3 models
> show #!4.1 models
> hide #!2 models
> show #2.1 models
> hide #2.1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #1 models
> show #1 models
> hide #!4 models
> select #1/A:28
22 atoms, 24 bonds, 1 residue, 1 model selected
> view sel
> show #2.1 models
> hide #2.1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #1 models
> show #1 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #1 models
> show #1 models
> select #1/A:43
22 atoms, 24 bonds, 1 residue, 1 model selected
> view sel
> hide #!4 models
> hide #1 models
> show #1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> select #1/A:78
22 atoms, 24 bonds, 1 residue, 1 model selected
> view sel
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #1 models
> show #1 models
> hide #!4.1 models
> select #1/A:80
20 atoms, 21 bonds, 1 residue, 1 model selected
> view sel
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> select #1/A:81
22 atoms, 24 bonds, 1 residue, 1 model selected
> view sel
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4.1 models
> hide #!4.1 models
> select #1/A:97
23 atoms, 25 bonds, 1 residue, 1 model selected
> view sel
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4.1 models
> select #1/A119
Nothing selected
> select #1/A:119
22 atoms, 24 bonds, 1 residue, 1 model selected
> view sel
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!4 models
> select #1/A:154
23 atoms, 25 bonds, 1 residue, 1 model selected
> view sel
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> select #1/A:171
22 atoms, 24 bonds, 1 residue, 1 model selected
> view sel
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> select #1/A:182
22 atoms, 24 bonds, 1 residue, 1 model selected
> view sel
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> select #1/A:183
22 atoms, 24 bonds, 1 residue, 1 model selected
> view sel
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> select #1/A:184
22 atoms, 24 bonds, 1 residue, 1 model selected
> view sel
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> view
> ui tool show Matchmaker
> matchmaker #!2-3#!4.1 to #1
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9ELY_Chiu_Nature.cif, chain A (#2), sequence alignment score = 810.8
RMSD between 185 pruned atom pairs is 0.770 angstroms; (across all 202 pairs:
1.377)
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9CXF_Toor_NatComm.cif, chain A (#3), sequence alignment score = 811.2
RMSD between 180 pruned atom pairs is 0.564 angstroms; (across all 200 pairs:
1.510)
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9G7C_Bujnicki_JMB.cif, chain A (#4.1), sequence alignment score = 562.4
RMSD between 130 pruned atom pairs is 1.210 angstroms; (across all 204 pairs:
6.174)
> show sel cartoons
> select clear
> show #1#!4.1 cartoons
> select clear
> show #2.1 models
> hide #2.1 models
> show #!3 models
Drag select of 14974 atoms, 16668 bonds, 2104 shapes, 411 residues
> select up
17460 atoms, 16668 bonds, 813 residues, 4 models selected
> select up
17474 atoms, 16685 bonds, 813 residues, 4 models selected
> select up
17836 atoms, 18555 bonds, 830 residues, 4 models selected
> select down
17474 atoms, 16685 bonds, 813 residues, 4 models selected
> ui tool show Matchmaker
> matchmaker #!2-3#!4.1 & sel to #1 & sel
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9ELY_Chiu_Nature.cif, chain A (#2), sequence alignment score = 810.8
RMSD between 185 pruned atom pairs is 0.770 angstroms; (across all 202 pairs:
1.377)
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9CXF_Toor_NatComm.cif, chain A (#3), sequence alignment score = 811.2
RMSD between 180 pruned atom pairs is 0.564 angstroms; (across all 200 pairs:
1.510)
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9G7C_Bujnicki_JMB.cif, chain A (#4.1), sequence alignment score = 556.2
RMSD between 129 pruned atom pairs is 1.205 angstroms; (across all 200 pairs:
3.390)
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
Alignment identifier is 2/A
Alignment identifier is 3/A
Alignment identifier is 4.1/A
Alignment identifier is 1/A
> ui tool show "Show Sequence Viewer"
> ui tool show Matchmaker
> matchmaker #!2-3#!4.1 to #1
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9ELY_Chiu_Nature.cif, chain A (#2), sequence alignment score = 810.8
RMSD between 185 pruned atom pairs is 0.770 angstroms; (across all 202 pairs:
1.377)
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9CXF_Toor_NatComm.cif, chain A (#3), sequence alignment score = 811.2
RMSD between 180 pruned atom pairs is 0.564 angstroms; (across all 200 pairs:
1.510)
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9G7C_Bujnicki_JMB.cif, chain A (#4.1), sequence alignment score = 562.4
RMSD between 130 pruned atom pairs is 1.210 angstroms; (across all 204 pairs:
6.174)
> ui tool show "Modeller Comparative"
Populating font family aliases took 123 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> showseqalignment
Unknown command: showseqalignment
> matchmaker
Missing or invalid "matchAtoms" argument: empty atom specifier
> matchmaker #2 to #1 showAlignment true
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9ELY_Chiu_Nature.cif, chain A (#2), sequence alignment score = 810.8
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, 9ELY_Chiu_Nature.cif #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 185 pruned atom pairs is 0.770 angstroms; (across all 202 pairs:
1.377)
> matchmaker #2 #3 to #1 showAlignment true
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9ELY_Chiu_Nature.cif, chain A (#2), sequence alignment score = 810.8
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, 9ELY_Chiu_Nature.cif #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 185 pruned atom pairs is 0.770 angstroms; (across all 202 pairs:
1.377)
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9CXF_Toor_NatComm.cif, chain A (#3), sequence alignment score = 811.2
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, 9CXF_Toor_NatComm.cif #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 180 pruned atom pairs is 0.564 angstroms; (across all 200 pairs:
1.510)
> matchmaker #4.1 to #1 showAlignment true
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9G7C_Bujnicki_JMB.cif, chain A (#4.1), sequence alignment score = 562.4
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, 9G7C_Bujnicki_JMB.cif #4.1/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 130 pruned atom pairs is 1.210 angstroms; (across all 204 pairs:
6.174)
> select add #2
17474 atoms, 16685 bonds, 189 pseudobonds, 813 residues, 5 models selected
> select subtract #2
13140 atoms, 11829 bonds, 611 residues, 3 models selected
> hide #!2 models
> hide #!3 models
> select subtract #3.2
13140 atoms, 11829 bonds, 611 residues, 3 models selected
> nucleotides sel & #1#!4.1 ladder
> nucleotides sel & #1#!4.1 slab
> style nucleic & sel & #1#!4.1 stick
Changed 8844 atom styles
> nucleotides sel & #1#!4.1 tube/slab shape box
> select clear
> select #4.1/A:53
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #4.1/A:53-54
42 atoms, 46 bonds, 2 residues, 1 model selected
> color sel red
> select #4.1/A:61
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #4.1/A:61-77
367 atoms, 410 bonds, 7 pseudobonds, 17 residues, 2 models selected
> color (#!4.1 & sel) red
> select #1/A:93
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #1/A:93-99
154 atoms, 173 bonds, 7 residues, 1 model selected
> color sel red
> select #1/A:102
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:102-104
60 atoms, 65 bonds, 3 residues, 1 model selected
> select #1/A:105
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:105-113
186 atoms, 205 bonds, 9 residues, 1 model selected
> select #4.1/A:110
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4.1/A:110-118
191 atoms, 212 bonds, 9 residues, 1 model selected
> select #4.1/A:157
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #4.1/A:157-159
66 atoms, 73 bonds, 3 residues, 1 model selected
> color sel red
> hide #!4 models
> open /Users/heyao/Desktop/raiA_model_refinement_20251112/Ns-raiA/Ns-
> raiA_flip2base_isolde_real_space_refine.pdb
Chain information for Ns-raiA_flip2base_isolde_real_space_refine.pdb #6
---
Chain | Description
A | No description available
Computing secondary structure
> hide #!6 models
> open /Users/heyao/Desktop/raiA_model_refinement_20251112/Mp-raiA/Mp-
> raiA_flip2base_isolde_real_space_refinement.pdb
Chain information for Mp-raiA_flip2base_isolde_real_space_refinement.pdb #7
---
Chain | Description
A | No description available
Computing secondary structure
> matchmaker #7 to #1 showAlignment true
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
Mp-raiA_flip2base_isolde_real_space_refinement.pdb, chain A (#7), sequence
alignment score = 328.1
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, Mp-
raiA_flip2base_isolde_real_space_refinement.pdb #7/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 113 pruned atom pairs is 0.894 angstroms; (across all 153 pairs:
13.905)
> select #7/A:60
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #7/A:60-71
259 atoms, 289 bonds, 12 residues, 1 model selected
> select #7/A:99
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #7/A:99-109
230 atoms, 255 bonds, 11 residues, 1 model selected
> select #7/A:110
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #7/A:110-121
264 atoms, 296 bonds, 12 residues, 1 model selected
