![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 13 months ago
Closed 13 months ago
#15996 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
The following bug report has been submitted:
Platform: macOS-15.0-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff84a3c6680 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, PIL._webp, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.segment._segment (total: 121)
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{
"uptime" : 120000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,3",
"coalitionID" : 4041,
"osVersion" : {
"train" : "macOS 15.0",
"build" : "24A335",
"releaseType" : "User"
},
"captureTime" : "2024-09-23 07:35:38.4636 -0700",
"codeSigningMonitor" : 0,
"incident" : "8802E38A-CE42-473C-897A-202EA40ED03D",
"pid" : 42349,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-09-22 09:22:05.3839 -0700",
"procStartAbsTime" : 96073272985143,
"procExitAbsTime" : 127411607754451,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"DED4BD1E-B392-5D25-B256-86E56CD2C686","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "586409D4-F6D0-0B06-6CD4-3641E818D7B4",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bootSessionUUID" : "AF665AEA-ACC5-43B5-8677-60987DFCF7DB",
"wakeTime" : 25,
"bridgeVersion" : {"build":"22P353","train":"9.0"},
"sleepWakeUUID" : "2CFAC2B7-7114-4B95-A883-175CFED9D4A6",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4558241792\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10fb14000-10fb18000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x000000000000000d, 0x0000000000000000","rawCodes":[13,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"UNKNOWN_0xD at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":42349},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4558241792\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10fb14000-10fb18000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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System Profile:
Network Service: Wi-Fi, AirPort, en0
Thunderbolt Bus: MacBook Pro, Apple Inc., 63.5
Boot Volume File System Type: apfs
Memory Module: BANK 0/ChannelA-DIMM0, 4 GB, LPDDR3, 2133 MHz, Samsung, K4E6E304ED-EGCG
Memory Module: BANK 2/ChannelB-DIMM0, 4 GB, LPDDR3, 2133 MHz, Samsung, K4E6E304ED-EGCG
USB Device: USB31Bus
USB Device: USB C Video Adaptor
USB Device: T2Bus
USB Device: Touch Bar Backlight
USB Device: Touch Bar Display
USB Device: Apple Internal Keyboard / Trackpad
USB Device: Headset
USB Device: Ambient Light Sensor
USB Device: FaceTime HD Camera (Built-in)
USB Device: Apple T2 Controller
Display: Color LCD, 2560 x 1600 Retina, Main, MirrorOff, Online
Display: C27F398, 1920 x 1080 (1080p FHD - Full High Definition), MirrorOff, Online
Model: MacBookPro16,3, BootROM 2069.0.0.0.0 (iBridge: 22.16.10353.0.0,0), 4 processors, Quad-Core Intel Core i5, 1.4 GHz, 8 GB, SMC
Graphics: Intel Iris Plus Graphics 645, Intel Iris Plus Graphics 645, Built-In
AirPort: spairport_wireless_card_type_wifi (0x14E4, 0x870), wl0: Jul 26 2024 20:45:01 version 16.20.380.0.3.6.130 FWID 01-c866e60e
AirPort:
Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> graphics silhouettes true width 1
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/petra/Downloads/cryosparc_P14_J268_011_volume_map_sharp.mrc
Opened cryosparc_P14_J268_011_volume_map_sharp.mrc as #1, grid size
420,420,420, pixel 0.65, shown at level 0.0111, step 2, values float32
> open /Users/petra/Downloads/cryosparc_P14_J268_011_volume_map.mrc
Opened cryosparc_P14_J268_011_volume_map.mrc as #2, grid size 420,420,420,
pixel 0.65, shown at level 0.0079, step 2, values float32
> surface dust #1 size 6.5
> surface dust #2 size 6.5
> color #2 #5e5e5eff models
> lighting soft
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #1 step 1
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #2 step 1
> volume #2 level 0.02448
> volume #1 level 0.06395
> volume #1 level 0.02915
> volume #1 level 0.03946
> volume #2 level 0.02579
> volume #1 level 0.05364
> volume #2 level 0.02317
> open
> /Users/petra/Desktop/GiGet345_Krios_Phenix/3.44A/input/Get345_For344AMap.pdb
Chain information for Get345_For344AMap.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> select add #3
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> show sel cartoons
> close #3
> open
> /Users/petra/Desktop/GiGet345_Krios_Phenix/3.44A/RealSpaceRefine_2/Get345_For344AMap_real_space_refined_002.pdb
Chain information for Get345_For344AMap_real_space_refined_002.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> select add #3
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> hide #!2 models
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 8196 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select subtract #3
Nothing selected
> show #!2 models
> select add #3
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> select subtract #3
Nothing selected
> select #3/D,c
3049 atoms, 3112 bonds, 392 residues, 1 model selected
> color sel #c08645ff
> select #3/A,B
4867 atoms, 4972 bonds, 6 pseudobonds, 609 residues, 3 models selected
> color (#!3 & sel) #4e6fafff
> select #3/E
345 atoms, 351 bonds, 43 residues, 1 model selected
> color sel #be1d3bff
> delete atoms sel
> delete bonds sel
> select add #3
7916 atoms, 8084 bonds, 6 pseudobonds, 1001 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.90501,0.30866,0.29272,-87.814,0.31206,-0.94937,0.036252,283.01,0.28909,0.058537,-0.95551,273.11
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.90501,0.30866,0.29272,-77.949,0.31206,-0.94937,0.036252,253.67,0.28909,0.058537,-0.95551,258.56
> view matrix models
> #3,0.90501,0.30866,0.29272,-131.66,0.31206,-0.94937,0.036252,240.27,0.28909,0.058537,-0.95551,252.93
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.98173,-0.04652,-0.18452,-0.92119,-0.058046,-0.99665,-0.05756,329.39,-0.18123,0.067219,-0.98114,338.06
> view matrix models
> #3,0.96026,0.12195,-0.25104,-15.516,0.12125,-0.99245,-0.01832,290.58,-0.25138,-0.012846,-0.9678,362.18
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.96026,0.12195,-0.25104,-16.449,0.12125,-0.99245,-0.01832,291.46,-0.25138,-0.012846,-0.9678,353.15
> fitmap #3 inMap #2
Fit molecule Get345_For344AMap_real_space_refined_002.pdb (#3) to map
cryosparc_P14_J268_011_volume_map.mrc (#2) using 7916 atoms
average map value = 0.05433, steps = 160
shifted from previous position = 7.29
rotated from previous position = 14.4 degrees
atoms outside contour = 1427, contour level = 0.023171
Position of Get345_For344AMap_real_space_refined_002.pdb (#3) relative to
cryosparc_P14_J268_011_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.99912478 0.03659391 -0.02026318 -41.48988537
0.03606792 -0.99901777 -0.02574207 310.83590142
-0.02118527 0.02498869 -0.99946326 310.37219628
Axis 0.99978113 0.01817227 -0.01036611
Axis point 0.00000000 153.82822852 156.94780746
Rotation angle (degrees) 178.54619666
Shift along axis -39.04956358
> select subtract #3
Nothing selected
> ui mousemode right translate
> ui tool show "Color Zone"
> color zone #2 near #3 distance 2
> color zone #2 near #3 distance 2.1
> color zone #2 near #3 distance 2.2
> color zone #2 near #3 distance 2.3
> color zone #2 near #3 distance 2.4
> color zone #2 near #3 distance 2.5
> color zone #2 near #3 distance 2.6
> color zone #2 near #3 distance 2.7
> color zone #2 near #3 distance 2.8
> color zone #2 near #3 distance 2.9
> color zone #2 near #3 distance 3
> color zone #2 near #3 distance 3.1
> color zone #2 near #3 distance 3.2
> color zone #2 near #3 distance 3.3
> color zone #2 near #3 distance 3.4
> color zone #2 near #3 distance 3.5
> color zone #2 near #3 distance 3.6
> color zone #2 near #3 distance 3.7
> color zone #2 near #3 distance 3.8
> color zone #2 near #3 distance 3.9
> color zone #2 near #3 distance 4
> color zone #2 near #3 distance 4.1
> color zone #2 near #3 distance 4
> color zone #2 near #3 distance 3.9
> color zone #2 near #3 distance 3.8
> color zone #2 near #3 distance 3.7
> color zone #2 near #3 distance 3.6
> color zone #2 near #3 distance 3.5
> color zone #2 near #3 distance 3.4
> color zone #2 near #3 distance 3.3
> color zone #2 near #3 distance 3.2
> color zone #2 near #3 distance 3.1
> color zone #2 near #3 distance 3
> color zone #2 near #3 distance 2.9
> color zone #2 near #3 distance 2.8
> color zone #2 near #3 distance 2.7
> color zone #2 near #3 distance 2.6
> color zone #2 near #3 distance 2.5
> color zone #2 near #3 distance 2.4
> color zone #2 near #3 distance 2.3
> color zone #2 near #3 distance 2.4
> color zone #2 near #3 distance 2.5
> color zone #2 near #3 distance 2.4
> color zone #2 near #3 distance 2.3
