![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 14 months ago
Closed 14 months ago
#15842 closed defect (nonchimerax)
Graphics crash, macOS 14.6.1, Intel Iris Plus Graphics
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.6.1-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00007ff854e1ddc0 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2772 in draw_elements
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1749 in draw
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 852 in _draw_geometry
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 787 in draw_self
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 780 in draw
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1567 in _draw_multiple
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1554 in draw_opaque
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 258 in _draw_scene
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 288 in render
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 113 in _redraw
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 100 in draw_new_frame
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.dssp._dssp, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw (total: 65)
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{
"uptime" : 4400,
"procRole" : "Background",
"version" : 2,
"userID" : 308582931,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"coalitionID" : 622,
"osVersion" : {
"train" : "macOS 14.6.1",
"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2024-08-29 14:57:23.4543 +0100",
"codeSigningMonitor" : 0,
"incident" : "517CCF1F-924F-4B5D-8ADF-FD15442450E8",
"pid" : 1048,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-08-29 13:44:41.5199 +0100",
"procStartAbsTime" : 38915539867,
"procExitAbsTime" : 4400855506579,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"5EF364FD-AD51-5765-AF50-22908BA5F9FF","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "EA0F72F8-F30B-35B0-0742-8DFF759A31C0",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bridgeVersion" : {"build":"21P6074","train":"8.6"},
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"termination" : {"flags":0,"code":6,"namespace":"SIGNAL","indicator":"Abort trap: 6","byProc":"ChimeraX","byPid":1048},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000002\n"],
"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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===== Log before crash start =====
Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/butryna/Desktop/Fig5/Fig5_ATPase.cxs
Opened vopmax_A_EMR.mrc as #5, grid size 440,440,440, pixel 0.95, shown at
level 0.21, step 2, values float32
Opened Unoccupied.mrc 0 as #1.1, grid size 440,440,440, pixel 0.95, shown at
level 2.04, step 1, values float32
Opened Orc1.mrc 1 as #1.2, grid size 440,440,440, pixel 0.95, shown at level
2.04, step 1, values float32
Opened Orc6.mrc 2 as #1.3, grid size 440,440,440, pixel 0.95, shown at level
2.04, step 1, values float32
Opened Lagging.mrc 3 as #1.4, grid size 440,440,440, pixel 0.95, shown at
level 2.04, step 1, values float32
Opened Leading.mrc 4 as #1.5, grid size 440,440,440, pixel 0.95, shown at
level 2.04, step 1, values float32
Opened Orc2.mrc 5 as #1.6, grid size 440,440,440, pixel 0.95, shown at level
2.04, step 1, values float32
Opened Mcm4.mrc 6 as #1.7, grid size 440,440,440, pixel 0.95, shown at level
2.04, step 1, values float32
Opened Mcm5.mrc 7 as #1.8, grid size 440,440,440, pixel 0.95, shown at level
2.04, step 1, values float32
Opened Orc4.mrc 8 as #1.9, grid size 440,440,440, pixel 0.95, shown at level