> color #7 #76d6ffff
> color #7 #b2b2b2ff
> select #1/A:2-59,70-86,88-92,169-201 #7/A:2-59,72-88,90-94,128-160
4858 atoms, 5435 bonds, 226 residues, 2 models selected
> select #7/A:163
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #1/A #7/A
7716 atoms, 8641 bonds, 2 pseudobonds, 359 residues, 3 models selected
MatchMaker Alignment [ID: 1] region chain A..chain A [1-206] RMSD: 13.905
> save /Users/heyao/Desktop/raiA_model_refinement_20251112/Mp-raiA/ca2mp
> format aln alignment 1
> matchmaker #7,#6 to #1 show true
Missing or invalid "matchAtoms" argument: only initial part "#7" of atom
specifier valid
> matchmaker #7 #6 to #1 showAlignment true
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
Mp-raiA_flip2base_isolde_real_space_refinement.pdb, chain A (#7), sequence
alignment score = 328.1
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, Mp-
raiA_flip2base_isolde_real_space_refinement.pdb #7/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 113 pruned atom pairs is 0.894 angstroms; (across all 153 pairs:
13.905)
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
Ns-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#6), sequence
alignment score = 412.4
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, Ns-
raiA_flip2base_isolde_real_space_refine.pdb #6/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 106 pruned atom pairs is 0.722 angstroms; (across all 193 pairs:
29.026)
> show #!6 models
> hide #!7 models
> select #6/A:1
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/A:1-25
530 atoms, 589 bonds, 25 residues, 1 model selected
> select #1/A:1
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:1-22
471 atoms, 526 bonds, 22 residues, 1 model selected
> matchmaker #6 to #1 showAlignment true
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
Ns-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#6), sequence
alignment score = 412.4
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, Ns-
raiA_flip2base_isolde_real_space_refine.pdb #6/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 106 pruned atom pairs is 0.722 angstroms; (across all 193 pairs:
29.026)
> hide #!6 models
> show #!7 models
> matchmaker #7 to #1 showAlignment true
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
Mp-raiA_flip2base_isolde_real_space_refinement.pdb, chain A (#7), sequence
alignment score = 328.1
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, Mp-
raiA_flip2base_isolde_real_space_refinement.pdb #7/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 113 pruned atom pairs is 0.894 angstroms; (across all 153 pairs:
13.905)
> select #7/A:119
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #7/A:119-121
69 atoms, 77 bonds, 3 residues, 1 model selected
> select #1/A:164
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #1/A:164-166
65 atoms, 72 bonds, 3 residues, 1 model selected
> select #7/A:110
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #7/A:110-121
264 atoms, 296 bonds, 12 residues, 1 model selected
> select #7/A:108
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #7/A:108-109
40 atoms, 43 bonds, 2 residues, 1 model selected
> show #!6 models
> hide #!7 models
> matchmaker #1 to #6 showAlignment true
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ns-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#6) with
Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1), sequence
alignment score = 412.4
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, Ns-
raiA_flip2base_isolde_real_space_refine.pdb #6/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 106 pruned atom pairs is 0.722 angstroms; (across all 193 pairs:
29.026)
> save /Users/heyao/Desktop/Ns2ca format aln alignment 1
> hide #!6 models
> show #!6 models
> select #6/A:60
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #6/A:60-72
278 atoms, 310 bonds, 13 residues, 1 model selected
> select #6/A:60-101,107-124,131-144,211-242 #1/A:23-64,74-91,98-111,162-193
4553 atoms, 5090 bonds, 212 residues, 2 models selected
> select #1/A:23
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #1/A:23-37
321 atoms, 358 bonds, 15 residues, 1 model selected
No sequence chosen for copying
> select #1/A:23
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #1/A:23-37
321 atoms, 358 bonds, 15 residues, 1 model selected
> color sel red
> select #1/A:70
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:70-73
80 atoms, 87 bonds, 4 residues, 1 model selected
> color sel yellow
> select #6/A:108
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #6/A:107
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #1/A:74
45 atoms, 49 bonds, 2 residues, 2 models selected
> select #1/A:93
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #1/A:93-96
89 atoms, 100 bonds, 4 residues, 1 model selected
> color sel lime
> select #1/A:113
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:113-114
42 atoms, 46 bonds, 2 residues, 1 model selected
> select clear
> color #6 #b2b2b2ff
> select #1/A:113
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:113-114
42 atoms, 46 bonds, 2 residues, 1 model selected
> color sel purple
> select clear
> select #1/A:115
23 atoms, 25 bonds, 1 residue, 1 model selected
> select clear
> select #6/A:144
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #1/A:111
43 atoms, 46 bonds, 2 residues, 2 models selected
> select #6/A:159
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/A:159-202
959 atoms, 1076 bonds, 44 residues, 1 model selected
> select #1/A:113
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:113-126
303 atoms, 339 bonds, 14 residues, 1 model selected
> select clear
> select #1/A:115
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #6/A:171
43 atoms, 46 bonds, 2 residues, 2 models selected
> select #6/A:172
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #1/A:185 #6/A:234
46 atoms, 50 bonds, 2 residues, 2 models selected
> select add #6/A:172
69 atoms, 75 bonds, 3 residues, 2 models selected
> select add #1/A:117
89 atoms, 96 bonds, 4 residues, 2 models selected
> select subtract #1/A:117
69 atoms, 75 bonds, 3 residues, 2 models selected
> select add #1/A:116
92 atoms, 100 bonds, 4 residues, 2 models selected
> select #6/A:171
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/A:172
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #1/A:116
46 atoms, 50 bonds, 2 residues, 2 models selected
> select #6/A:172
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #6/A:172-178
158 atoms, 178 bonds, 7 residues, 1 model selected
> select add #1/A:116
181 atoms, 203 bonds, 8 residues, 2 models selected
> select #1/A:111
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:111
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:112
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:112-115
85 atoms, 94 bonds, 4 residues, 1 model selected
> select #6/A:159
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/A:159-167
193 atoms, 215 bonds, 9 residues, 1 model selected
> select #1/A:128
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #1/A:128-130
65 atoms, 72 bonds, 3 residues, 1 model selected
> matchmaker #1 to #6 matrix Nucleic showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ns-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#6) with
Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1), sequence
alignment score = 412.4
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, Ns-
raiA_flip2base_isolde_real_space_refine.pdb #6/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 106 pruned atom pairs is 0.722 angstroms; (across all 193 pairs:
29.026)
> select add #1/A:65
85 atoms, 93 bonds, 4 residues, 1 model selected
> select #6/A:197
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #6/A:189
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #6/A:190
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #1/A:133
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #1/A:134
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #6/A:191
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> hide #!6 models
> show #!4 models
> matchmaker #4.1 to #1 matrix Nucleic showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ca-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#1) with
9G7C_Bujnicki_JMB.cif, chain A (#4.1), sequence alignment score = 562.4
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: Ca-
raiA_flip2base_isolde_real_space_refine.pdb #1/A, 9G7C_Bujnicki_JMB.cif #4.1/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 130 pruned atom pairs is 1.210 angstroms; (across all 204 pairs:
6.174)
> select #1/A:105
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:105-111
146 atoms, 161 bonds, 7 residues, 1 model selected
> select #1/A:112
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:112-113
40 atoms, 43 bonds, 2 residues, 1 model selected
> select #1/A:105
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:105-113
186 atoms, 205 bonds, 9 residues, 1 model selected
> select clear
> select #4.1/A:159
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #4.1/A:159-166
172 atoms, 192 bonds, 1 pseudobond, 8 residues, 2 models selected
> select #4.1/A:133
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #4.1/A:133-137
109 atoms, 121 bonds, 5 residues, 1 model selected
> select #1/A:114
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #1/A:114-120