> color zone #2 near #3 distance 2.2
> color zone #2 near #3 distance 2.1
> color zone #2 near #3 distance 2
> color zone #2 near #3 distance 1.9
> color zone #2 near #3 distance 1.8
> color zone #2 near #3 distance 1.7
> color zone #2 near #3 distance 1.6
> color zone #2 near #3 distance 1.5
> color zone #2 near #3 distance 1.4
> color zone #2 near #3 distance 1.3
> color zone #2 near #3 distance 1.2
> color zone #2 near #3 distance 1.1
> color zone #2 near #3 distance 1.2
> color zone #2 near #3 distance 1.3
> color zone #2 near #3 distance 1.4
> color zone #2 near #3 distance 1.5
> color zone #2 near #3 distance 1.6
> color zone #2 near #3 distance 1.7
> color zone #2 near #3 distance 1.8
> color zone #2 near #3 distance 1.9
> color zone #2 near #3 distance 2
> color zone #2 near #3 distance 2.1
> color zone #2 near #3 distance 2.2
> color zone #2 near #3 distance 2.3
> color zone #2 near #3 distance 2.4
> color zone #2 near #3 distance 2.5
> color zone #2 near #3 distance 2.6
> color zone #2 near #3 distance 2.7
> color zone #2 near #3 distance 2.8
> volume splitbyzone #2
Opened cryosparc_P14_J268_011_volume_map.mrc 0 as #4.1, grid size 420,420,420,
pixel 0.65, shown at level 0.0232, step 1, values float32
Opened cryosparc_P14_J268_011_volume_map.mrc 1 as #4.2, grid size 420,420,420,
pixel 0.65, shown at level 0.0232, step 1, values float32
Opened cryosparc_P14_J268_011_volume_map.mrc 2 as #4.3, grid size 420,420,420,
pixel 0.65, shown at level 0.0232, step 1, values float32
> volume #4.3 level 0.02165
> surface dust #4.1 size 6.5
> surface dust #4.2 size 6.5
> surface dust #4.3 size 6.5
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> volume #4.2 level 0.03145
> volume #4.3 level 0.03659
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> hide #!4.2 models
> hide #!4.3 models
> show #!4.1 models
> ui mousemode right "map eraser"
> volume erase #4.1 center 125.1,98.73,141.79 radius 13.098
> volume erase #4.1 center 108.69,140.84,114.59 radius 13.098
> volume erase #4.1 center 112.27,138.44,134.77 radius 13.098
> ui mousemode right "translate selected models"
> show #!4.2 models
> show #!4.3 models
> volume #4.2 level 0.02541
> color #4.1 #5e5e5e81 models
> color #4.1 #5e5e5e93 models
> color #4.1 #5e5e5e9f models
> color #4.1 #d6d6d6ff models
> color #4.1 #ebebebff models
> color #4.1 darkgrey models
> color #4.1 #a9a9a983 models
> color #4.1 silver models
> color #4.1 #929292ff models
> color #4.1 #919191ff models
> color #4.1 #797979ff models
> color #4.1 #5e5e5eff models
> color #4.1 #5e5e5e8b models
> set bgColor white
> color #4.1 #424242ff models
> color #4.1 #5e5e5eff models
> color #4.1 #5e5e5e93 models
> lighting full
> lighting soft
> lighting simple
> lighting soft
> color #4.1 darkgrey models
> color #4.1 #919191ff models
> color #4.1 #919191ec models
> save /Users/petra/Desktop/G345A2.56.tif width 1088 height 850 supersample 4
> transparentBackground true
> save /Users/petra/Desktop/G345A2.56_Bottom.tif width 1088 height 850
> supersample 4 transparentBackground true
> volume #4.2 level 0.03324
> show #!3 models
> color #4.2 #c0864594 models
> ui mousemode right select
Drag select of 4.1 cryosparc_P14_J268_011_volume_map.mrc 0 , 4.2
cryosparc_P14_J268_011_volume_map.mrc 1 , 4.3
cryosparc_P14_J268_011_volume_map.mrc 2 , 65 atoms, 784 residues, 1
pseudobonds, 66 bonds
> ui mousemode right "translate selected models"
> select add #3
7916 atoms, 8084 bonds, 6 pseudobonds, 1001 residues, 9 models selected
> select subtract #3
6 models selected
> select add #4
7 models selected
> select subtract #4
Nothing selected
> select #3/E,A,B
4867 atoms, 4972 bonds, 6 pseudobonds, 609 residues, 3 models selected
> select #3/,A,B,D
Expected an objects specifier or a keyword
> select #3/,A,B,D
Expected an objects specifier or a keyword
> select add #3
7916 atoms, 8084 bonds, 6 pseudobonds, 1001 residues, 3 models selected
> select subtract #3
Nothing selected
> select #3/,A,B,D
Expected an objects specifier or a keyword
> select #3/A,B,D
6157 atoms, 6293 bonds, 6 pseudobonds, 774 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> ui mousemode right "map eraser"
> ui mousemode right "translate selected models"
> hide #!4.2 models
> show #!4.2 models
> hide #!4.3 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4 models
> show #!4 models
> ui mousemode right "map eraser"
Can only have one displayed volume when erasing
> select add #3
7916 atoms, 8084 bonds, 6 pseudobonds, 1001 residues, 3 models selected
> select subtract #3
Nothing selected
Can only have one displayed volume when erasing
> hide #!3 models
Can only have one displayed volume when erasing
> hide #!4.1 models
> volume erase #4.2 center 141.51,140.95,91.454 radius 20.338
> volume erase #4.2 center 133.72,132.85,103.75 radius 20.338
> volume erase #4.2 center 144.67,127.79,105.06 radius 20.338
> show #!4.1 models
Can only have one displayed volume when erasing
> hide #!4.2 models
> volume erase #4.1 center 127.81,160.19,132.25 radius 20.338
> volume erase #4.1 center 140.86,160.8,136.83 radius 20.338
> ui mousemode right translate
> show #!4.2 models
> show #!4.3 models
> hide #!4.3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> volume #4.1 level 0.02411
> select #3/E
Nothing selected
> open
> /Users/petra/Desktop/GiGet345_Krios_Phenix/3.44A/RealSpaceRefine_2/Get345_For344AMap_real_space_refined_002.pdb
Chain information for Get345_For344AMap_real_space_refined_002.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> select add #5
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 8196 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> color #5 #c08645ff
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select #5/A,B,D
6157 atoms, 6293 bonds, 6 pseudobonds, 774 residues, 3 models selected
> hide sel atoms
> hide sel cartoons
> select #5/E
345 atoms, 351 bonds, 43 residues, 1 model selected
> color sel #be1d3bff
> select add #5
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> select subtract #5
Nothing selected
> select add #5
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> select subtract #5
Nothing selected
> select add #5
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,-66.717,0,1,0,-48.191,0,0,1,20.778
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.99608,0.085066,-0.024433,-78.214,0.08255,-0.9925,-0.090126,307.35,-0.031917,0.087755,-0.99563,265.47
> view matrix models
> #5,0.99914,0.030228,0.028502,-75.645,0.032823,-0.99489,-0.095474,317.14,0.02547,0.096327,-0.99502,253.84
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.99914,0.030228,0.028502,-70.399,0.032823,-0.99489,-0.095474,338.81,0.02547,0.096327,-0.99502,267.33
> ui mousemode right translate
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.99914,0.030228,0.028502,-62.441,0.032823,-0.99489,-0.095474,317.25,0.02547,0.096327,-0.99502,292
> view matrix models
> #5,0.99914,0.030228,0.028502,-48.849,0.032823,-0.99489,-0.095474,314.53,0.02547,0.096327,-0.99502,292.7
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.99816,-0.03592,0.048859,-39.379,-0.031416,-0.99545,-0.090012,325.14,0.05187,0.088311,-0.99474,289.5
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.99816,-0.03592,0.048859,-36.582,-0.031416,-0.99545,-0.090012,330.38,0.05187,0.088311,-0.99474,285.18
> select subtract #5
Nothing selected
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #!3 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
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 Get345_For344AMap_real_space_refined_002.pdb, chain A (#5) with
Get345_For344AMap_real_space_refined_002.pdb, chain A (#3), sequence alignment
score = 1579.4
RMSD between 303 pruned atom pairs is 0.000 angstroms; (across all 303 pairs:
0.000)
> select #3/A,B,D
6157 atoms, 6293 bonds, 6 pseudobonds, 774 residues, 3 models selected
> hide sel atoms
> hide sel cartoons
> view matrix models
> #3,0.99816,-0.03592,0.048859,-47.63,-0.031416,-0.99545,-0.090012,329.7,0.05187,0.088311,-0.99474,281.05
> undo
> select add #3
7916 atoms, 8084 bonds, 6 pseudobonds, 1001 residues, 3 models selected
> view matrix models
> #3,0.99816,-0.03592,0.048859,-38.585,-0.031416,-0.99545,-0.090012,330.33,0.05187,0.088311,-0.99474,284.72
> undo
> select subtract #3
Nothing selected
> hide #!3 models
> hide #!4 models
> hide #!4.1 models
> hide #!4.2 models
> ui mousemode right select
> select #5/E:17
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!4 models
> hide #!4 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> select #5/E:16
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #5/E:15
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #5/E:14
26 atoms, 23 bonds, 3 residues, 1 model selected