2.04, step 1, values float32
Opened Orc3.mrc 9 as #1.10, grid size 440,440,440, pixel 0.95, shown at level
2.04, step 1, values float32
Opened vopmax_A_EMR.mrc 10 as #1.11, grid size 440,440,440, pixel 0.95, shown
at level 2.04, step 1, values float32
Opened Cdt1.mrc 11 as #1.12, grid size 440,440,440, pixel 0.95, shown at level
2.04, step 1, values float32
Opened Mcm7.mrc 12 as #1.13, grid size 440,440,440, pixel 0.95, shown at level
2.04, step 1, values float32
Opened Mcm2.mrc 13 as #1.14, grid size 440,440,440, pixel 0.95, shown at level
2.04, step 1, values float32
Opened Mcm3.mrc 14 as #1.15, grid size 440,440,440, pixel 0.95, shown at level
2.04, step 1, values float32
Opened Orc5.mrc 15 as #1.16, grid size 440,440,440, pixel 0.95, shown at level
2.04, step 1, values float32
opened ChimeraX session
> open
> /Users/butryna/Documents/Phenix/krios_5RA/RealSpaceRefine_123/OCCM_vopmaxA_isolde_noH-
> coot-17_OXT_real_space_refined_123.pdb
Chain information for OCCM_vopmaxA_isolde_noH-
coot-17_OXT_real_space_refined_123.pdb #2
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
X Y | No description available
> show cartoons
> hide atoms
> hide #!3 models
> dssp
> ui tool show "Side View"
> select #2/y
861 atoms, 965 bonds, 42 residues, 1 model selected
> color sel red
> select #2/x
861 atoms, 965 bonds, 42 residues, 1 model selected
> ui tool show "Color Actions"
> select #2/x
861 atoms, 965 bonds, 42 residues, 1 model selected
> select clear
> select #2/x
861 atoms, 965 bonds, 42 residues, 1 model selected
> color sel #ffffffff
> color sel white
> select clear
> select #2/2
5087 atoms, 5174 bonds, 6 pseudobonds, 639 residues, 3 models selected
> color (#!2 & sel) #00ff77ff
> color (#!2 & sel) #b7ff9dff
> select #2/6
5436 atoms, 5524 bonds, 12 pseudobonds, 679 residues, 3 models selected
> color (#!2 & sel) #246b05ff
> select #2/7
4542 atoms, 4609 bonds, 11 pseudobonds, 578 residues, 3 models selected
> color (#!2 & sel) #6b8e23ff
> select #2/3
4583 atoms, 4661 bonds, 4 pseudobonds, 585 residues, 2 models selected
> color (#!2 & sel) #7fff00ff
> select #2/5
5087 atoms, 5160 bonds, 11 pseudobonds, 640 residues, 3 models selected
> color (#!2 & sel) #228b22ff
> select clear
> select #2/8
4047 atoms, 4123 bonds, 3 pseudobonds, 505 residues, 2 models selected
> color (#!2 & sel) #d3d3d3ff
> select #2/a
961 atoms, 971 bonds, 120 residues, 1 model selected
> color sel #8b4513ff
> select #2/f
324 atoms, 328 bonds, 38 residues, 1 model selected
> color sel #e1bae0ff
> select #2/b
1845 atoms, 1892 bonds, 3 pseudobonds, 222 residues, 2 models selected
> color (#!2 & sel) #ff7f50ff
> select #2/d
3573 atoms, 3639 bonds, 3 pseudobonds, 435 residues, 2 models selected
> color (#!2 & sel) #ffa500ff
> select #2/c
4618 atoms, 4717 bonds, 3 pseudobonds, 557 residues, 2 models selected
> color (#!2 & sel) #e9967aff
> select #2/e
3475 atoms, 3559 bonds, 3 pseudobonds, 421 residues, 2 models selected
> color (#!2 & sel) #8b0000ff
> select #2/4
4992 atoms, 5053 bonds, 13 pseudobonds, 628 residues, 3 models selected
> color (#!2 & sel) #b7ff9dff
> select clear
> select #2/2:1-472/3:1-338/4:1-498/5:1-344/6:1-508/7:1-385/x/y/8/a/b/c/d/e/f
33268 atoms, 34093 bonds, 31 pseudobonds, 3968 residues, 2 models selected
> cartoon hide (#!2 & sel)
> select #2/x/y
1722 atoms, 1930 bonds, 84 residues, 1 model selected
> cartoon sel
> select clear
> select #2/2:1-472/3:1-338/4:1-498/5:1-344/6:1-508/7:1-385
12703 atoms, 12934 bonds, 16 pseudobonds, 1586 residues, 2 models selected
> select up