156 atoms, 175 bonds, 7 residues, 1 model selected
> select #4.1/A:158
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #4.1/A:158
20 atoms, 21 bonds, 1 residue, 1 model selected
> color sel black
> select add #4.1/A:121
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #4.1/A:122
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #4.1/A:123
87 atoms, 94 bonds, 4 residues, 1 model selected
> hide #1 models
> show #!6 models
> matchmaker #4.1 to #6 matrix Nucleic showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Ns-raiA_flip2base_isolde_real_space_refine.pdb, chain A (#6) with
9G7C_Bujnicki_JMB.cif, chain A (#4.1), sequence alignment score = 476.2
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 9G7C_Bujnicki_JMB.cif #4.1/A,
Ns-raiA_flip2base_isolde_real_space_refine.pdb #6/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 101 pruned atom pairs is 1.063 angstroms; (across all 207 pairs:
23.093)
Drag select of 236 atoms, 35 residues, 258 bonds, 79 shapes
> select clear
Drag select of 260 atoms, 59 residues, 286 bonds, 132 shapes
> select up
10179 atoms, 11394 bonds, 473 residues, 2 models selected
> select down
1262 atoms, 286 bonds, 59 residues, 2 models selected
> select clear
> select add #4.1/A:116
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #6/A:149
42 atoms, 45 bonds, 2 residues, 2 models selected
Drag select of 260 atoms, 50 residues, 286 bonds, 115 shapes
> select clear
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!6 models
> show #!6 models
> select #6/A:134
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #6/A:134-141
166 atoms, 183 bonds, 8 residues, 1 model selected
> color sel red
> select #6/A:142
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/A:142-146
106 atoms, 117 bonds, 5 residues, 1 model selected
> color sel red
> select #6/A:147
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #6/A:147-152
125 atoms, 138 bonds, 6 residues, 1 model selected
> color sel red
> undo
> select #6/A:146
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #6/A:142
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/A:142-146
106 atoms, 117 bonds, 5 residues, 1 model selected
> select add #4.1/A:113
129 atoms, 142 bonds, 6 residues, 2 models selected
> select clear
> select #4.1/A:113
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #4.1/A:112
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #4.1/A:111
66 atoms, 71 bonds, 3 residues, 1 model selected
> select add #4.1/A:110
86 atoms, 92 bonds, 4 residues, 1 model selected
> select add #6/A:146
109 atoms, 117 bonds, 5 residues, 2 models selected
> select clear
> select #6/A:146
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #4.1/A:113
46 atoms, 50 bonds, 2 residues, 2 models selected
> select #6/A:147
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #6/A:148
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #6/A:149
63 atoms, 67 bonds, 3 residues, 1 model selected
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/heyao/My Drive/RaiA_2024/Figures/fig1.cxs"
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "ZoneColor" returned None
restore_snapshot for "Redust" returned None
[Repeated 1 time(s)]
restore_snapshot for "ZoneColor" returned None
restore_snapshot for "Redust" returned None
[Repeated 1 time(s)]
restore_snapshot for "ZoneColor" returned None
[Repeated 3 time(s)]
restore_snapshot for "Redust" returned None
Log from Mon Dec 16 22:23:52 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/heyao/Desktop/fig1.cxs
Opened cryosparc_P44_J306_007_volume_map.mrc as #2, grid size 256,256,256,
pixel 0.856, shown at level 0.06, step 1, values float32
Opened cryosparc_P44_J306_007_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 0.856, shown at level 0.148, step 1, values float32
Opened cryosparc_P44_J306_007_volume_map.mrc as #4, grid size 256,256,256,
pixel 0.856, shown at level 0.0478, step 1, values float32
Opened cryosparc_P44_J208_006_volume_map.mrc as #5, grid size 256,256,256,
pixel 0.856, shown at level 0.0521, step 1, values float32
Opened cryosparc_P44_J208_006_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 0.856, shown at level 0.0951, step 1, values float32
Opened cryosparc_P44_J119_007_volume_map.mrc as #8, grid size 256,256,256,
pixel 0.856, shown at level 0.05, step 1, values float32
Opened cryosparc_P44_J119_007_volume_map_sharp.mrc as #10, grid size
256,256,256, pixel 0.856, shown at level 0.0712, step 1, values float32
Log from Sat Dec 14 18:45:20 2024You can double click a model's Name or ID in
the model panel to edit those fields
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/heyao/My Drive/RaiA_2024/PDB_deposition/raiA_3.0A/raiA_OD-
> coot-35_isolda_real_space_refined_delH_new_real_space_refined_051_isolda.pdb"
Chain information for raiA_OD-
coot-35_isolda_real_space_refined_delH_new_real_space_refined_051_isolda.pdb
#1
---
Chain | Description
A | No description available
> set bgColor white
> lighting soft
> graphics silhouettes true
> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA_3.0A/cryosparc_P44_J306_007_volume_map.mrc"
Opened cryosparc_P44_J306_007_volume_map.mrc as #2, grid size 256,256,256,
pixel 0.856, shown at level 0.0213, step 1, values float32
> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA_3.0A/cryosparc_P44_J306_007_volume_map_sharp.mrc"
Opened cryosparc_P44_J306_007_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 0.856, shown at level 0.0348, step 1, values float32
> ui mousemode right zoom
> hide #!2 models
> show atoms
> style stick
Changed 6580 atom styles
> nucleotides atoms
> style nucleic stick
Changed 6575 atom styles
> select H
2195 atoms, 204 residues, 1 model selected
> delete sel
> select clear
> show #!2 models
> volume #2 level 0.06175
> view
> select clear
> show #!3 models
> hide #!2 models
> hide #1 models
> volume #3 level 0.1598
> volume #3 level 0.2398
> show #1 models
> hide #!3 models
> cartoon style sel xsection oval width 1.6 thickness 1.6
> select clear
Drag select of 3161 atoms, 204 residues, 3480 bonds
> cartoon style sel xsection oval width 1.6 thickness 1.6
> select clear
> select #1
4385 atoms, 4907 bonds, 209 residues, 1 model selected
> select #1/1-14
Nothing selected
> select #1/A:1-14
298 atoms, 332 bonds, 14 residues, 1 model selected
> select #1/A:1-14,191-204
593 atoms, 661 bonds, 28 residues, 1 model selected
> color sel orange red
> select clear
> color #1/A:1-14,191-204 orange red
> select /A:190
23 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:183
22 atoms, 24 bonds, 1 residue, 1 model selected
> select /A:23
22 atoms, 24 bonds, 1 residue, 1 model selected
> color #1/A:15-23,183-190 purple
> select clear
> select add /A:185
23 atoms, 25 bonds, 1 residue, 1 model selected
> select clear
> select add /A:183
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add /A:184
44 atoms, 48 bonds, 2 residues, 1 model selected
> color sel gray
> select clear
> select /A:185
23 atoms, 25 bonds, 1 residue, 1 model selected
> color #1/A:15-23,185-190 purple
> select clear
> select /A:185
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add /A:186
45 atoms, 49 bonds, 2 residues, 1 model selected
> select /A:185
23 atoms, 25 bonds, 1 residue, 1 model selected
> color #1/A:15-23,186-190 purple
> color sel light gray
> select clear
[Repeated 2 time(s)]
> select /A:24
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add /A:25
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add /A:26
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add /A:27
86 atoms, 92 bonds, 4 residues, 1 model selected
> select add /A:50
106 atoms, 113 bonds, 5 residues, 1 model selected
> select add /A:49
128 atoms, 137 bonds, 6 residues, 1 model selected
> select add /A:48
151 atoms, 162 bonds, 7 residues, 1 model selected
> select add /A:47
171 atoms, 183 bonds, 8 residues, 1 model selected
> select add /A:46
193 atoms, 207 bonds, 9 residues, 1 model selected
> select add /A:45
215 atoms, 231 bonds, 10 residues, 1 model selected
> color #1/A:24-27,45-50 royal blue
> color sel cornflower blue
> select clear
> color #1/A:24-27,45-50 cornflower blue
> select /A:28
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add /A:29
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add /A:30
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add /A:31
85 atoms, 91 bonds, 4 residues, 1 model selected
> select add /A:32
105 atoms, 112 bonds, 5 residues, 1 model selected
> color #1/A:28-32,40-44 yellow
> select clear
> color #1/A:33-39 green
> select /A:90
20 atoms, 21 bonds, 1 residue, 1 model selected
> color #1/A:33-39,85-90 green
> select clear
> select /A:84
23 atoms, 25 bonds, 1 residue, 1 model selected
> select clear
> select /A:33
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel gray
> select clear
> select /A:29
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select /A:33
22 atoms, 24 bonds, 1 residue, 1 model selected
> select clear
> select /A:35
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select /A:34
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add /A:35
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add /A:36
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add /A:37
86 atoms, 92 bonds, 4 residues, 1 model selected
> select add /A:38
106 atoms, 113 bonds, 5 residues, 1 model selected
> select add /A:39
128 atoms, 137 bonds, 6 residues, 1 model selected
> select /A:85