> select add #5/E:13
31 atoms, 27 bonds, 4 residues, 1 model selected
> select add #5/E:12
37 atoms, 32 bonds, 5 residues, 1 model selected
> select add #5/E:11
45 atoms, 39 bonds, 6 residues, 1 model selected
> select add #5/E:9
56 atoms, 49 bonds, 7 residues, 1 model selected
> select add #5/E:10
64 atoms, 56 bonds, 8 residues, 1 model selected
> select add #5/E:8
73 atoms, 64 bonds, 9 residues, 1 model selected
> select add #5/E:7
81 atoms, 71 bonds, 10 residues, 1 model selected
> select add #5/E:6
93 atoms, 83 bonds, 11 residues, 1 model selected
> select add #5/E:5
102 atoms, 91 bonds, 12 residues, 1 model selected
> select add #5/E:4
113 atoms, 101 bonds, 13 residues, 1 model selected
> select add #5/E:3
120 atoms, 107 bonds, 14 residues, 1 model selected
> select add #5/E:2
128 atoms, 114 bonds, 15 residues, 1 model selected
> select add #5/E:1
136 atoms, 121 bonds, 16 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> surface dust #4.1 size 6.5
> show #!4.2 models
> show #!4.3 models
> hide #!4.3 models
Drag select of 4.2 cryosparc_P14_J268_011_volume_map.mrc 1 , 2 residues
> ui mousemode right select
> ui mousemode right translate
> select add #4
14 atoms, 2 residues, 8 models selected
> select subtract #4
14 atoms, 2 residues, 1 model selected
> select add #5
8125 atoms, 8298 bonds, 6 pseudobonds, 1028 residues, 3 models selected
> select subtract #5
Nothing selected
> volume #4.1 level 0.02579
> volume #4.1 level 0.02186
> volume #4.1 level 0.02897
> volume #4.1 level 0.02036
> volume #4.1 color #919191a5
> save /Users/petra/Desktop/G45.tif width 1088 height 850 supersample 4
> transparentBackground true
> save /Users/petra/Desktop/G45B.tif width 1088 height 850 supersample 4
> transparentBackground true
> save /Users/petra/Desktop/G45C.tif width 1088 height 850 supersample 4
> transparentBackground true
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> ui mousemode right "map eraser"
> volume erase #4.1 center 147.64,133.87,186.24 radius 8.0875
> volume erase #4.1 center 136.49,155.54,93.582 radius 8.0875
> volume erase #4.1 center 136.18,147.39,96.829 radius 8.0875
> volume erase #4.1 center 136,137.41,99.882 radius 8.0875
> volume erase #4.1 center 153.58,101,121.03 radius 8.0875
> volume erase #4.1 center 143.5,98.564,127.24 radius 8.0875
> volume erase #4.1 center 148.32,109.94,138.88 radius 8.0875
> volume erase #4.1 center 128.28,107.49,121.55 radius 8.0875
> volume erase #4.1 center 127.47,139.02,102.4 radius 8.0875
> show #!4.3 models
> show #!4.2 models
> hide #6 models
> hide #!4.3 models
> show #!5 models
> ui mousemode right "translate selected models"
> volume #4.1 color darkgrey
> volume #4.1 color #a9a9a96b
> volume #4.1 color silver
> volume #4.1 color #ebebeb
> volume #4.1 color #ebebeb93
> volume #4.1 color silver
> volume #4.1 color #c0c0c08c
> volume #4.1 color #797979
> volume #4.1 color #7979798e
> volume #4.1 color #79797977
> save /Users/petra/Desktop/45.tif width 1088 height 850 supersample 4
> transparentBackground true
> hide #!4.2 models
> hide #!4.1 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> select #5/A,B,D
6157 atoms, 6293 bonds, 6 pseudobonds, 774 residues, 3 models selected
> show sel atoms
> show sel cartoons
> hide #!5 models
> select add #5
8125 atoms, 8298 bonds, 6 pseudobonds, 1028 residues, 3 models selected
> close #5
> open
> /Users/petra/Desktop/GiGet345_Krios_Phenix/3.44A/RealSpaceRefine_2/Get345_For344AMap_real_space_refined_002.pdb
Chain information for Get345_For344AMap_real_space_refined_002.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> hide #!5 models
> show #!5 models
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 8196 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select #5/C,D
3049 atoms, 3112 bonds, 392 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #5/E
345 atoms, 351 bonds, 43 residues, 1 model selected
> hide sel cartoons
> view matrix models #5,1,0,0,12.615,0,1,0,6.4817,0,0,1,-3.253
> select add #5
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> select subtract #5
Nothing selected
> show #!2 models
> hide #!2 models
> select add #2
2 models selected
> select subtract #2
Nothing selected
> show #!1 models
> hide #!1 models
> show #!1 models
> select add #5
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> view matrix models #5,1,0,0,-48.85,0,1,0,-32.22,0,0,1,2.1119
> view matrix models #5,1,0,0,-39.715,0,1,0,-43.732,0,0,1,-43.54
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.94847,0.24647,-0.19914,293.56,-0.23962,-0.96912,-0.058174,356.06,-0.20733,-0.0074582,0.97824,-2.0325
> fitmap #5 inMap #1
Fit molecule Get345_For344AMap_real_space_refined_002.pdb (#5) to map
cryosparc_P14_J268_011_volume_map_sharp.mrc (#1) using 8261 atoms
average map value = 0.02748, steps = 248
shifted from previous position = 1.43
rotated from previous position = 15.2 degrees
atoms outside contour = 6575, contour level = 0.053637
Position of Get345_For344AMap_real_space_refined_002.pdb (#5) relative to
cryosparc_P14_J268_011_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99501491 0.09924115 -0.00982555 294.92748352
-0.09681729 -0.98491328 -0.14343035 349.79464057
-0.02391151 -0.14176405 0.98961165 -11.63082783
Axis 0.00847684 0.07165843 -0.99739321
Axis point 155.98331159 167.20436612 0.00000000
Rotation angle (degrees) 174.35955370
Shift along axis 39.16629409
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.99501,0.099241,-0.0098255,296.1,-0.096817,-0.98491,-0.14343,350.68,-0.023912,-0.14176,0.98961,-14.515
> fitmap #5 inMap #1
Fit molecule Get345_For344AMap_real_space_refined_002.pdb (#5) to map
cryosparc_P14_J268_011_volume_map_sharp.mrc (#1) using 8261 atoms
average map value = 0.08277, steps = 120
shifted from previous position = 2.71
rotated from previous position = 5.22 degrees
atoms outside contour = 3958, contour level = 0.053637
Position of Get345_For344AMap_real_space_refined_002.pdb (#5) relative to
cryosparc_P14_J268_011_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99956076 0.01741815 0.02397739 303.90776233
-0.02113321 -0.98612905 -0.16462960 343.29796952
0.02077725 -0.16506400 0.98606399 -18.08439602
Axis -0.01122886 0.08271987 -0.99650958
Axis point 153.70459615 169.42112914 0.00000000
Rotation angle (degrees) 178.89164722
Shift along axis 43.00629928
> select subtract #5
Nothing selected
> volume #1 level 0.114
> volume #1 color #b2b2b28d
> volume #1 level 0.1644
> ui mousemode right zoom
> volume #1 level 0.2068
> select #5/B
2427 atoms, 2480 bonds, 1 pseudobond, 303 residues, 2 models selected
> volume #1 color #d6d6d6
> volume #1 color silver
> volume #1 color #c0c0c09c
> color (#!5 & sel) dark gray
> color (#!5 & sel) dim gray
> color (#!5 & sel) #b3aea4ff
> select add #5
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> select subtract #5
Nothing selected
> ui mousemode right select
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> color sel byelement
> volume #1 level 0.1671
> select add #5
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> select subtract #5
Nothing selected
> select add #5/A:401@O1A
1 atom, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> ui tool show "Color Zone"
> color zone #2 near #3 distance 2.8
> color zone #2 near #3 distance 2.76
> color zone #2 near #3 distance 1.47
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 1.47
> color zone #2 near sel distance 1.41
> color zone #2 near sel distance 1.45
> volume splitbyzone #2
Opened cryosparc_P14_J268_011_volume_map.mrc 0 as #6.1, grid size 420,420,420,
pixel 0.65, shown at level 0.0232, step 1, values float32
Opened cryosparc_P14_J268_011_volume_map.mrc 1 as #6.2, grid size 420,420,420,
pixel 0.65, shown at level 0.0232, step 1, values float32
Opened cryosparc_P14_J268_011_volume_map.mrc 2 as #6.3, grid size 420,420,420,
pixel 0.65, shown at level 0.0232, step 1, values float32
Opened cryosparc_P14_J268_011_volume_map.mrc 3 as #6.4, grid size 420,420,420,
pixel 0.65, shown at level 0.0232, step 1, values float32
Opened cryosparc_P14_J268_011_volume_map.mrc 4 as #6.5, grid size 420,420,420,
pixel 0.65, shown at level 0.0232, step 1, values float32
> select add #5
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> select subtract #5
Nothing selected
> hide #!5 models
> hide #!6 models
> hide #!6.1 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> hide #!6.2 models
> hide #!6.3 models
> hide #!6.4 models
> hide #!6.5 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> hide #!3 models
> select add #5/A:401@O2B
1 atom, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color zone #1 near sel distance 3.9
> volume splitbyzone #1
Opened cryosparc_P14_J268_011_volume_map_sharp.mrc 0 as #7.1, grid size