12783 atoms, 13012 bonds, 16 pseudobonds, 1596 residues, 2 models selected
> select up
20297 atoms, 20624 bonds, 16 pseudobonds, 2582 residues, 2 models selected
> select #2/c/6:902-1500/4:730-1500/5:706-1500
7194 atoms, 7324 bonds, 8 pseudobonds, 867 residues, 2 models selected
> select #2/c/6:902-1500/4:854-1500/5:706-1500
6407 atoms, 6529 bonds, 5 pseudobonds, 768 residues, 2 models selected
> cartoon hide (#!2 & sel)
> save Fig4.cxs format session
> select #2/2:1-472/3:1-338/4:1-498/5:1-344/6:1-508/7:1-385/x/y/8/a/b/c/d/e/f
33268 atoms, 34093 bonds, 31 pseudobonds, 3968 residues, 2 models selected
> select #2/2473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500
14121 atoms, 14297 bonds, 16 pseudobonds, 1799 residues, 2 models selected
> surface (#!2 & sel)
> transparency (#!2 & sel) 70
> select #2
50292 atoms, 51340 bonds, 72 pseudobonds, 6131 residues, 3 models selected
> cartoon hide (#!2 & sel)
> select
> #2/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467/y/x
3185 atoms, 3389 bonds, 2 pseudobonds, 284 residues, 2 models selected
> cartoon (#!2 & sel)
> select clear
> lighting simple
> select #2/2473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500
14121 atoms, 14297 bonds, 16 pseudobonds, 1799 residues, 2 models selected
> select #2/2:473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500
17002 atoms, 17222 bonds, 17 pseudobonds, 2162 residues, 2 models selected
> surface (#!2 & sel)
> transparency (#!2 & sel) 70
> select clear
> select #2/2:473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500
17002 atoms, 17222 bonds, 17 pseudobonds, 2162 residues, 2 models selected
> select
> #2/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467/y/x
3185 atoms, 3389 bonds, 2 pseudobonds, 284 residues, 2 models selected
> select #2
50292 atoms, 51340 bonds, 72 pseudobonds, 6131 residues, 3 models selected
> surface hidePatches (#!2 & sel)
> select
> #2/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467/y/x
3185 atoms, 3389 bonds, 2 pseudobonds, 284 residues, 2 models selected
> select ~sel & ##selected
47107 atoms, 47951 bonds, 70 pseudobonds, 5847 residues, 3 models selected
> surface (#!2 & sel)
> select up
47130 atoms, 47951 bonds, 70 pseudobonds, 5870 residues, 16 models selected
> select up
47271 atoms, 48092 bonds, 70 pseudobonds, 5870 residues, 16 models selected
> select up
47456 atoms, 48276 bonds, 70 pseudobonds, 5899 residues, 16 models selected
> select up
48570 atoms, 49410 bonds, 70 pseudobonds, 6047 residues, 16 models selected
> select up
50292 atoms, 51340 bonds, 72 pseudobonds, 6131 residues, 16 models selected
> select up
50292 atoms, 51340 bonds, 72 pseudobonds, 6131 residues, 16 models selected
> select up
50292 atoms, 51340 bonds, 72 pseudobonds, 6131 residues, 16 models selected
> select #2/2:1-472/3:1-338/4:1-498/5:1-344/6:1-508/7:1-385/x/y/8/a/b/c/d/e/f
33268 atoms, 34093 bonds, 31 pseudobonds, 3968 residues, 2 models selected
> surface (#!2 & sel)
> surface hidePatches (#!2 & sel)
> select #2
50292 atoms, 51340 bonds, 72 pseudobonds, 6131 residues, 3 models selected
> surface (#!2 & sel)
> select #2/2:1-472/3:1-338/4:1-498/5:1-344/6:1-508/7:1-385/x/y/8/a/b/c/d/e/f
33268 atoms, 34093 bonds, 31 pseudobonds, 3968 residues, 2 models selected
> surface hidePatches (#!2 & sel)
> select up
33348 atoms, 34171 bonds, 31 pseudobonds, 3978 residues, 17 models selected
> select up
40862 atoms, 41783 bonds, 31 pseudobonds, 4964 residues, 17 models selected
> select up
41021 atoms, 41939 bonds, 31 pseudobonds, 4986 residues, 17 models selected
> select up