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add /A:34
43 atoms, 46 bonds, 2 residues, 1 model selected
> select clear
> select /A:85
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add /A:90
40 atoms, 42 bonds, 2 residues, 1 model selected
> color #1/A:34-39,85-90 green
> select clear
> select /A:51
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add /A:52
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add /A:53
62 atoms, 66 bonds, 3 residues, 1 model selected
> select add /A:54
82 atoms, 87 bonds, 4 residues, 1 model selected
> color sel cyan
> select clear
> select add /A:51
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add /A:52
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add /A:53
62 atoms, 66 bonds, 3 residues, 1 model selected
> select add /A:54
82 atoms, 87 bonds, 4 residues, 1 model selected
> select /A:177
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add /A:176
46 atoms, 50 bonds, 2 residues, 1 model selected
> select add /A:175
66 atoms, 71 bonds, 3 residues, 1 model selected
> select add /A:174
89 atoms, 96 bonds, 4 residues, 1 model selected
> select /A:174
23 atoms, 25 bonds, 1 residue, 1 model selected
> color #1/A:51-54, 174-177 cyan
> select clear
> select /A:55
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add /A:79
46 atoms, 50 bonds, 2 residues, 1 model selected
> color #1/A:55-79 orange
> select clear
> view
[Repeated 1 time(s)]
> color #1/A:55-79 goldenrod rod
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #1/A:55-79 goldenrod
> select /A:80
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add /A:81
42 atoms, 45 bonds, 2 residues, 1 model selected
> select clear
> select /A:82
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add /A:83
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add /A:84
66 atoms, 71 bonds, 3 residues, 1 model selected
> select clear
> select /A:84
23 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:80
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:81
22 atoms, 24 bonds, 1 residue, 1 model selected
> select clear
> select /A:84
23 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:83
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add /A:82
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add /A:181
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add /A:182
85 atoms, 91 bonds, 4 residues, 1 model selected
> select add /A:170
108 atoms, 116 bonds, 5 residues, 1 model selected
> select add /A:121
130 atoms, 140 bonds, 6 residues, 1 model selected
> select subtract /A:170
107 atoms, 115 bonds, 5 residues, 1 model selected
> select subtract /A:121
85 atoms, 91 bonds, 4 residues, 1 model selected
> select add /A:81
107 atoms, 115 bonds, 5 residues, 1 model selected
> select add /A:180
127 atoms, 136 bonds, 6 residues, 1 model selected
> select add /A:179
150 atoms, 161 bonds, 7 residues, 1 model selected
> select add /A:178
173 atoms, 186 bonds, 8 residues, 1 model selected
> ui tool show "Color Actions"
> color sel salmon
> color sel dark salmon
> color sel salmon
> color sel light salmon
> select clear
> select add /A:178
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add /A:179
46 atoms, 50 bonds, 2 residues, 1 model selected
> select add /A:180
66 atoms, 71 bonds, 3 residues, 1 model selected
> select add /A:181
86 atoms, 92 bonds, 4 residues, 1 model selected
> select add /A:182
108 atoms, 116 bonds, 5 residues, 1 model selected
> select clear
> select /A:81
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add /A:82
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add /A:83
65 atoms, 70 bonds, 3 residues, 1 model selected
> select clear
> select add /A:178
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add /A:179
46 atoms, 50 bonds, 2 residues, 1 model selected
> select /A:180
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add /A:181
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add /A:182
62 atoms, 66 bonds, 3 residues, 1 model selected
> color #1/A:81-83, 178-182 salmon
> select clear
> select add /A:184
22 atoms, 24 bonds, 1 residue, 1 model selected
> color #1/A:81-83, 178-184 salmon
> select clear
> select add /A:183
22 atoms, 24 bonds, 1 residue, 1 model selected
> select clear
> select /A:183@C3'
1 atom, 1 residue, 1 model selected
> select clear
> select /A:173
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add /A:172
43 atoms, 46 bonds, 2 residues, 1 model selected
> select clear
> select /A:91
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select /A:99
22 atoms, 24 bonds, 1 residue, 1 model selected
> select /A:100
22 atoms, 24 bonds, 1 residue, 1 model selected
> select /A:101
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add /A:100
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add /A:99
67 atoms, 73 bonds, 3 residues, 1 model selected
> select subtract /A:99
45 atoms, 49 bonds, 2 residues, 1 model selected
> select /A:103
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add /A:168
43 atoms, 46 bonds, 2 residues, 1 model selected
> select clear
> color #1/A:119-163 hotpink
> select clear
> select /A:163
22 atoms, 24 bonds, 1 residue, 1 model selected
> select clear
> select /A:118
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add /A:106
46 atoms, 50 bonds, 2 residues, 1 model selected
> select /A:101
23 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:118
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add /A:108
43 atoms, 46 bonds, 2 residues, 1 model selected
> color #1/A:108-118 blue
> color #1/A:108-118 royalblue
> color #1/A:108-118 lblue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/A:108-118 blue
> select clear
> color #1/A:108-118 darkblue
> select /A:107
20 atoms, 21 bonds, 1 residue, 1 model selected
> color #1/A:101-107,164-170 limegreen
> select clear
> color #1/A:101-107,164-170 lime
> select clear
> select add /A:171
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add /A:172
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add /A:173
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add /A:100
87 atoms, 94 bonds, 4 residues, 1 model selected
> select add /A:91
107 atoms, 115 bonds, 5 residues, 1 model selected
> color #1/A:91-100, 171-173 lightgray
> color #1/A:91-100, 171-173 gray
> color #1/A:91-100, 171-173 darkgray
> select clear
> select /A:185
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add /A:183
45 atoms, 49 bonds, 2 residues, 1 model selected
> select /A:185
23 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:185
23 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:185
23 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:165
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select /A:84
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add /A:33
45 atoms, 49 bonds, 2 residues, 1 model selected
> color #1/A:33, 84, 91-100, 171-173 darkgray
> select clear
> select add /A:29
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select add /A:29
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:185
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add /A:183
45 atoms, 49 bonds, 2 residues, 1 model selected
> color #1/A:33, 84, 91-100, 171-173, 183,185 darkgray
> select clear
> color byhetero
> select clear
[Repeated 1 time(s)]
> undo
[Repeated 4 time(s)]
> select clear
> view
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!2 models
> volume #2 level 0.06614
> hide #!2 models
> view
[Repeated 1 time(s)]
> show #!2 models
> volume #2 level 0.07928
> volume #2 color #b2b2b283
> view
[Repeated 1 time(s)]
> show #!3 models
> hide #!3 models
> hide #!2 models
> save "/Users/heyao/Google Drive/My Drive/RaiA_2024/Figures/fig1.cxs"
> show #!2 models
> hide #!2 models
> select Mg
5 atoms, 5 residues, 1 model selected
> hide sel target a
> select clear
Drag select of 3156 atoms, 204 residues, 3480 bonds
> show #!2 models
> ui tool show "Color Zone"
> color zone #2 near #1 distance 5.14
> select clear
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select clear
> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA_3.0A/cryosparc_P44_J306_007_volume_map.mrc"
Opened cryosparc_P44_J306_007_volume_map.mrc as #4, grid size 256,256,256,
pixel 0.856, shown at level 0.0213, step 1, values float32
> volume #4 level 0.04781
> volume #4 color #b2b2b27a
> select clear
> view
> hide #!2 models
> show #!2 models
> hide #1 models
> hide #!4 models
> volume #2 level 0.06335
> select clear
> view
> view name p1
> ui tool show "Side View"
> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true
> surface dust size 3
Missing or invalid "surfaces" argument: invalid surfaces specifier
> surface dust
Missing or invalid "surfaces" argument: empty atom specifier
> surface dust #2 size 3
> select clear
> view p1
> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true
> turn x 90
> save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3
> transparentBackground true
> turn x 90
[Repeated 2 time(s)]
> color single #2
> show #1 models
> hide #!2 models
> select clear
Drag select of 3156 atoms, 204 residues, 3480 bonds
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!2 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color zone #2 near sel distance 5.14
> select clear
> hide #1 models
> select clear
> view p1
> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true
> turn x 90
> save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3