420,420,420, pixel 0.65, shown at level 0.167, step 1, values float32
Opened cryosparc_P14_J268_011_volume_map_sharp.mrc 1 as #7.2, grid size
420,420,420, pixel 0.65, shown at level 0.167, step 1, values float32
Opened cryosparc_P14_J268_011_volume_map_sharp.mrc 2 as #7.3, grid size
420,420,420, pixel 0.65, shown at level 0.167, step 1, values float32
Opened cryosparc_P14_J268_011_volume_map_sharp.mrc 3 as #7.4, grid size
420,420,420, pixel 0.65, shown at level 0.167, step 1, values float32
Opened cryosparc_P14_J268_011_volume_map_sharp.mrc 4 as #7.5, grid size
420,420,420, pixel 0.65, shown at level 0.167, step 1, values float32
> hide #!4 models
> select add #5
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> select subtract #5
Nothing selected
> hide #!7 models
> show #!7 models
> hide #!7.1 models
> show #!7.1 models
> hide #!7.1 models
> hide #!7.2 models
> show #!7.2 models
> hide #!7.2 models
> show #!7.2 models
> hide #!7.3 models
> show #!7.3 models
> hide #!7.3 models
> show #!7.3 models
> hide #!7.4 models
> show #!7.4 models
> hide #!7.5 models
> show #!7.5 models
> hide #!7.5 models
> close #7
> hide #!5 models
> show #!5 models
> show #!1 models
> undo
> show #!1 models
> undo
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!6.3 models
> hide #!6.3 models
> show #!6.3 models
> show #!6.4 models
> close #6
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4.1 models
> show #!4.2 models
> hide #!4.2 models
> hide #!4.1 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> color #1 #d6d6d6ff models
> color #1 #ebebebff models
> color #1 white models
> color #1 #d6d6d6ff models
> color #1 silver models
> color #1 #d6d6d6ff models
> color #1 darkgrey models
> hide #!1 models
> show #!1 models
> color #1 #a9a9a98e models
> show #!5 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> color #5 #919191ff
> color #1 #009193ff models
> color #1 #531b93ff models
> color #1 silver models
> select add #5
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> color #5 #011993ff
> color zone #1 near sel distance 3.9
> color zone #1 near sel distance 3.86
> color zone #1 near sel distance 1.07
> select subtract #5
Nothing selected
> color #5 #00fdffff
> color #1 #d6d6d6ff models
> color #1 darkgrey models
> color #1 #a9a9a98b models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> color sel magenta
> color zone #1 near sel distance 1.07
> color zone #1 near sel distance 1.08
> color zone #1 near sel distance 1.62
> volume splitbyzone #1
Opened cryosparc_P14_J268_011_volume_map_sharp.mrc 0 as #6.1, grid size
420,420,420, pixel 0.65, shown at level 0.167, step 1, values float32
Opened cryosparc_P14_J268_011_volume_map_sharp.mrc 1 as #6.2, grid size
420,420,420, pixel 0.65, shown at level 0.167, step 1, values float32
> surface dust #6.1 size 6.5
> surface dust #6.2 size 6.5
> select add #5
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> select subtract #5
Nothing selected
> hide #!5 models
> hide #!6 models
> show #!6 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.1 models
> hide #!6 models
> show #!6 models
> show #!6.1 models
> hide #!6.1 models
> show #!1 models
> hide #!1 models
> hide #!6.2 models
> show #!6.2 models
> hide #!6.2 models
> show #!5 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> color sel byelement
> select add #5/A:61
36 atoms, 37 bonds, 2 residues, 1 model selected
> select #5/A,B
4867 atoms, 4972 bonds, 6 pseudobonds, 609 residues, 3 models selected
> color (#!5 & sel) dark gray
> select add #5
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> select subtract #5
Nothing selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
31 atoms, 33 bonds, 1 residue, 1 model selected
> color sel byelement
> select add #5
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> select subtract #5
Nothing selected
> show #!6.2 models
> volume #6.2 level 0.1326
> color #6.2 darkgrey models
> color #6.2 #531b93ff models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #6.2 style mesh
> color #6.2 #5e1eaaff models
> color #6.2 #5822aaff models
> color #6.2 #5422aaff models
> color #6.2 #4722aaff models
> color #6.2 #2b24aaff models
> color #6.2 #6770aaff models
> color #6.2 #5c35aaff models
> color #6.2 #5930aaff models
> color #6.2 #3b28aaff models
> color #6.2 #3215aaff models
> color #6.2 #2e0caaff models
> color #6.2 #412faaff models
> color #6.2 #4837aaff models
> color #6.2 #4a27aaff models
> color #6.2 #5833aaff models
> color #6.2 #634baaff models
> color #6.2 #6e61aaff models
> color #6.2 #513aaaff models
> color #6.2 #4425aaff models
Drag select of 3 residues
> select add #5
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> select subtract #5
Nothing selected
> ui mousemode right "translate selected models"
> ui mousemode right select
> select #5/A:501@MG
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> ui mousemode right translate
> save /Users/petra/Desktop/ATP1.tif width 1088 height 850 supersample 4
> transparentBackground true
> color #6.2 #3f229dff models
> color #6.2 #3b2094ff models
> select add #5
8261 atoms, 8435 bonds, 6 pseudobonds, 1044 residues, 3 models selected
> select subtract #5
Nothing selected
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!6.2 models
> show #!6.2 models
> color #6.2 #5239b1ff models
> color #6.2 #47329bff models
> color #6.2 #422e8fff models
> color #6.2 #3b2980ff models
> color #6.2 #271b56ff models
> color #6.2 #1d1540ff models
> color #6.2 #39277bff models
> color #6.2 #463197ff models
> color #6.2 #553bb7ff models
> color #6.2 #4c35a6ff models
> color #6.2 #432f91ff models
> save /Users/petra/Desktop/EMBO.cxs includeMaps true
> cootmode #6.2
Unknown command: cootmode #6.2
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6.1 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.1 models
> hide #!6.2 models
> show #!6.2 models
> hide #!6 models
> show #!6 models
> show #!6.1 models
> hide #!6.1 models
> cootmode #6
Unknown command: cootmode #6
> color #6.2 #005fffff models
> undo
> color #6.2 #225fffff models
> color #6.2 #4f5fffff models
> color #6.2 #4f00ffff models
> color #6.2 #4f08ffff models
> color #6.2 #4f08c1ff models
> color #6.2 #4f08a0ff models
> volume #6 style mesh level 0.8
> hide #!6.2 models
> show #!6.2 models
> show #!6.1 models
> hide #!6.1 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!6.1 models
> hide #!6.1 models
> volume #6.2 level 0.128
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #6.2 step 4
> volume #6.2 step 1
> volume #6.2 step 8
> volume #6.2 level -0.005278
> volume #6.2 step 1
> volume #6.2 level 0.1305
> undo
> volume #6.2 level 0.1331
> volume #6 level 0.5 style mesh
> volume #6.2 level 0.1723
> volume #6.2 level 0.132
> volume #6 divisions 80
Expected a keyword
> volume #6 meshLighting divisions 80
Invalid "meshLighting" argument: Expected true or false (or 1 or 0)
> volume #6 divisions 80 mesh
Expected a keyword
> volume #6 subdivideSurface true subdivisionLevels 1
> volume #6 subdivideSurface true subdivisionLevels 2
> volume #6 subdivideSurface true subdivisionLevels .5
Invalid "subdivisionLevels" argument: Expected an integer
> volume #6 subdivideSurface true subdivisionLevels 1
> volume #6.2 level 0.04486
> show #!6.1 models
> volume #6.2 level 0.1411
> color #6.2 #4f53a0ff models
> color #6.2 #4f5ea0ff models
> color #6.2 #4f12a0ff models
> color #6.2 #4f63a0ff models
> color #6.2 #0063a0ff models
> color #6.2 #5863a0ff models
> color #6.2 #4f63a0ff models
> color #6.2 #4f42a0ff models
> hide #!6.1 models
> show #!6.1 models
> hide #!6.1 models
> volume #6.1 level 0.2093
> hide #!6.1 models
> hide #!6 models
> show #!6 models
> hide #!6.2 models
> show #!6.2 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> open /Users/petra/Downloads/ScGet4_ScGet5/pred.model_idx_4.cif
pred.model_idx_4.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.model_idx_4.cif #7
---
Chain | Description
A B | protein-0-1
C D | protein-1-1
Color pred.model_idx_4.cif by residue attribute pLDDT_score
> hide #!5 models
> hide #!6 models
> hide #!6.2 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #7/A
1672 atoms, 1708 bonds, 212 residues, 1 model selected
> select #7/B
1672 atoms, 1708 bonds, 212 residues, 1 model selected
> select #7/C
2566 atoms, 2627 bonds, 312 residues, 1 model selected
> hide sel cartoons
> select #7/D
2566 atoms, 2627 bonds, 312 residues, 1 model selected
> hide sel cartoons
> select #7/A
1672 atoms, 1708 bonds, 212 residues, 1 model selected
> hide sel cartoons
> open
> /Users/petra/Downloads/fold_scget45_fl_22/fold_scget45_fl_22_model_4.cif
Chain information for fold_scget45_fl_22_model_4.cif #8
---
Chain | Description
A B | .