45238 atoms, 46217 bonds, 31 pseudobonds, 5515 residues, 17 models selected
> select up
45336 atoms, 46312 bonds, 31 pseudobonds, 5527 residues, 17 models selected
> select up
48585 atoms, 49618 bonds, 31 pseudobonds, 5927 residues, 17 models selected
> select up
48632 atoms, 49663 bonds, 31 pseudobonds, 5934 residues, 17 models selected
> select up
49678 atoms, 50722 bonds, 31 pseudobonds, 6061 residues, 17 models selected
> select up
49709 atoms, 50751 bonds, 31 pseudobonds, 6065 residues, 17 models selected
> select up
50071 atoms, 51117 bonds, 31 pseudobonds, 6109 residues, 17 models selected
> select
> #2/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467
1463 atoms, 1459 bonds, 2 pseudobonds, 200 residues, 2 models selected
> surface hidePatches (#!2 & sel)
> select clear
> select
> #2/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467
1463 atoms, 1459 bonds, 2 pseudobonds, 200 residues, 2 models selected
> surface (#!2 & sel)
> select #2/2473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500
14121 atoms, 14297 bonds, 16 pseudobonds, 1799 residues, 2 models selected
> surface (#!2 & sel)
> select clear
> select #2/2:473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500
17002 atoms, 17222 bonds, 17 pseudobonds, 2162 residues, 2 models selected
> surface (#!2 & sel)
> select clear
> select #2/7/3
9125 atoms, 9270 bonds, 15 pseudobonds, 1163 residues, 3 models selected
> cartoon hide (#!2 & sel)
> surface hidePatches (#!2 & sel)
> select #2/c/6:902-1500/4:854-1500/5:706-1500
6407 atoms, 6529 bonds, 5 pseudobonds, 768 residues, 2 models selected
> surface hidePatches (#!2 & sel)
> select #2/7/3
9125 atoms, 9270 bonds, 15 pseudobonds, 1163 residues, 3 models selected
> surface (#!2 & sel)
> select clear
> select #2/7/3
9125 atoms, 9270 bonds, 15 pseudobonds, 1163 residues, 3 models selected
> surface hidePatches (#!2 & sel)
> select #2/3:339-1500/7:386-1500
4844 atoms, 4902 bonds, 4 pseudobonds, 624 residues, 2 models selected
> surface (#!2 & sel)
> transparency (#!2 & sel) 0
> select clear
> close #1
> close #3,5
> open
> /Users/butryna/Documents/Phenix/2RA/RealSpaceRefine_38/ref11_ref13_DNAFFed-
> coot-12_isolde_noH_Zn_OXT_real_space_refined_038.pdb
Chain information for ref11_ref13_DNAFFed-
coot-12_isolde_noH_Zn_OXT_real_space_refined_038.pdb #1
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
8 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
X Y | No description available
> hide atoms
> hide cartoons
> show cartoons
> mmaker #1/6 to #2/6
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 OCCM_vopmaxA_isolde_noH-coot-17_OXT_real_space_refined_123.pdb,
chain 6 (#2) with ref11_ref13_DNAFFed-
coot-12_isolde_noH_Zn_OXT_real_space_refined_038.pdb, chain 6 (#1), sequence
alignment score = 3301.1
RMSD between 640 pruned atom pairs is 0.993 angstroms; (across all 672 pairs:
1.114)
> dssp
> select #1/2:1-472/3:1-338/4:1-498/5:1-344/6:1-508/7:1-385/x/y/8/a/b/c/d/e/f
35198 atoms, 36055 bonds, 36 pseudobonds, 4204 residues, 2 models selected
> hide sel cartoons
> select
> #1/2:1-472/3:1-338/4:1-498/5:1-344/6:1-508/7:1-385/x/y/8/a/b/c/d/e/f/8
35198 atoms, 36055 bonds, 36 pseudobonds, 4204 residues, 2 models selected
> hide sel cartoons
> hide #!2 models
> show #!2 models
> hide #!1 models
> select
> #2/2:1-472/3:1-338/4:1-498/5:1-344/6:1-508/7:1-385/x/y/8/a/b/c/d/e/f/8
33268 atoms, 34093 bonds, 31 pseudobonds, 3968 residues, 2 models selected
> hide sel cartoons
> select #2/c/6:902-1500/4:854-1500/5:706-1500
6407 atoms, 6529 bonds, 5 pseudobonds, 768 residues, 2 models selected
> hide sel cartoons