> transparentBackground true
> turn x 90
[Repeated 2 time(s)]
> turn y 90
[Repeated 1 time(s)]
> save /Users/heyao/Desktop/3.png width 2000 height 2000 supersample 3
> transparentBackground true
> turn x 90
> save /Users/heyao/Desktop/4.png width 2000 height 2000 supersample 3
> transparentBackground true
> view name p2
> view p1
> turn y 90
[Repeated 1 time(s)]
> turn y 190
[Repeated 1 time(s)]
> view p1
> view
> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA+P2_3.0A/cryosparc_P44_J208_006_volume_map.mrc"
Opened cryosparc_P44_J208_006_volume_map.mrc as #5, grid size 256,256,256,
pixel 0.856, shown at level 0.0194, step 1, values float32
> volume #5 color #b2b2b2
> volume #5 level 0.04769
> ui mousemode right "rotate selected models"
> select add #5
2 models selected
> view matrix models
> #5,0.98908,-0.10981,-0.098248,23.585,0.018638,0.75465,-0.65586,89.971,0.14617,0.64687,0.74846,-68.003
> fitmap #5 inMap #2
Fit map cryosparc_P44_J208_006_volume_map.mrc in map
cryosparc_P44_J306_007_volume_map.mrc using 57510 points
correlation = 0.6961, correlation about mean = 0.1762, overlap = 166.5
steps = 160, shift = 7.08, angle = 13.6 degrees
Position of cryosparc_P44_J208_006_volume_map.mrc (#5) relative to
cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.99520792 0.09266609 -0.03121206 -1.90478254
-0.08638041 0.68359534 -0.72473156 121.64881794
-0.04582162 0.72395470 0.68832403 -45.65379273
Axis 0.99239916 0.01000804 -0.12265292
Axis point 0.00000000 113.18746461 118.36999355
Rotation angle (degrees) 46.87724941
Shift along axis 4.92673271
> select clear
> select add #5
2 models selected
> view matrix models
> #5,-0.28863,-0.93163,0.22081,242.43,0.58353,-0.35401,-0.73086,165.17,0.75907,-0.082096,0.64582,-41.296
> view matrix models
> #5,-0.86039,-0.42794,0.27676,244.86,0.12692,-0.70587,-0.69688,256.01,0.49358,-0.56446,0.66164,44.269
> fitmap #5 inMap #2
Fit map cryosparc_P44_J208_006_volume_map.mrc in map
cryosparc_P44_J306_007_volume_map.mrc using 57510 points
correlation = 0.9304, correlation about mean = 0.7264, overlap = 384.4
steps = 420, shift = 27.3, angle = 61.9 degrees
Position of cryosparc_P44_J208_006_volume_map.mrc (#5) relative to
cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
-0.82309682 0.56737562 0.02442404 134.59045503
-0.45808180 -0.63789380 -0.61907396 298.40293952
-0.33566753 -0.52074601 0.78495280 110.25649577
Axis 0.09010312 0.32997103 -0.93968109
Axis point 119.35289183 147.39940598 0.00000000
Rotation angle (degrees) 146.93150884
Shift along axis 6.98539970
> select clear
> view p1
> select clear
> hide #!2 models
> open "/Users/heyao/My Drive/RaiA_2024/PDB_deposition/raiA+P2_3.0A/KN-
> coot-13_isolde_real_space_refined_065_isolde.pdb"
Chain information for KN-coot-13_isolde_real_space_refined_065_isolde.pdb #6
---
Chain | Description
A | No description available
> select add #6
5353 atoms, 5988 bonds, 1 pseudobond, 249 residues, 2 models selected
> view matrix models
> #6,-0.90858,0.1578,-0.38676,255.46,0.17715,-0.69294,-0.6989,251.02,-0.37829,-0.70352,0.60164,171.11
> view matrix models
> #6,-0.51182,0.84433,-0.15861,100.53,-0.62781,-0.49363,-0.60182,317.23,-0.58643,-0.20844,0.78272,119.21
> fitmap #6 inMap #5
Fit molecule KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) to map
cryosparc_P44_J208_006_volume_map.mrc (#5) using 5353 atoms
average map value = 0.01605, steps = 132
shifted from previous position = 4.23
rotated from previous position = 9.84 degrees
atoms outside contour = 4651, contour level = 0.047687
Position of KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) relative
to cryosparc_P44_J208_006_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
0.86772792 -0.39727738 0.29869543 2.06277270
0.42913695 0.90201861 -0.04694588 -47.94991180
-0.25077830 0.16891749 0.95319313 19.39883446
Axis 0.21254395 0.54102425 0.81370623
Axis point 94.65981773 -21.12486692 0.00000000
Rotation angle (degrees) 30.51798290
Shift along axis -9.71868299
> view matrix models
> #6,-0.62963,0.75199,0.19515,92.984,-0.76605,-0.55911,-0.3171,317.86,-0.12935,-0.34915,0.9281,70.549
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.62963,0.75199,0.19515,68.108,-0.76605,-0.55911,-0.3171,313.96,-0.12935,-0.34915,0.9281,63.027
> view matrix models
> #6,-0.62963,0.75199,0.19515,68.366,-0.76605,-0.55911,-0.3171,300.24,-0.12935,-0.34915,0.9281,53.164
> fitmap #6 inMap #5
Fit molecule KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) to map
cryosparc_P44_J208_006_volume_map.mrc (#5) using 5353 atoms
average map value = 0.07683, steps = 172
shifted from previous position = 10.1
rotated from previous position = 25.4 degrees
atoms outside contour = 1263, contour level = 0.047687
Position of KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) relative
to cryosparc_P44_J208_006_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
0.99999995 0.00001997 0.00032109 -0.03981368
-0.00001996 1.00000000 -0.00003851 0.01104931
-0.00032109 0.00003851 0.99999995 0.04171659
Axis 0.11885500 0.99099744 -0.06162443
Axis point 130.60221565 0.00000000 125.36760562
Rotation angle (degrees) 0.01856408
Shift along axis 0.00364702
> ui mousemode right zoom
> select clear
> view p1
> select clear
> view p1
> hide #!5 models
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> select clear
Drag select of 249 residues, 1 pseudobonds, 498 shapes
> nucleotides sel atoms
> style nucleic & sel stick
Changed 5353 atom styles
> cartoon style sel xsection oval width 1.6 thickness 1.6
> select clear
> show #1 models
> hide #!6 models
> show #!6 models
> select #6/A:240
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #6/A:14
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #6/A:240
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #6/A:1
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/A:253
22 atoms, 24 bonds, 1 residue, 1 model selected
> P1a and P1b color #6/A:1-14,240-253 orange red
Unknown command: P1a and P1b color #6/A:1-14,240-253 orange red
> color #6/A:1-14,240-253 orange red
> select clear
[Repeated 1 time(s)]
> select #6/A:15
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select #6/A:239
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #6/A:238
45 atoms, 49 bonds, 2 residues, 1 model selected
> select #6/A:235
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #6/A:239
45 atoms, 49 bonds, 2 residues, 1 model selected
> select clear
> select #6/A:15
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #6/A:20
43 atoms, 46 bonds, 2 residues, 1 model selected
> select #6/A:19
20 atoms, 21 bonds, 1 residue, 1 model selected
> color #6/A:15-19,235-239 purple
> select #6/A:92
23 atoms, 25 bonds, 1 residue, 1 model selected
> select clear
> hide #1 models
> select #6/A:60
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #6/A:59
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #6/A:20
65 atoms, 70 bonds, 3 residues, 1 model selected
> ui tool show "Color Actions"
> color #6/A:20-60 darkgoldenrod
> select clear
> view
> select clear
> show #!2 models
> hide #!2 models
> show #1 models
> hide #1 models
> color #6/A:20-60 pylegoldenrod
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #6/A:20-60 palegoldenrod
> select clear
> view
> show #!2 models
> hide #!2 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> color #6/A:20-60 tan
> select clear
[Repeated 1 time(s)]
> show #!2 models
> hide #!2 models
> show #1 models
> hide #!6 models
> show #!6 models
> select #1/A:23
22 atoms, 24 bonds, 1 residue, 1 model selected
> select clear
> select #6/A:60
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel purple
> select clear
> select #6/A:20
23 atoms, 25 bonds, 1 residue, 1 model selected
> color sel purple
> select clear
[Repeated 1 time(s)]
> hide #1 models
> select #6/A:20
23 atoms, 25 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!6 models
> show #!6 models
> select #6/A:60
22 atoms, 24 bonds, 1 residue, 1 model selected
> select clear
> select #6/A:59
20 atoms, 21 bonds, 1 residue, 1 model selected
> color #6/A:15-20,60,235-239 purple
> select clear
> hide #1 models
> show #!2 models
> show #1 models
> hide #!2 models
> color #6/A:21-59 tan
> hide #1 models
> show #1 models
> select #6/A:61
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #6/A:64
46 atoms, 50 bonds, 2 residues, 1 model selected
> select add #1/A:50
66 atoms, 71 bonds, 3 residues, 2 models selected
> select subtract #1/A:50
46 atoms, 50 bonds, 2 residues, 1 model selected
> select add #6/A:87
66 atoms, 71 bonds, 3 residues, 1 model selected
> select add #6/A:82
88 atoms, 95 bonds, 4 residues, 1 model selected
> color #6/A:61-64,82-87 cornflower blue
> select #6/A:65
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #1/A:33
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #6/A:65
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #6/A:69
42 atoms, 45 bonds, 2 residues, 1 model selected
> select #6/A:81
22 atoms, 24 bonds, 1 residue, 1 model selected
> color #6/A:65-69,77-81 yellow
> select clear
[Repeated 1 time(s)]
> select #6/A:70
22 atoms, 24 bonds, 1 residue, 1 model selected
> select clear
> select #6/A:71
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #6/A:76
45 atoms, 49 bonds, 2 residues, 1 model selected
> select clear
> select #6/A:71
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #6/A:76
45 atoms, 49 bonds, 2 residues, 1 model selected
> select clear