C D | .
> hide #7 models
> select add #7
8476 atoms, 8670 bonds, 1048 residues, 1 model selected
> select #7/B
1672 atoms, 1708 bonds, 212 residues, 1 model selected
> select add #7
8476 atoms, 8670 bonds, 1048 residues, 1 model selected
> select subtract #7
Nothing selected
> select #8/B
1673 atoms, 1709 bonds, 212 residues, 1 model selected
> select #8/C
2567 atoms, 2628 bonds, 312 residues, 1 model selected
> hide sel cartoons
> select #8/D
2567 atoms, 2628 bonds, 312 residues, 1 model selected
> hide sel cartoons
> open /Users/petra/Downloads/fold_scget45_fl/fold_scget45_fl_model_4.cif
Chain information for fold_scget45_fl_model_4.cif #9
---
Chain | Description
A | .
B | .
> hide #8 models
> select add #8
8480 atoms, 8674 bonds, 1048 residues, 1 model selected
> select subtract #8
Nothing selected
> hide #9 models
> show #9 models
> select #9/B
2567 atoms, 2628 bonds, 312 residues, 1 model selected
> hide sel cartoons
> select add #9
4240 atoms, 4337 bonds, 524 residues, 1 model selected
> select subtract #9
Nothing selected
> show #8 models
> hide #9 models
> show #7 models
> hide #8 models
> select add #7
8476 atoms, 8670 bonds, 1048 residues, 1 model selected
> select subtract #7
Nothing selected
> select #7/B
1672 atoms, 1708 bonds, 212 residues, 1 model selected
> select #7/A
1672 atoms, 1708 bonds, 212 residues, 1 model selected
> show sel cartoons
> select add #7
8476 atoms, 8670 bonds, 1048 residues, 1 model selected
> select subtract #7
Nothing selected
> lighting soft
> view
> ui tool show "Side View"
> view
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> select add #7
8476 atoms, 8670 bonds, 1048 residues, 1 model selected
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> select #7/C,D
5132 atoms, 5254 bonds, 624 residues, 1 model selected
> hide sel cartoons
> select add #7
8476 atoms, 8670 bonds, 1048 residues, 1 model selected
> select subtract #7
Nothing selected
> show #8 models
> hide #8 models
> hide #7 models
> show #8 models
> hide #8 models
> show #7 models
> ui mousemode right select
> select add #7/A:210
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
144 atoms, 145 bonds, 18 residues, 1 model selected
> select add #7/A:178
151 atoms, 152 bonds, 19 residues, 1 model selected
> select add #7/A:180
159 atoms, 159 bonds, 20 residues, 1 model selected
> select up
458 atoms, 468 bonds, 59 residues, 1 model selected
> select down
159 atoms, 159 bonds, 20 residues, 1 model selected
> select #7/A:188
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
93 atoms, 94 bonds, 11 residues, 1 model selected
> select add #7/A:201
101 atoms, 101 bonds, 12 residues, 1 model selected
> select up
237 atoms, 239 bonds, 29 residues, 1 model selected
> select add #7/A:190
248 atoms, 250 bonds, 30 residues, 1 model selected
> select add #7/A:191
257 atoms, 258 bonds, 31 residues, 1 model selected
> select add #7/A:192
265 atoms, 265 bonds, 32 residues, 1 model selected
> select add #7/A:193
273 atoms, 272 bonds, 33 residues, 1 model selected
> select add #7/A:212
282 atoms, 280 bonds, 34 residues, 1 model selected
> select add #7/B:209
288 atoms, 285 bonds, 35 residues, 1 model selected
> select up
426 atoms, 431 bonds, 52 residues, 1 model selected
> select add #7/B:193
434 atoms, 438 bonds, 53 residues, 1 model selected
> select add #7/B:192
442 atoms, 445 bonds, 54 residues, 1 model selected
> select add #7/B:191
451 atoms, 453 bonds, 55 residues, 1 model selected
> select add #7/B:190
462 atoms, 464 bonds, 56 residues, 1 model selected
> select add #7/B:185
470 atoms, 471 bonds, 57 residues, 1 model selected
> select up
555 atoms, 563 bonds, 67 residues, 1 model selected
> select add #7/B:178
562 atoms, 570 bonds, 68 residues, 1 model selected
> select add #7/B:177
569 atoms, 576 bonds, 69 residues, 1 model selected
> color sel dark gray
> select add #7/B:212
578 atoms, 584 bonds, 70 residues, 1 model selected
> color sel dark gray
> ui mousemode right translate
> ui mousemode right select
> select #7/B:58
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #7
8476 atoms, 8670 bonds, 1048 residues, 1 model selected
> select subtract #7
Nothing selected
Drag select of 464 residues
> color sel dim gray
> lighting soft
> lighting full
> lighting flat
> lighting full
> select clear
> select add #7/A:209
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #7/B:203
17 atoms, 15 bonds, 2 residues, 1 model selected
> select add #7/B:182
25 atoms, 22 bonds, 3 residues, 1 model selected
> select add #7/A:187
34 atoms, 30 bonds, 4 residues, 1 model selected
> select up
474 atoms, 478 bonds, 58 residues, 1 model selected
> select add #7/A:212
483 atoms, 486 bonds, 59 residues, 1 model selected
> select add #7/B:212
492 atoms, 494 bonds, 60 residues, 1 model selected
> select add #7/A:190
503 atoms, 505 bonds, 61 residues, 1 model selected
> select add #7/A:191
512 atoms, 513 bonds, 62 residues, 1 model selected
> select add #7/A:192
520 atoms, 520 bonds, 63 residues, 1 model selected
> select add #7/A:193
528 atoms, 527 bonds, 64 residues, 1 model selected
> select add #7/A:178
535 atoms, 534 bonds, 65 residues, 1 model selected
> select add #7/A:177
542 atoms, 540 bonds, 66 residues, 1 model selected
> select add #7/B:192
550 atoms, 547 bonds, 67 residues, 1 model selected
> select add #7/B:190
561 atoms, 558 bonds, 68 residues, 1 model selected
> select add #7/B:191
570 atoms, 566 bonds, 69 residues, 1 model selected
> select add #7/B:193
578 atoms, 573 bonds, 70 residues, 1 model selected
> color sel #009193ff
> color sel #005493ff
> color sel #531b93ff
> color sel #942193ff
> color sel #009051ff
> color sel #4f8f00ff
> color sel #945200ff
> color sel #941100ff
> color sel #ff2600ff
> color sel #fffb00ff
> color sel #8efa00ff
> color sel #00fa92ff
> color sel #0433ffff
> color sel #ff40ffff
> color sel #ff2f92ff
> color sel #73fcd6ff
> color sel #fffc79ff
> color sel #ffd479ff
> color sel #ff7e79ff
> color sel #ff40ffff
> color sel #00fdffff
> color sel #0433ffff
> color sel #ff40ffff
> color sel #942192ff
> color sel #ff2600ff
> color sel #fffb00ff
> color sel #ffffffff
> color sel #aa7942ff
> color sel #0433ffff
> color sel #000000ff
> color sel #942192ff
> color sel #fffb00ff
> color sel #ff2600ff
> color sel #ff9300ff
> color sel #ff2600ff
> color sel #ff40ffff
> color sel #00fdffff
> color sel #0433ffff
> color sel #000000ff
> color sel #1a1a1aff
> color sel #ff453aff
> color sel #32d74bff
> color sel #0a84ffff
> color sel #ff453aff
> color sel #bf5af2ff
> color sel #6ac4dcff
> color sel #5e5ce6ff
> color sel #63e6e2ff
> color sel #5ac8f5ff
> color sel #419cffff
> color sel #ffffff3f
> color sel #419cffff
> color sel #98989dff
> color sel #5ac8f5ff
> color sel #63e6e2ff
> color sel #73fdffff
> color sel #ff2f92ff
> color sel #ffd479ff
> color sel #fffc79ff
> color sel #73fa79ff
> color sel #73fcd6ff
> color sel #73fdffff
> color sel #76d6ffff
> color sel #7a81ffff
> color sel #d783ffff
> color sel #78b1c1ff
> color sel #3f5196ff
> color sel #79a0d1ff
> color sel #c3d8bdff
> color sel #ff6800ff
> color sel #be1d3bff
> color sel #365053ff
> color sel #ff8340ff
> color sel #b2a788ff
> color sel #c08645ff
> color sel #6d2d39ff
> color sel #86799dff
> color sel #fe6d7fff
> color sel #00fdffff
> color sel #00fa92ff
> color sel #00fdffff
> color sel #0096ffff
> color sel #0433ffff
> color sel #ff40ffff
> color sel #ff7e79ff