> select #1/c/6:902-1500/4:854-1500/5:706-1500
5948 atoms, 6059 bonds, 5 pseudobonds, 716 residues, 2 models selected
> hide #!2 cartoons
> select #1/c/6:902-1500/4:854-1500/5:706-1500
5948 atoms, 6059 bonds, 5 pseudobonds, 716 residues, 2 models selected
> select #2/2:473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500
17002 atoms, 17222 bonds, 17 pseudobonds, 2162 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> select
> #2/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467/y/x
3185 atoms, 3389 bonds, 2 pseudobonds, 284 residues, 2 models selected
> show sel cartoons
> show #!1 models
> hide #!2 models
> select #1/6:902-1500/4:854-1500/5:706-1500
1367 atoms, 1380 bonds, 1 pseudobond, 164 residues, 2 models selected
> select #1/6:902-1500/4:854-1500/5:706-1500/7:740-1500
1819 atoms, 1838 bonds, 1 pseudobond, 218 residues, 2 models selected
> hide sel cartoons
> select #1/2
4709 atoms, 4787 bonds, 3 pseudobonds, 592 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!1 & sel) #00ff77ff
> select #1/4
5253 atoms, 5318 bonds, 11 pseudobonds, 660 residues, 3 models selected
> color (#!1 & sel) #b7ff9dff
> select #1/6
5448 atoms, 5538 bonds, 11 pseudobonds, 681 residues, 3 models selected
> color (#!1 & sel) #246b05ff
> select #1/7
5156 atoms, 5233 bonds, 10 pseudobonds, 653 residues, 3 models selected
> color (#!1 & sel) #6b8e23ff
> select #1/3
4516 atoms, 4594 bonds, 6 pseudobonds, 574 residues, 2 models selected
> color (#!1 & sel) #7fff00ff
> select #1/5
4488 atoms, 4550 bonds, 10 pseudobonds, 568 residues, 3 models selected
> color (#!1 & sel) #228b22ff
> select #1/y
861 atoms, 965 bonds, 42 residues, 1 model selected
> color sel #ff0000ff
> select #1/x
861 atoms, 965 bonds, 42 residues, 1 model selected
> color sel #ffffffff
> select #1/x/y
1722 atoms, 1930 bonds, 84 residues, 1 model selected
> show sel cartoons
> show #!2 models
> hide #!2 models
> select
> #1/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467/y/x
3282 atoms, 3488 bonds, 1 pseudobond, 298 residues, 2 models selected
> select up
3430 atoms, 3635 bonds, 1 pseudobond, 323 residues, 2 models selected
> select up
13067 atoms, 13426 bonds, 1 pseudobond, 1562 residues, 2 models selected
> select
> #1/2:473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500/y/x
18884 atoms, 19314 bonds, 14 pseudobonds, 2269 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
> select ~sel & ##selected
33497 atoms, 34150 bonds, 56 pseudobonds, 4120 residues, 3 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1
18884 atoms, 19314 bonds, 14 pseudobonds, 2269 residues, 2 models selected
> show sel cartoons
> select #1/6:902-1500/4:854-1500/5:706-1500/7:740-1500
1819 atoms, 1838 bonds, 1 pseudobond, 218 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> show #!2 models
> hide #!1 models
> select
> #1/2:473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500/y/x
17065 atoms, 17476 bonds, 10 pseudobonds, 2051 residues, 2 models selected
> select
> #2/2:473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500/y/x
18724 atoms, 19152 bonds, 17 pseudobonds, 2246 residues, 2 models selected
> select ~sel & ##selected
31568 atoms, 32188 bonds, 55 pseudobonds, 3885 residues, 3 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> save Fig4.cxs format session
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> ui tool show "Selection Inspector"
> setattr =sel p display false
Assigning display attribute to 1 item
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #2/5/2/4/6
12158 atoms, 12320 bonds, 13 pseudobonds, 1538 residues, 2 models selected