> select #6/A:123
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/A:118
20 atoms, 21 bonds, 1 residue, 1 model selected
> color #1/A:71-76,118-123 green
> undo
> color #6/A:71-76,118-123 green
> select clear
> hide #1 models
> show #1 models
> select #6/A:88
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #6/A:91
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #6/A:92
63 atoms, 67 bonds, 3 residues, 1 model selected
> select subtract #6/A:92
40 atoms, 42 bonds, 2 residues, 1 model selected
> select #6/A:226
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #6/A:223
46 atoms, 50 bonds, 2 residues, 1 model selected
> select subtract #6/A:223
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #6/A:223
46 atoms, 50 bonds, 2 residues, 1 model selected
> color #6/A:88-91,223-226 cyan
> select clear
> select #1/A:55
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #6/A:92
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #6/A:112
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> select #6/A:92
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #6/A:112
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide #1 models
> show #1 models
> hide #!6 models
> select #1/A:80
20 atoms, 21 bonds, 1 residue, 1 model selected
> color #1/A:33,80,84,91-100,171-173,183,185 darkgray
> select clear
> show #!2 models
> hide #1 models
> show #1 models
> hide #!2 models
> select clear
Drag select of 3156 atoms, 204 residues, 3480 bonds
> show #!2 models
> color #2 near 1 distance 5
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> colorzone #2 near 1 distance 5
Unknown command: colorzone #2 near 1 distance 5
> color zone #2 near 1 distance 5
Invalid "near" argument: invalid atoms specifier
> color zone #2 near #1 distance 5
> select clear
> hide #!2 models
> hide #1 models
> view p1
> show #1 models
> show #!2 models
> hide #1 models
> show #!6 models
> hide #!2 models
> color #6/A:92-112 goldenrod
> select clear
> show #!2 models
> hide #!2 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #1 models
> show #!2 models
> hide #!2 models
> show #1 models
> hide #1 models
> select #6/A:70
22 atoms, 24 bonds, 1 residue, 1 model selected
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #1 models
> select #1/A:81
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #6/A:114
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #6/A:115
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #6/A:116
65 atoms, 70 bonds, 3 residues, 1 model selected
> select #6/A:227
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #6/A:233
22 atoms, 24 bonds, 1 residue, 1 model selected
> color #6/A:114-116,227-233 salmon
> hide #1 models
> show #1 models
> hide #!6 models
> show #!6 models
> select #1/A:183
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #6/A:232
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #1/A:185
23 atoms, 25 bonds, 1 residue, 1 model selected
> hide #1 models
> show #1 models
> hide #1 models
> select #6/A:234
23 atoms, 25 bonds, 1 residue, 1 model selected
> color #6/A:70,232,234 darkgray
> select clear
> show #!2 models
> hide #!2 models
> show #1 models
> hide #1 models
> show #1 models
> select #1/A:170
23 atoms, 25 bonds, 1 residue, 1 model selected
> select clear
> select #6/A:219
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #1/A:170
23 atoms, 25 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #1/A:170
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #6/A:219
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #6/A:213
46 atoms, 50 bonds, 2 residues, 1 model selected
> select #6/A:140
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/A:134
23 atoms, 25 bonds, 1 residue, 1 model selected
> select clear
> color #6/A:134-140,213-219 lime
> select #6/A:141
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/A:174
23 atoms, 25 bonds, 1 residue, 1 model selected
> color #6/A:141-174 darkblue
> select clear
> select #6/A:212
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #6/A:175
22 atoms, 24 bonds, 1 residue, 1 model selected
> color #6/A:175-212 hotpink
> hide #1 models
> view p1
> select clear
> show #1 models
> hide #1 models
> select #6/A:124
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #6/A:133
42 atoms, 45 bonds, 2 residues, 1 model selected
> select #6/A:222
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #6/A:220
42 atoms, 45 bonds, 2 residues, 1 model selected
> color #6/A:70,113,117,124-133,220-222,232,234 darkgray
> select clear
> view p1
> show #!5 models
> volume #5 level 0.05695
> ui tool show "Color Zone"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color zone #5 near #6 distance 5.14
> color zone #5 near #6 distance 5.1
> color zone #5 near #6 distance 5
[Repeated 2 time(s)]
> hide #!5 models
> show #!5 models
> hide #!6 models
> volume #5 level 0.05886
> volume #5 level 0.05504
> show #!2 models
> hide #!2 models
> show #1 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!2 models
> hide #1 models
> save /Users/heyao/Desktop/fig1.cxs
> show #!6 models
> hide #!2 models
> show #!2 models
> hide #!6 models
> show #1 models
> hide #!2 models
> show #!2 models
> hide #1 models
> view p1
> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true
> turn y 180
> save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3
> transparentBackground true
> view p2
> save /Users/heyao/Desktop/3.png width 2000 height 2000 supersample 3
> transparentBackground true
> turn y 180
[Repeated 1 time(s)]
> turn x 180
[Repeated 1 time(s)]
> turn z 180
> save /Users/heyao/Desktop/4.png width 2000 height 2000 supersample 3
> transparentBackground true
> show #1 models
> hide #1 models
> hide #!2 models
> show #!6 models
> hide #!6 models
> show #!5 models
> ui tool show "Hide Dust"
> surface dust #5 size 5.14
> surface dust #5 size 4.94
> surface dust #5 size 1.19
> surface dust #5 size 1.74
> surface dust #5 size 1
> surface dust #5 size 3
[Repeated 1 time(s)]
> save /Users/heyao/Desktop/14.png width 2000 height 2000 supersample 3
> transparentBackground true
> turn z 180
> save /Users/heyao/Desktop/13.png width 2000 height 2000 supersample 3
> transparentBackground true
> view p1
> save /Users/heyao/Desktop/11.png width 2000 height 2000 supersample 3
> transparentBackground true
> turn y 180
> save /Users/heyao/Desktop/12.png width 2000 height 2000 supersample 3
> transparentBackground true
> view
[Repeated 3 time(s)]
> select clear
> volume #5 level 0.07883
> view p1
> volume #5 level 0.04591
> view p1
> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA+P2_3.0A/cryosparc_P44_J208_006_volume_map_sharp.mrc"
Opened cryosparc_P44_J208_006_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 0.856, shown at level 0.0321, step 1, values float32
> volume #7 level 0.09953
> select add #7
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.76381,0.63589,-0.11064,143.02,-0.52039,-0.70812,-0.47725,309.35,-0.38182,-0.30695,0.87178,93.617
> fitmap #7 inMap #5
Fit map cryosparc_P44_J208_006_volume_map_sharp.mrc in map
cryosparc_P44_J208_006_volume_map.mrc using 33096 points
correlation = 0.9546, correlation about mean = 0.7783, overlap = 698.7
steps = 164, shift = 18.4, angle = 13.5 degrees
Position of cryosparc_P44_J208_006_volume_map_sharp.mrc (#7) relative to
cryosparc_P44_J208_006_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
0.99999995 -0.00009731 0.00030468 -0.02233620
0.00009737 0.99999998 -0.00018529 0.01126621
-0.00030466 0.00018532 0.99999994 0.01925316
Axis 0.50131231 0.82422219 0.26333202
Axis point 60.44868633 0.00000000 78.51712028
Rotation angle (degrees) 0.02117924
Shift along axis 0.00315842
> select clear
> hide #!5 models
> volume #7 level 0.1479
> volume #7 level 0.1142
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> surface dust #7 size 5.14
> color zone #7 near #6 distance 5.14
> select clear
> volume #7 level 0.09513
> surface dust #7 size 5.17
> surface dust #7 size 2.59
> hide #!7 models
> show #1 models
> hide #1 models
> show #!2 models
> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA-P8_3.5A/cryosparc_P44_J119_007_volume_map.mrc"
Opened cryosparc_P44_J119_007_volume_map.mrc as #8, grid size 256,256,256,
pixel 0.856, shown at level 0.0109, step 1, values float32
> volume #8 level 0.05676
> select add #8
2 models selected
> view matrix models
> #8,-0.7258,0.66222,0.18623,91.252,0.62651,0.52455,0.57647,-87.693,0.28407,0.53508,-0.79561,134.51
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.7258,0.66222,0.18623,96.465,0.62651,0.52455,0.57647,-78.886,0.28407,0.53508,-0.79561,111.51
> view matrix models
> #8,-0.7258,0.66222,0.18623,95.693,0.62651,0.52455,0.57647,-77.05,0.28407,0.53508,-0.79561,109.84
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.59361,-0.78521,0.17626,238.98,-0.41119,0.48422,0.77231,14.761,-0.69177,0.38597,-0.61031,208.04
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
Must specify one map, got 0
> fitmap #8 inMap #2
Fit map cryosparc_P44_J119_007_volume_map.mrc in map
cryosparc_P44_J306_007_volume_map.mrc using 32003 points
correlation = 0.7141, correlation about mean = 0.06117, overlap = 96.41
steps = 120, shift = 7.63, angle = 7.11 degrees
Position of cryosparc_P44_J119_007_volume_map.mrc (#8) relative to
cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
-0.67932839 -0.70734554 0.19538482 233.17463966
-0.32924966 0.53174106 0.78028592 -1.20521285