Drag select of 109 residues
> select subtract #7/B:172
775 atoms, 100 residues, 1 model selected
> select subtract #7/B:173
766 atoms, 99 residues, 1 model selected
> select subtract #7/B:171
759 atoms, 98 residues, 1 model selected
> select subtract #7/B:169
752 atoms, 97 residues, 1 model selected
> select subtract #7/B:170
747 atoms, 96 residues, 1 model selected
> color sel #00fdffff
> color sel #00fa92ff
> color sel #fffb00ff
> color sel #8efa00ff
> color sel #00f900ff
> color sel #942193ff
> color sel #531b93ff
> color sel #942193ff
> color sel #941751ff
> color sel #ff2600ff
> color sel #011993ff
> color sel #005493ff
> color sel #009193ff
> color sel #008f00ff
> color sel #4f8f00ff
> color sel #009193ff
> color sel #009051ff
> color sel #009193ff
Drag select of 105 residues
> color sel #011993ff
> color sel #009193ff
> select add #7/B:4
760 atoms, 5 bonds, 98 residues, 1 model selected
> select add #7/B:1
768 atoms, 12 bonds, 99 residues, 1 model selected
> select add #7
8476 atoms, 8670 bonds, 1048 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #7/A:12
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #7/B:14
17 atoms, 16 bonds, 2 residues, 1 model selected
> select up
214 atoms, 220 bonds, 26 residues, 1 model selected
> select add #7/A:22
222 atoms, 227 bonds, 27 residues, 1 model selected
> select add #7/A:23
229 atoms, 233 bonds, 28 residues, 1 model selected
> select add #7/A:25
236 atoms, 240 bonds, 29 residues, 1 model selected
> select add #7/A:26
245 atoms, 248 bonds, 30 residues, 1 model selected
> select add #7/B:7
249 atoms, 251 bonds, 31 residues, 1 model selected
> select add #7/B:6
255 atoms, 256 bonds, 32 residues, 1 model selected
> select add #7/B:4
261 atoms, 261 bonds, 33 residues, 1 model selected
> select add #7/A:5
266 atoms, 265 bonds, 34 residues, 1 model selected
> select up
372 atoms, 381 bonds, 48 residues, 1 model selected
> select add #7/A:7
376 atoms, 384 bonds, 49 residues, 1 model selected
> select subtract #7/A:8
369 atoms, 376 bonds, 48 residues, 1 model selected
> select add #7/A:6
375 atoms, 381 bonds, 49 residues, 1 model selected
> select add #7/A:1
383 atoms, 388 bonds, 50 residues, 1 model selected
> select add #7/A:8
390 atoms, 395 bonds, 51 residues, 1 model selected
> select add #7/B:23
397 atoms, 401 bonds, 52 residues, 1 model selected
> select add #7/B:24
406 atoms, 409 bonds, 53 residues, 1 model selected
> select add #7/B:22
414 atoms, 416 bonds, 54 residues, 1 model selected
> select add #7/B:1
422 atoms, 423 bonds, 55 residues, 1 model selected
> select add #7/B:2
428 atoms, 428 bonds, 56 residues, 1 model selected
> select subtract #7/B:3
421 atoms, 421 bonds, 55 residues, 1 model selected
> select subtract #7/B:5
416 atoms, 415 bonds, 54 residues, 1 model selected
> select add #7/B:5
421 atoms, 419 bonds, 55 residues, 1 model selected
> select add #7/A:37
429 atoms, 426 bonds, 56 residues, 1 model selected
> select add #7/A:35
437 atoms, 433 bonds, 57 residues, 1 model selected
> select up
547 atoms, 561 bonds, 71 residues, 1 model selected
> select add #7/B:35
555 atoms, 568 bonds, 72 residues, 1 model selected
> select up
572 atoms, 586 bonds, 74 residues, 1 model selected
> color sel #008f00ff
> color sel #929000ff
> color sel #945200ff
> color sel #941100ff
> color sel #945200ff
> color sel #008f00ff
> color sel #009193ff
> color sel #005493ff
> select add #7
8476 atoms, 8670 bonds, 1048 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #7/A:5
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
18 atoms, 17 bonds, 3 residues, 1 model selected
> select up
1672 atoms, 1708 bonds, 212 residues, 1 model selected
> select down
18 atoms, 17 bonds, 3 residues, 1 model selected
> select add #7/A:1
26 atoms, 24 bonds, 4 residues, 1 model selected
> select add #7/A:2
32 atoms, 29 bonds, 5 residues, 1 model selected
> select add #7/A:7
36 atoms, 32 bonds, 6 residues, 1 model selected
> select add #7/A:6
42 atoms, 37 bonds, 7 residues, 1 model selected
> select add #7/B:6
48 atoms, 42 bonds, 8 residues, 1 model selected
> select add #7/B:3
55 atoms, 48 bonds, 9 residues, 1 model selected
> select add #7/B:5
60 atoms, 52 bonds, 10 residues, 1 model selected
> select add #7/B:4
66 atoms, 57 bonds, 11 residues, 1 model selected
> select add #7/B:1
74 atoms, 64 bonds, 12 residues, 1 model selected
> select add #7/B:2
80 atoms, 69 bonds, 13 residues, 1 model selected
> select add #7/B:7
84 atoms, 72 bonds, 14 residues, 1 model selected
> hide sel cartoons
> select add #7/B:178
91 atoms, 79 bonds, 15 residues, 1 model selected
> select add #7/B:177
98 atoms, 85 bonds, 16 residues, 1 model selected
> color sel #feaaa3ff
> select add #7
8476 atoms, 8670 bonds, 1048 residues, 1 model selected
> select subtract #7
Nothing selected
Drag select of 9 residues
> select add #7
8476 atoms, 8670 bonds, 1048 residues, 1 model selected
> select subtract #7
Nothing selected
> ui mousemode right translate
> ui mousemode right select
> select add #7/A:170
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #7/A:171
12 atoms, 11 bonds, 2 residues, 1 model selected
> select add #7/A:172
19 atoms, 18 bonds, 3 residues, 1 model selected
> select add #7/A:173
28 atoms, 26 bonds, 4 residues, 1 model selected
> select add #7/A:175
36 atoms, 33 bonds, 5 residues, 1 model selected
> select add #7/A:174
45 atoms, 41 bonds, 6 residues, 1 model selected
> select add #7/A:196
50 atoms, 45 bonds, 7 residues, 1 model selected
> select add #7/B:176
57 atoms, 51 bonds, 8 residues, 1 model selected
> select subtract #7/A:196
52 atoms, 47 bonds, 7 residues, 1 model selected
> select add #7/B:175
60 atoms, 54 bonds, 8 residues, 1 model selected
> select add #7/B:173
69 atoms, 62 bonds, 9 residues, 1 model selected
> select add #7/B:174
78 atoms, 70 bonds, 10 residues, 1 model selected
> select add #7/B:172
85 atoms, 77 bonds, 11 residues, 1 model selected
> select add #7/B:171
92 atoms, 84 bonds, 12 residues, 1 model selected
> select add #7/B:169
99 atoms, 91 bonds, 13 residues, 1 model selected
> select add #7/B:170
104 atoms, 95 bonds, 14 residues, 1 model selected
> color sel #5e5e5eff
> color sel #797979ff
> color sel #919191ff
> color sel #c0c0c0ff
> color sel #a9a9a9ff
> color sel #424242ff
> color sel #7d7d7dff
> select add #7
8476 atoms, 8670 bonds, 1048 residues, 1 model selected
> select subtract #7
Nothing selected
> save /Users/petra/Desktop/scg45.tif width 875 height 670 supersample 4
> transparentBackground true
Drag select of 3 residues
> select add #7
8476 atoms, 8670 bonds, 1048 residues, 1 model selected
> select subtract #7
Nothing selected
> ui mousemode right translate
> save /Users/petra/Desktop/scg45.tif width 875 height 670 supersample 4
> transparentBackground true
> open
> /Users/petra/Downloads/prediction_GiGet5_GiGet5_a0e96/rank_2_model_4_ptm_seed_0_unrelaxed.pdb
Chain information for rank_2_model_4_ptm_seed_0_unrelaxed.pdb #10
---
Chain | Description
A B | No description available
> hide #7 models
> select add #10
2336 atoms, 2374 bonds, 294 residues, 1 model selected
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> ui mousemode right select
> select subtract #10/B:120
2329 atoms, 2366 bonds, 293 residues, 1 model selected
> select up
2336 atoms, 2374 bonds, 294 residues, 1 model selected
> select subtract #10/A:125
2327 atoms, 2364 bonds, 293 residues, 1 model selected
> select up