> transparency (#!2 & sel) 70
> select clear
> select #2/3/7
4844 atoms, 4902 bonds, 4 pseudobonds, 624 residues, 2 models selected
> surface hidePatches (#!2 & sel)
> hide sel cartoons
> show #!1 models
> hide #!2 models
> select #2/3
2409 atoms, 2437 bonds, 2 pseudobonds, 309 residues, 2 models selected
> hide #!1 cartoons
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> select #1
17065 atoms, 17476 bonds, 10 pseudobonds, 2051 residues, 2 models selected
> show sel cartoons
> select #1/3
2370 atoms, 2399 bonds, 3 pseudobonds, 302 residues, 2 models selected
> hide sel cartoons
> select #1/3
2370 atoms, 2399 bonds, 3 pseudobonds, 302 residues, 2 models selected
> show sel cartoons
> select #1/3
2370 atoms, 2399 bonds, 3 pseudobonds, 302 residues, 2 models selected
> hide sel cartoons
> select #1/5/7
5162 atoms, 5227 bonds, 2 pseudobonds, 666 residues, 2 models selected
> surface (#!1 & sel)
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> select #1
17065 atoms, 17476 bonds, 10 pseudobonds, 2051 residues, 3 models selected
> surface (#!1 & sel)
> select #1/x/y
1722 atoms, 1930 bonds, 84 residues, 1 model selected
> surface hidePatches (#!1 & sel)
> select #1/2/4/6/5
10376 atoms, 10516 bonds, 7 pseudobonds, 1329 residues, 2 models selected
> transparency (#!1 & sel) 70
> select #1/3
2370 atoms, 2399 bonds, 3 pseudobonds, 302 residues, 2 models selected
> surface hidePatches (#!1 & sel)
> select #1
17065 atoms, 17476 bonds, 10 pseudobonds, 2051 residues, 5 models selected
> surface hidePatches (#!1 & sel)
> select clear
> select #1
17065 atoms, 17476 bonds, 10 pseudobonds, 2051 residues, 5 models selected
> select #1/2/3/4/5/6/7
15343 atoms, 15546 bonds, 10 pseudobonds, 1967 residues, 2 models selected
> surface (#!1 & sel)
> transparency (#!1 & sel) 70
> select #2/2/3/4/5/6/7
17002 atoms, 17222 bonds, 17 pseudobonds, 2162 residues, 2 models selected
> surface #1
> transparency #1 70
> hide #!1 models
> show #!2 models
> select #2
18724 atoms, 19152 bonds, 17 pseudobonds, 2246 residues, 2 models selected
> surface (#!2 & sel)
> select #2/x/y
1722 atoms, 1930 bonds, 84 residues, 1 model selected
> surface hidePatches (#!2 & sel)
> select #2
18724 atoms, 19152 bonds, 17 pseudobonds, 2246 residues, 2 models selected
> transparency (#!2 & sel) 70
> show #!1 models
> hide #!2 models
> select #1/x/y
1722 atoms, 1930 bonds, 84 residues, 1 model selected
> surface hidePatches (#!1 & sel)
> select #1/2/3/4/5/6/7
15343 atoms, 15546 bonds, 10 pseudobonds, 1967 residues, 2 models selected
> hide sel cartoons
> hide #!1 models
> show #!2 models
> show #!2 cartoons
> hide #!2 cartoons
> show #!2 cartoons
> hide #!2 cartoons
> select #2/x/y
1722 atoms, 1930 bonds, 84 residues, 1 model selected
> show sel cartoons
> show #!1 models
> hide #!2 models
> select
> #2/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467
1463 atoms, 1459 bonds, 2 pseudobonds, 200 residues, 2 models selected
> hide #!1 models
> show #!2 models
> show sel cartoons
> show #!1 models
> hide #!2 models
> select
> #1/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467
1560 atoms, 1558 bonds, 1 pseudobond, 214 residues, 2 models selected
> show sel cartoons
> select clear
> save Fig4.cxs format session
Enter a PDB ID in the entry field
> open 5v8f fromDatabase pdb format mmcif
Summary of feedback from opening 5v8f fetched from pdb
---
warning | Atom CE has no neighbors to form bonds with according to residue
template for MET /6:313
5v8f title:
Structural basis of MCM2-7 replicative helicase loading by ORC-Cdc6 and Cdt1
[more info...]