-0.65582589 0.46573999 -0.59412007 187.73366128
Axis -0.31995815 0.86585704 0.38460157
Axis point 145.04886475 0.00000000 58.92440994
Rotation angle (degrees) 150.55799757
Shift along axis -3.44700659
> select clear
> select add #8
2 models selected
> view matrix models
> #8,0.92597,-0.247,0.28559,-0.62486,-0.33951,-0.87565,0.34347,206.09,0.16524,-0.41501,-0.89469,231.71
> fitmap #8 inMap #2
Fit map cryosparc_P44_J119_007_volume_map.mrc in map
cryosparc_P44_J306_007_volume_map.mrc using 32003 points
correlation = 0.918, correlation about mean = 0.5232, overlap = 217.2
steps = 132, shift = 2.14, angle = 21.9 degrees
Position of cryosparc_P44_J119_007_volume_map.mrc (#8) relative to
cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.98172391 0.09005861 0.16765326 -29.84294848
-0.01268335 -0.84802486 0.52980466 149.11768328
0.18988760 -0.52224830 -0.83138403 232.76992784
Axis -0.99504515 -0.02102952 -0.09717466
Axis point 0.00000000 108.37326391 96.40524730
Rotation angle (degrees) 148.08599472
Shift along axis 3.93986945
> select clear
> hide #!8 models
> show #!8 models
> hide #!2 models
> show #!2 models
> select clear
> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA-P8_3.5A/initial_model_AN-
> coot-11_isolde.pdb"
Chain information for initial_model_AN-coot-11_isolde.pdb #9
---
Chain | Description
A | No description available
> select add #9
3336 atoms, 3734 bonds, 2 pseudobonds, 155 residues, 2 models selected
> hide #!2 models
> view matrix models
> #9,0.92235,0.35553,0.15123,-47.92,0.17678,-0.73639,0.65305,87.261,0.34354,-0.57561,-0.74206,237.51
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.92235,0.35553,0.15123,-46.908,0.17678,-0.73639,0.65305,102.26,0.34354,-0.57561,-0.74206,218.07
> fitmap #9 inMap #8
Fit molecule initial_model_AN-coot-11_isolde.pdb (#9) to map
cryosparc_P44_J119_007_volume_map.mrc (#8) using 3336 atoms
average map value = 0.06906, steps = 132
shifted from previous position = 6.96
rotated from previous position = 16.8 degrees
atoms outside contour = 1046, contour level = 0.056762
Position of initial_model_AN-coot-11_isolde.pdb (#9) relative to
cryosparc_P44_J119_007_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.99999922 0.00120715 0.00033324 -0.17137916
-0.00120711 0.99999926 -0.00015796 0.15354463
-0.00033343 0.00015757 0.99999994 0.01154017
Axis 0.12499238 0.26409247 -0.95636399
Axis point 125.34278901 142.88874346 0.00000000
Rotation angle (degrees) 0.07231914
Shift along axis 0.00809228
> select clear
> ui mousemode right zoom
> view p1
> select clear
> hide #!8 models
> select clear
Drag select of 155 residues, 2 pseudobonds, 310 shapes
> nucleotides sel atoms
> style nucleic & sel stick
Changed 3336 atom styles
> cartoon style sel xsection oval width 1.6 thickness 1.6
> select clear
> show #!8 models
> hide #!8 models
> show #1 models
> select clear
> select #1/A:191
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #9/A:150
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #9/A:14
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #9/A:150
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #9/A:163
23 atoms, 25 bonds, 1 residue, 1 model selected
> color #9/A:1-14,150-163 orange red
> select clear
> select #1/A:190
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #1/A:15
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #9/A:23
42 atoms, 45 bonds, 2 residues, 2 models selected
> select #1/A:190
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #9/A:149
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #9/A:145
22 atoms, 24 bonds, 1 residue, 1 model selected
> color #6/A:15-23,145-149 purple
[Repeated 1 time(s)]
> undo
[Repeated 2 time(s)]
> hide #1 models
> hide #!9 models
> show #!5 models
> hide #!5 models
> show #!6 models
> show #!9 models
> hide #!6 models
> undo
[Repeated 10 time(s)]No undo action is available
> undo
No undo action is available
> undo
No undo action is available
> undo
No undo action is available
> select clear
[Repeated 1 time(s)]
> color #9/A:15-23,145-149 purple
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> select #1/A:24
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #1/A:27
46 atoms, 50 bonds, 2 residues, 1 model selected
> select add #1/A:50
66 atoms, 71 bonds, 3 residues, 1 model selected
> select add #9/A:45
88 atoms, 95 bonds, 4 residues, 2 models selected
> color #9/A:24-27,45-50 cornflower blue
> select clear
> hide #!9 models
> show #!9 models
> hide #1 models
> show #1 models
> select #9/A:28
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #9/A:32
42 atoms, 45 bonds, 2 residues, 1 model selected
> select #9/A:40
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #9/A:44
45 atoms, 49 bonds, 2 residues, 1 model selected
> color #9/A:28-32,40-44 yellow
> select clear
> select #1/A:33
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #1/A:34
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #9/A:34
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #9/A:39
46 atoms, 50 bonds, 2 residues, 1 model selected
> select #9/A:92
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/A:87
20 atoms, 21 bonds, 1 residue, 1 model selected
> color #9/A:34-39,87-92 green
> select clear
> hide #1 models
> show #1 models
> hide #1 models
> select #9/A:33
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel darg gray
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel darkgray
> select clear
> show #!2 models
> hide #!2 models
> show #1 models
> hide #1 models
> show #1 models
> hide #!9 models
> show #!9 models
> select #1/A:51
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/A:51
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #9/A:54
40 atoms, 42 bonds, 2 residues, 1 model selected
> select clear
> select #9/A:136
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #9/A:133
46 atoms, 50 bonds, 2 residues, 1 model selected
> color #9/A:51-54,133-136 cyan
> select clear
> hide #1 models
> show #1 models
> select #9/A:55
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #9/A:81
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide #1 models
> select clear
> select #9/A:81
20 atoms, 21 bonds, 1 residue, 1 model selected
> show #1 models
> color #9/A:55-81 goldenrod
> select clear
> hide #1 models
> show #1 models
> select #9/A:83
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #9/A:85
45 atoms, 49 bonds, 2 residues, 1 model selected
> select #1/A:81
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/A:83
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #9/A:85
45 atoms, 49 bonds, 2 residues, 1 model selected
> select #1/A:184
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/A:143
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/A:143
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/A:137
23 atoms, 25 bonds, 1 residue, 1 model selected
> color #9/A:83-85,137-143 salmon
> select clear
> select #1/A:183
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #1/A:185
45 atoms, 49 bonds, 2 residues, 1 model selected
> hide #1 models
> show #1 models
> hide #1 models
> select add #9/A:142
67 atoms, 73 bonds, 3 residues, 2 models selected
> select add #9/A:144
89 atoms, 97 bonds, 4 residues, 2 models selected
> color #9/A:33, 82, 86, 142,144 darkgray
> select clear
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> select #9/A:93
20 atoms, 21 bonds, 1 residue, 1 model selected
> show #1 models
> select #9/A:121
23 atoms, 25 bonds, 1 residue, 1 model selected
> hide #1 models
> select add #9/A:108
43 atoms, 46 bonds, 2 residues, 1 model selected
> show #1 models
> hide #1 models
> color #9/A:108-121 darkblue
> select clear
> select add #9/A:107
20 atoms, 21 bonds, 1 residue, 1 model selected
> show #1 models
> select add #1/A:101
43 atoms, 46 bonds, 2 residues, 2 models selected
> select add #9/A:102
65 atoms, 70 bonds, 3 residues, 2 models selected
> select #1/A:102
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:101
23 atoms, 25 bonds, 1 residue, 1 model selected
> hide #!9 models
> show #!9 models
> hide #1 models
> select #9/A:107
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #9/A:128
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #9/A:127
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #9/A:126
66 atoms, 71 bonds, 3 residues, 1 model selected
> show #1 models
> select add #9/A:129
88 atoms, 95 bonds, 4 residues, 1 model selected
> select #9/A:103
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #9/A:107
43 atoms, 46 bonds, 2 residues, 1 model selected
> select clear
> color #9/A:103-107,126-129 lime
> select clear
> hide #1 models
> select #9/A:102
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #9/A:130
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #9/A:132
42 atoms, 45 bonds, 2 residues, 1 model selected
> select #9/A:93
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #9/A:102
42 atoms, 45 bonds, 2 residues, 1 model selected
> color #9/A:33,82,86,93-102,130-132,142,144 darkgray
> select clear
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> save /Users/heyao/Desktop/fig1.cxs
> show #!8 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color zone #8 near #9 distance 5.14
> color zone #8 near #9 distance 4.96
> color zone #8 near #9 distance 3.98
> surface dust #8 size 5.14
> volume #8 level 0.06701
> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA-P8_3.5A/cryosparc_P44_J119_007_volume_map_sharp.mrc"