2336 atoms, 2374 bonds, 294 residues, 1 model selected
> select subtract #10
Nothing selected
> select add #10/A:125
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
115 atoms, 114 bonds, 14 residues, 1 model selected
> select add #10/A:128
122 atoms, 120 bonds, 15 residues, 1 model selected
> select up
136 atoms, 135 bonds, 17 residues, 1 model selected
> select add #10/B:118
141 atoms, 139 bonds, 18 residues, 1 model selected
> select up
251 atoms, 249 bonds, 31 residues, 1 model selected
> select add #10/B:129
256 atoms, 253 bonds, 32 residues, 1 model selected
> select up
272 atoms, 270 bonds, 34 residues, 1 model selected
> show sel target ab
> hide sel atoms
> show sel atoms
> hide sel atoms
> select helix
22815 atoms, 23043 bonds, 2795 residues, 6 models selected
> select #10/A:141
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #10/A:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/A:127
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #10/A:129
13 atoms, 11 bonds, 2 residues, 1 model selected
> select up
136 atoms, 135 bonds, 17 residues, 1 model selected
> select add #10/B:126
147 atoms, 145 bonds, 18 residues, 1 model selected
> select add #10/B:129
152 atoms, 149 bonds, 19 residues, 1 model selected
> select up
272 atoms, 270 bonds, 34 residues, 1 model selected
> select coil
14134 atoms, 14196 bonds, 4 pseudobonds, 1840 residues, 8 models selected
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
Drag select of 10 residues
> select #10/A:123
9 atoms, 8 bonds, 1 residue, 1 model selected
> dssp
> select add #10/B:125
18 atoms, 16 bonds, 2 residues, 1 model selected
> select add #10/A:129
23 atoms, 20 bonds, 3 residues, 1 model selected
> select add #10/B:146
34 atoms, 31 bonds, 4 residues, 1 model selected
> select add #10/B:128
41 atoms, 37 bonds, 5 residues, 1 model selected
> select subtract #10/B:146
30 atoms, 26 bonds, 4 residues, 1 model selected
> select up
272 atoms, 270 bonds, 34 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ss_type 1
Assigning ss_type attribute to 34 items
> setattr sel r ss_type 0
Assigning ss_type attribute to 34 items
> setattr sel r ss_type 1
Assigning ss_type attribute to 34 items
> setattr sel r ss_type 0
Assigning ss_type attribute to 34 items
> setattr sel r ss_type 1
Assigning ss_type attribute to 34 items
> setattr sel r ss_type 2
Assigning ss_type attribute to 34 items
> setattr sel r ss_type 1
Assigning ss_type attribute to 34 items
Cannot increment value
> ui tool show "Selection Inspector"
> size sel ballScale 0.26
Changed 1 ball scales
> size sel ballScale 0.27
Changed 1 ball scales
> size sel ballScale 0.28
Changed 1 ball scales
> size sel ballScale 0.29
Changed 1 ball scales
> size sel ballScale 0.28
Changed 1 ball scales
> size sel ballScale 0.27
Changed 1 ball scales
> size sel ballScale 0.26
Changed 1 ball scales
> setattr sel structures autochain false
Assigning autochain attribute to 1 item
> show sel atoms
> hide sel atoms
> style sel ball
Changed 272 atom styles
> style sel sphere
Changed 272 atom styles
> style sel stick
Changed 272 atom styles
> setattr sel r thin_rings false
Assigning thin_rings attribute to 34 items
> setattr sel r thin_rings true
Assigning thin_rings attribute to 34 items
> setattr sel r ss_type 0
Assigning ss_type attribute to 34 items
> setattr sel r ss_type 0
Assigning ss_type attribute to 34 items
> setattr sel r ss_type 1
Assigning ss_type attribute to 34 items
Cannot increment value
> dssp
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select add #10
2336 atoms, 2374 bonds, 294 residues, 1 model selected
> select subtract #10
Nothing selected
> show #8 models
> hide #8 models
> show #9 models
> hide #9 models
> show #7 models
> hide #10 models
> hide #7 models
> show #7 models
> select #7/C,D
5132 atoms, 5254 bonds, 624 residues, 1 model selected
> hide sel cartoons
> select add #7
8476 atoms, 8670 bonds, 1048 residues, 1 model selected
> select subtract #7
Nothing selected
> ui mousemode right translate
> ui mousemode right select
> select add #7/A:4
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #7/A:5
11 atoms, 9 bonds, 2 residues, 1 model selected
> select add #7/A:2
17 atoms, 14 bonds, 3 residues, 1 model selected
> select add #7/A:1
25 atoms, 21 bonds, 4 residues, 1 model selected
> select add #7/A:3
32 atoms, 27 bonds, 5 residues, 1 model selected
> select add #7/A:6
38 atoms, 32 bonds, 6 residues, 1 model selected
> select add #7/A:7
42 atoms, 35 bonds, 7 residues, 1 model selected
> select add #7/B:5
47 atoms, 39 bonds, 8 residues, 1 model selected
> select add #7/B:1
55 atoms, 46 bonds, 9 residues, 1 model selected
> select add #7/B:2
61 atoms, 51 bonds, 10 residues, 1 model selected
> select add #7/B:4
67 atoms, 56 bonds, 11 residues, 1 model selected
> select add #7/B:3
74 atoms, 62 bonds, 12 residues, 1 model selected
> select add #7/B:6
80 atoms, 67 bonds, 13 residues, 1 model selected
> select add #7/B:7
84 atoms, 70 bonds, 14 residues, 1 model selected
> color sel #043660ff
> select add #7
8476 atoms, 8670 bonds, 1048 residues, 1 model selected
> select subtract #7
Nothing selected
> save /Users/petra/Desktop/455sc.tif width 875 height 670 supersample 4
> transparentBackground true
> hide #7 models
> show #10 models
> hide #10 models
> show #10 models
Drag select of 2 residues
> ui mousemode right translate
> select add #10
2336 atoms, 2374 bonds, 294 residues, 1 model selected
> select subtract #10
Nothing selected
> open
> /Users/petra/Downloads/prediction_GiGet5_GiGet5_a0e96/rank_1_model_2_ptm_seed_0_unrelaxed.pdb
Chain information for rank_1_model_2_ptm_seed_0_unrelaxed.pdb #11
---
Chain | Description
A B | No description available
> hide #10 models
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> hide #11 models
> open
> /Users/petra/Downloads/prediction_GiGet5_GiGet5_a0e96/rank_5_model_5_ptm_seed_0_unrelaxed.pdb
Chain information for rank_5_model_5_ptm_seed_0_unrelaxed.pdb #12
---
Chain | Description
A B | No description available
> hide #12 models
> close #12
> show #11 models
> close #11
> show #10 models
> select #10/A
1168 atoms, 1187 bonds, 147 residues, 1 model selected
> color sel gray
> cd ../Documents
Current working directory is: /Users/petra/Documents
> runscript colormaps_viridis.py
New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`
Default colormap for `rainbow` set to 'turbo'
To unpatch, run `runscript viridis_colormaps.py --reset_defaults`
> rainbow #10/B palette viridis
> select add #10
2336 atoms, 2374 bonds, 294 residues, 1 model selected
> select subtract #10
Nothing selected
> save /Users/petra/Desktop/55gi.tif width 875 height 670 supersample 4
> transparentBackground true
> hide #10 models
> open /Users/petra/Downloads/cryosparc_P705_J120_012_volume_map.mrc
Opened cryosparc_P705_J120_012_volume_map.mrc as #11, grid size 200,200,200,
pixel 1.5, shown at level 0.0394, step 1, values float32
> surface dust #11 size 15
> volume #11 level 0.1373
> volume #11 level 0.2155
> volume #11 level 0.3634
> open /Users/petra/Downloads/cryosparc_P705_J120_012_volume_map_sharp.mrc
Opened cryosparc_P705_J120_012_volume_map_sharp.mrc as #12, grid size
200,200,200, pixel 1.5, shown at level 0.0541, step 1, values float32
> surface dust #11 size 15
> surface dust #12 size 15
> volume #12 level 0.2503
> hide #!11 models
> volume #12 level 0.4393
> volume #12 level 0.6646
> volume #12 level 0.5774