Chain information for 5v8f #3
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868
3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-961
4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
7 | DNA replication licensing factor MCM7 | MCM7_YEAST 1-800
8 | Cell division cycle protein CDT1 | CDT1_YEAST 1-604
9 | Cell division control protein 6 | CDC6_YEAST 1-513
A | Origin recognition complex subunit 1 | ORC1_YEAST 1-913
B | Origin recognition complex subunit 2 | ORC2_YEAST 1-620
C | Origin recognition complex subunit 3 | ORC3_YEAST 1-616
D | Origin recognition complex subunit 4 | ORC4_YEAST 1-529
E | Origin recognition complex subunit 5 | ORC5_YEAST 1-479
F | Origin recognition complex subunit 6 | ORC6_YEAST 1-435
M | DNA (39-MER) |
N | DNA (39-MER) |
Non-standard residues in 5v8f #3
---
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
> hide #!1,3 atoms
> hide #!1 models
> select #3/2473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500
15194 atoms, 15386 bonds, 7 pseudobonds, 1941 residues, 2 models selected
> show sel cartoons
> select #3/2/473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500
19960 atoms, 20228 bonds, 10 pseudobonds, 2545 residues, 2 models selected
> select
> #3/2/473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500/m/n
21559 atoms, 22020 bonds, 83 pseudobonds, 2623 residues, 3 models selected
> show sel cartoons
> select ~sel & ##selected
38027 atoms, 38739 bonds, 39 pseudobonds, 4682 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> select #1/6:902-1500/4:854-1500/5:706-1500/7:740-1500
Nothing selected
> select #3/6:902-1500/4:854-1500/5:706-1500/7:740-1500
1705 atoms, 1722 bonds, 205 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/3:892-1500
565 atoms, 573 bonds, 69 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/7:731
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
133 atoms, 133 bonds, 16 residues, 1 model selected
> select down
7 atoms, 6 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select #3/7:732
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
126 atoms, 125 bonds, 15 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/7:733
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
118 atoms, 117 bonds, 14 residues, 1 model selected
> select down
9 atoms, 8 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/7:734
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
109 atoms, 108 bonds, 13 residues, 1 model selected
> select down
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select #3/7:734-739
47 atoms, 46 bonds, 6 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select
> #3/2:473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500/m/n
17306 atoms, 17707 bonds, 78 pseudobonds, 2097 residues, 3 models selected
> select ~sel & ##selected
1912 atoms, 1946 bonds, 2 pseudobonds, 243 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> select #3/5:335
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
74 atoms, 72 bonds, 10 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/2
2854 atoms, 2896 bonds, 1 pseudobond, 361 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!3 & sel) #00ff77ff
> select #3/4
2718 atoms, 2755 bonds, 348 residues, 1 model selected
> color sel #b7ff9dff
> select #3/6
2536 atoms, 2573 bonds, 326 residues, 1 model selected
> color sel #246b05ff
> select #3/7
2623 atoms, 2657 bonds, 1 pseudobond, 339 residues, 2 models selected
> color (#!3 & sel) #6b8e23ff
> select #3/3
2474 atoms, 2503 bonds, 1 pseudobond, 320 residues, 2 models selected
> color (#!3 & sel) #7fff00ff
> select #3/5
2428 atoms, 2458 bonds, 1 pseudobond, 315 residues, 2 models selected
> color (#!3 & sel) #228b22ff
> select #3/y
Nothing selected
> color #3 #ffffffff
> color #3 #ff0000ff
> select #3/x
Nothing selected
> color #3 #ffffffff
> select #3/x
Nothing selected
> select #3/2
2854 atoms, 2896 bonds, 1 pseudobond, 361 residues, 2 models selected
> color (#!3 & sel) #00ff77ff
> select #3/4
2718 atoms, 2755 bonds, 348 residues, 1 model selected
> color sel #b7ff9dff
> select #3/6
2536 atoms, 2573 bonds, 326 residues, 1 model selected
> color sel #246b05ff
> select #3/7
2623 atoms, 2657 bonds, 1 pseudobond, 339 residues, 2 models selected
> color (#!3 & sel) #6b8e23ff
> select #3/3
2474 atoms, 2503 bonds, 1 pseudobond, 320 residues, 2 models selected
> color (#!3 & sel) #7fff00ff
> select #3/5
2428 atoms, 2458 bonds, 1 pseudobond, 315 residues, 2 models selected
> color (#!3 & sel) #228b22ff
> select #3/m
795 atoms, 886 bonds, 39 residues, 1 model selected
> color sel #ff0000ff
> select #3/n
804 atoms, 906 bonds, 39 residues, 1 model selected
> color sel #ffffffff