Opened cryosparc_P44_J119_007_volume_map_sharp.mrc as #10, grid size
256,256,256, pixel 0.856, shown at level 0.0198, step 1, values float32
> volume #10 level 0.1802
> select add #10
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #10,-0.97132,-0.23766,0.0077356,235.93,-0.15228,0.64668,0.7474,-32.131,-0.18263,0.72479,-0.66433,134.13
> volume #10 level 0.08858
> view matrix models
> #10,0.93215,0.020628,0.36147,-38.767,-0.19435,-0.81384,0.54762,154.01,0.30548,-0.58072,-0.75462,233.48
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.93215,0.020628,0.36147,-35.457,-0.19435,-0.81384,0.54762,162.59,0.30548,-0.58072,-0.75462,224.58
Must specify one map, got 0
> fitmap #10 inMap #8
Fit map cryosparc_P44_J119_007_volume_map_sharp.mrc in map
cryosparc_P44_J119_007_volume_map.mrc using 27855 points
correlation = 0.931, correlation about mean = 0.5914, overlap = 393.1
steps = 120, shift = 6.72, angle = 13 degrees
Position of cryosparc_P44_J119_007_volume_map_sharp.mrc (#10) relative to
cryosparc_P44_J119_007_volume_map.mrc (#8) coordinates:
Matrix rotation and translation
0.99999985 0.00045450 0.00030702 -0.07641814
-0.00045451 0.99999989 0.00002918 0.05384633
-0.00030700 -0.00002931 0.99999995 0.03236712
Axis -0.05324606 0.55895242 -0.82748840
Axis point 109.35316698 167.30731259 0.00000000
Rotation angle (degrees) 0.03147028
Shift along axis 0.00738308
> select clear
> save /Users/heyao/Desktop/fig1.cxs
> surface dust #10 size 5.14
> color zone #10 near #9 distance 5.14
> hide #!8 models
> hide #!9 models
> volume #10 level 0.08349
> view p1
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!10 models
> show #!8 models
> hide #!10 models
> show #!10 models
> hide #!8 models
> volume #10 level 0.08172
> volume #10 level 0.07116
> show #!8 models
> volume #8 level 0.05258
> volume #8 level 0.04487
> select #8
2 models selected
> show #!9 models
> hide #!8 models
> select clear
> show #!8 models
> color #8 #d6d6d6ff models
> color #8 silver models
> color zone #10 near #9 distance 5.14
[Repeated 1 time(s)]
> color zone #8 near #9 distance 5.14
> select clear
> hide #!8 models
> hide #!9 models
> show #1 models
> hide #1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> color #3 #b2b2b2ff models
> color zone #3 near #1 distance 5.14
> view
> view p1
> volume #3 level 0.1706
> volume #3 level 0.19
> volume #3 level 0.2
> volume #3 level 0.1481
> view
> view p1
> show #1 models
> hide #!2 models
Drag select of 3156 atoms, 204 residues, 3480 bonds
> show #!2 models
> ui tool show "Color Zone"
> color zone #2 near sel distance 5
> hide #!2 models
> show #!2 models
> hide #1 models
> view p1
> volume #2 level 0.07
> volume #2 level 0.05
> volume #2 level 0.06
> view p1
> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true
> turn y 180
> save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3
> transparentBackground true
> view p2
> turn z 180
> save /Users/heyao/Desktop/3.png width 2000 height 2000 supersample 3
> transparentBackground true
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!4 models
> show #!2 models
> hide #!2 models
> show #1 models
> hide #1 models
> show #!3 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> view p1
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!5 models
> volume #5 level 0.05207
> view p1
> save /Users/heyao/Desktop/11.png width 2000 height 2000 supersample 3
> transparentBackground true
> turn y 180
> save /Users/heyao/Desktop/12.png width 2000 height 2000 supersample 3
> transparentBackground true
> view p2
> turn z 180
> save /Users/heyao/Desktop/13.png width 2000 height 2000 supersample 3
> transparentBackground true
> hide #!5 models
> show #!10 models
> show #!8 models
> hide #!10 models
> view p1
> volume #8 level 0.05187
> volume #8 level 0.04053
> view p1
> view
> view p1
> save /Users/heyao/Desktop/21.png width 2000 height 2000 supersample 3
> transparentBackground true
> turn y 180
> save /Users/heyao/Desktop/22.png width 2000 height 2000 supersample 3
> transparentBackground true
> view p2
> turn z 180
> save /Users/heyao/Desktop/23.png width 2000 height 2000 supersample 3
> transparentBackground true
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!10 models
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!8 models
> view p1
> hide #!8 models
> show #!8 models
> hide #!2 models
> volume #8 level 0.05
> view p1
> save /Users/heyao/Desktop/21.png width 2000 height 2000 supersample 3
> transparentBackground true
> turn y 180
> save /Users/heyao/Desktop/22.png width 2000 height 2000 supersample 3
> transparentBackground true
> view p2
[Repeated 1 time(s)]
> turn z 180
> save /Users/heyao/Desktop/23.png width 2000 height 2000 supersample 3
> transparentBackground true
> save /Users/heyao/Desktop/fig1.cxs
——— End of log from Sat Dec 14 18:45:20 2024 ———
opened ChimeraX session
> ui mousemode right translate
> ui mousemode right zoom
> hide #!8 models
> show #1 models
> view p1
> select clear
> ui tool show "Side View"
> save /Users/heyao/Desktop/101.png width 2000 height 2000 supersample 3
> transparentBackground true
> view p1
> turn y 180
> save /Users/heyao/Desktop/102.png width 2000 height 2000 supersample 3
> transparentBackground true
> view p1
> save /Users/heyao/Desktop/101.png width 2000 height 2000 supersample 3
> transparentBackground true
> turn y 180
> save /Users/heyao/Desktop/102.png width 2000 height 2000 supersample 3
> transparentBackground true
> show #!3 models
> hide #1 models
> show #!2 models
> hide #!3 models
> view p2
> turn z 180
> turn y 180
> turn z 180
> select clear
> save /Users/heyao/Desktop/103.png width 2000 height 2000 supersample 3
> transparentBackground true
> show #1 models
> hide #!2 models
> save /Users/heyao/Desktop/104.png width 2000 height 2000 supersample 3
> transparentBackground true
> show #!2 models
> hide #1 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!6 models
> hide #!5 models
> save /Users/heyao/Desktop/105.png width 2000 height 2000 supersample 3
> transparentBackground true
> view p1
> hide #6.1 models
> save /Users/heyao/Desktop/106.png width 2000 height 2000 supersample 3
> transparentBackground true
> turn y 180
> save /Users/heyao/Desktop/107.png width 2000 height 2000 supersample 3
> transparentBackground true
> show #!5 models
> hide #!6 models
> view p1
> turn z 90
[Repeated 3 time(s)]
> turn x 90
[Repeated 2 time(s)]
> view p2
> turn x 90
[Repeated 1 time(s)]
> turn z 90
[Repeated 1 time(s)]
> save /Users/heyao/Desktop/108.png width 2000 height 2000 supersample 3
> transparentBackground true
> hide #!5 models
> show #!6 models
> save /Users/heyao/Desktop/105.png width 2000 height 2000 supersample 3
> transparentBackground true
> hide #!6 models
> show #!9 models
> hide #9.1 models
> hide #!9 models
> show #!6 models
> view name p3
> show #!9 models
> hide #!9 models
> hide #!6 models
> show #!9 models
> hide #!9 models
> show #!6 models
> view p1
> show #6.1 models
> hide #6.1 models
> show #6.1 models
> hide #!6 models
Cell requested for row 9 is out of bounds for table with 12 rows! Resizing
table model.
> show #!9 models
> view p1
> save /Users/heyao/Desktop/111.png width 2000 height 2000 supersample 3
> transparentBackground true
> turn y 180
> save /Users/heyao/Desktop/112.png width 2000 height 2000 supersample 3
> transparentBackground true
> view p3
> save /Users/heyao/Desktop/113.png width 2000 height 2000 supersample 3
> transparentBackground true
> hide #!9 models
> show #!8 models
> save /Users/heyao/Desktop/114.png width 2000 height 2000 supersample 3
> transparentBackground true
> hide #!8 models
> show #!9 models
> show #9.1 models
> view p1
[Repeated 1 time(s)]
> turn y 180
> view p3
> save /Users/heyao/Desktop/fig1.cxs
——— End of log from Mon Dec 16 22:23:52 2024 ———
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGQ3LL/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 13822.41.1
OS Loader Version: 13822.41.1
Software:
System Software Overview:
System Version: macOS 26.1 (25B78)
Kernel Version: Darwin 25.1.0
Time since boot: 10 days, 2 hours, 50 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2717D:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
DELL U2417H:
Resolution: 1080 x 1920
UI Looks like: 1080 x 1920 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: 270
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
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: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
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-Clipper: 0.25.2
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
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: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.10.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
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: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 3 weeks ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 2 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
The ChimeraX bug report panel said what we know about this crash:
"This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX."
The ChimeraX daily build and release candidates that will be on the download page this week use a newer Qt (version 6.9.2) and we have not seen these Mac crashes waking from sleep in the newer Qt, so you may want to try it.
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Reported by Yao He