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!6.1 models
> hide #!6.1 models
> show #!3 models
> hide #!3 models
> volume #12 level 0.1341
> hide #!12 models
> open /Users/petra/Downloads/cryosparc_P14_J275_012_volume_map_sharp.mrc
Opened cryosparc_P14_J275_012_volume_map_sharp.mrc as #13, grid size
320,320,320, pixel 0.853, shown at level 0.0285, step 2, values float32
> surface dust #13 size 8.53
> volume #13 step 1
> volume #13 level 0.1596
> volume #13 level 0.1249
> volume #13 level 0.1442
> volume #13 level 0.2869
> volume #13 level 0.1288
> volume #13 level 0.03238
> volume #13 level 0.2329
> open /Users/petra/Downloads/cryosparc_P14_J268_011_volume_map_sharp.mrc
Opened cryosparc_P14_J268_011_volume_map_sharp.mrc as #14, grid size
420,420,420, pixel 0.65, shown at level 0.0111, step 2, values float32
> surface dust #13 size 8.53
> surface dust #14 size 6.5
> hide #!13 models
> volume #14 step 1
> volume #14 level 0.02058
> volume #14 level 0.05039
> volume #14 level 0.07206
> volume gaussian #14 sDev 2
Opened cryosparc_P14_J268_011_volume_map_sharp.mrc gaussian as #15, grid size
420,420,420, pixel 0.65, shown at step 1, values float32
> volume #14 level 0.03684
> volume #14 level 0.04497
> volume #13 color #cccc9994
> volume #13 color #cccc9980
> volume #15 color #ffffb293
> volume #15 level 0.007784
> volume #14 level 0.03277
> volume #14 level 0.07071
> volume #15 level 0.01202
> volume #14 level 0.05445
> volume #15 level 0.01003
> ui tool show "Segment Map"
Segmenting cryosparc_P14_J268_011_volume_map_sharp.mrc gaussian, density
threshold 0.010034
Only showing 60 of 68 regions.
Showing 60 of 68 region surfaces
237 watershed regions, grouped to 68 regions
Showing cryosparc_P14_J268_011_volume_map_sharp gaussian.seg - 68 regions, 60
surfaces
> ui mousemode right select
Drag select of 357, 33582 of 44336 triangles, 328, 20590 of 33400 triangles,
353, 69 of 27844 triangles, 298, 20265 of 29640 triangles, 347, 13570 of 27408
triangles, 312, 23048 of 31028 triangles, 350, 25745 of 26620 triangles, 333,
24989 of 25176 triangles, 280, 356, 19338 of 24772 triangles, 346, 21669 of
22100 triangles, 360, 22647 of 23088 triangles, 362, 334, 21422 of 23492
triangles, 284, 12462 of 20628 triangles, 261, 19330 of 19532 triangles, 348,
20235 of 20596 triangles, 349, 12883 of 19992 triangles, 286, 2767 of 19448
triangles, 355, 12681 of 18452 triangles, 340, 6493 of 19140 triangles, 301,
17575 of 19008 triangles, 341, 293, 10754 of 15496 triangles, 332, 307, 12237
of 14872 triangles, 297, 13398 of 13568 triangles, 281, 4908 of 15056
triangles, 305, 7378 of 13488 triangles, 302, 306, 7983 of 14892 triangles,
152, 11757 of 14420 triangles, 253, 313, 9252 of 12728 triangles, 156, 9000 of
12560 triangles, 262, 3269 of 12368 triangles, 315, 1843 of 11992 triangles,
288, 14 cryosparc_P14_J268_011_volume_map_sharp.mrc , 15
cryosparc_P14_J268_011_volume_map_sharp.mrc gaussian
> select #16.5
1 model selected
Segmenting cryosparc_P14_J268_011_volume_map_sharp.mrc gaussian, density
threshold 0.010034
Only showing 60 of 68 regions.
Showing 60 of 68 region surfaces
237 watershed regions, grouped to 68 regions
Showing cryosparc_P14_J268_011_volume_map_sharp gaussian.seg - 68 regions, 60
surfaces
> select #16.5
1 model selected
> select add #16.53
2 models selected
> select add #16.33
3 models selected
> select add #16.3
4 models selected
> select add #16.30
5 models selected
> select add #16.1
6 models selected
> select subtract #16.1
5 models selected
> select add #16.1
6 models selected
> select add #16.55
7 models selected
> select add #16.37
8 models selected
> select add #16.27
9 models selected
> select add #16.50
10 models selected
> select add #16.23
11 models selected
> select add #16.36
12 models selected
> select add #16.58
13 models selected
> select add #16.10
14 models selected
> select add #16.8
15 models selected
> select add #16.39
16 models selected
> select add #16.22
17 models selected
> select add #16.38
18 models selected
> select add #16.16
21 models selected
> select add #16.14
22 models selected
> select add #16.35
23 models selected
> select add #16.57
24 models selected
> select #16.5
1 model selected
> select #15
2 models selected
> hide #!14 models
> hide #!15 models
> show #!15 models
> select subtract #15
Nothing selected
> hide #!6 models
> show #!6 models
> select #15
2 models selected
> hide #!16 models
> hide #!15 models
> show #!16 models
> hide #!16 models
> select subtract #15
Nothing selected
> show #!16 models
> close #16
> show #!15 models
Segmenting cryosparc_P14_J268_011_volume_map_sharp.mrc gaussian, density
threshold 0.010034
Only showing 60 of 68 regions.
Showing 60 of 68 region surfaces
237 watershed regions, grouped to 68 regions
Showing cryosparc_P14_J268_011_volume_map_sharp gaussian.seg - 68 regions, 60
surfaces
> hide #!15 models
> hide #!16 models
> select add #15
2 models selected
> select subtract #15
Nothing selected
> show #!15 models
Drag select of 15 cryosparc_P14_J268_011_volume_map_sharp.mrc gaussian
> select subtract #15
Nothing selected
> show #!16 models
> hide #!15 models
> volume #15 level 0.009105
> volume #15 level 0.01061
> hide #!15 models
> volume #15 level 0.01352
> close #16
> close #15
> show #!14 models
Drag select of 14 cryosparc_P14_J268_011_volume_map_sharp.mrc
> select subtract #14
Nothing selected
> ui mousemode right select
> ui mousemode right translate
> volume #14 level 0.03186
> volume #14 level 0.05207
> volume #14 level 0.03781
> volume #14 level 0.02441
> open /Users/petra/Downloads/cryosparc_P10_J333_010_volume_map_sharp(1).mrc
Opened cryosparc_P10_J333_010_volume_map_sharp(1).mrc as #15, grid size
420,420,420, pixel 0.832, shown at level 0.00759, step 2, values float32
> surface dust #14 size 6.5
> surface dust #15 size 8.32
> hide #!14 models
> volume #15 step 1
> volume #15 level 0.03931
> volume #15 level 0.06627
> volume #15 level 0.1043
> volume #15 level 0.07737
> volume #15 level 0.05675
> close #15
> show #!14 models
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
> graphics silhouettes true width 1
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/petra/Downloads/cryosparc_P705_J122_011_volume_map.mrc
Opened cryosparc_P705_J122_011_volume_map.mrc as #1, grid size 360,360,360,
pixel 0.832, shown at level 0.00755, step 2, values float32
OpenGL version: 4.1 INTEL-23.0.21
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,3
Processor Name: Quad-Core Intel Core i5
Processor Speed: 1.4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 2069.0.0.0.0 (iBridge: 22.16.10353.0.0,0)
OS Loader Version: 582~1023
Software:
System Software Overview:
System Version: macOS 15.0 (24A335)
Kernel Version: Darwin 24.0.0
Time since boot: 4 days, 15 hours, 44 minutes
Graphics/Displays:
Intel Iris Plus Graphics 645:
Chipset Model: Intel Iris Plus Graphics 645
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea6
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
C27F398:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: HTQHA00700
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: DVI or HDMI
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 13 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 13 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Mac Qt 6.6 crash in _NSViewHierarchyDidChangeBackingProperties connecting or disconnecting display or waking from sleep.