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> mmaker #3/6 to #1/6
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 ref11_ref13_DNAFFed-
coot-12_isolde_noH_Zn_OXT_real_space_refined_038.pdb, chain 6 (#1) with 5v8f,
chain 6 (#3), sequence alignment score = 2422.7
RMSD between 305 pruned atom pairs is 0.851 angstroms; (across all 319 pairs:
1.052)
> show #!2 models
> show #!1 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!2 models
> select #2
18724 atoms, 19152 bonds, 17 pseudobonds, 2246 residues, 2 models selected
> surface hidePatches (#!2 & sel)
> select #2/6:902-1500/4:854-1500/5:706-1500/7:740-1500
1790 atoms, 1812 bonds, 2 pseudobonds, 212 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/2/3/4/5/6/7
15212 atoms, 15410 bonds, 12 pseudobonds, 1950 residues, 2 models selected
> surface (#!2 & sel)
> select clear
> show #!1 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!1 models
> hide #!2 models
> select #3
17232 atoms, 17634 bonds, 77 pseudobonds, 2087 residues, 3 models selected
> surface (#!3 & sel)
> transparency (#!3 & sel) 70
> select #3/m/n
1599 atoms, 1792 bonds, 73 pseudobonds, 78 residues, 2 models selected
> surface hidePatches (#!3 & sel)
> select
> #3/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467/m/n
3207 atoms, 3399 bonds, 73 pseudobonds, 300 residues, 2 models selected
> select ~sel & ##selected
14025 atoms, 14235 bonds, 4 pseudobonds, 1787 residues, 2 models selected
> cartoon hide (#!3 & sel)
> select clear
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> select #3/m
795 atoms, 886 bonds, 39 residues, 1 model selected
> color (#!3 & sel) white
> select #3/n
804 atoms, 906 bonds, 39 residues, 1 model selected
> color (#!3 & sel) red
> select clear
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> select #3/3
2474 atoms, 2503 bonds, 1 pseudobond, 320 residues, 2 models selected
> hide sel cartoons
> surface hidePatches (#!3 & sel)
> select #3/7
2623 atoms, 2657 bonds, 1 pseudobond, 339 residues, 2 models selected
> surface hidePatches (#!3 & sel)
> hide sel cartoons
> select #3/4
2718 atoms, 2755 bonds, 348 residues, 1 model selected
> surface hidePatches (#!3 & sel)
> cartoon hide (#!3 & sel)
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting full
> select #3
17232 atoms, 17634 bonds, 77 pseudobonds, 2087 residues, 7 models selected
> transparency (#!3 & sel) 80
> select clear
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!3 models
> select #1/3/7
4967 atoms, 5030 bonds, 3 pseudobonds, 638 residues, 2 models selected
> surface hidePatches (#!1 & sel)
> hide sel cartoons
> select #1/3/7/4
7424 atoms, 7517 bonds, 6 pseudobonds, 955 residues, 2 models selected
> cartoon hide (#!1 & sel)
> surface hidePatches (#!1 & sel)
> show #!3 models
> hide #!3 models
> select #1/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516
741 atoms, 737 bonds, 102 residues, 1 model selected
> color (#!1 & sel) red
> select clear
> select #1/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467
819 atoms, 821 bonds, 1 pseudobond, 112 residues, 2 models selected
> color (#!1 & sel) light gray
> select clear
> select #1/5/2/4
7897 atoms, 8002 bonds, 6 pseudobonds, 1010 residues, 2 models selected
> select #1/5/2/6
7919 atoms, 8029 bonds, 4 pseudobonds, 1012 residues, 2 models selected
> transparency (#!1 & sel) 0
> select #1/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467
819 atoms, 821 bonds, 1 pseudobond, 112 residues, 2 models selected
> transparency (#!1 & sel) 80
> select #1/2:633/3:499/4:658/5:506/6:665/7:550
54 atoms, 48 bonds, 6 residues, 1 model selected
> select #1/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516
741 atoms, 737 bonds, 102 residues, 1 model selected
> transparency (#!1 & sel) 80
> select clear
> lighting simple
> select #1/5
2565 atoms, 2596 bonds, 2 pseudobonds, 330 residues, 2 models selected
> ui tool show "Color Actions"
> color (#!1 & sel) #228b22ff
> select #1/5:500-516
123 atoms, 122 bonds, 17 residues, 1 model selected
> transparency (#!1 & sel) 80
> select #1/5:448-467
155 atoms, 157 bonds, 20 residues, 1 model selected
> transparency (#!1 & sel) 80
> select clear
> select #1/6
2479 atoms, 2514 bonds, 1 pseudobond, 319 residues, 2 models selected
> surface hidePatches (#!1 & sel)
> hide sel cartoons
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> select #1/
Expected an objects specifier or a keyword
> surface (#!1 & sel)
> select #1
17065 atoms, 17476 bonds, 10 pseudobonds, 2051 residues, 11 models selected
> surface (#!1 & sel)
> select #1/n/m
Nothing selected
> surface hidePatches #1
> select #1
17065 atoms, 17476 bonds, 10 pseudobonds, 2051 residues, 13 models selected
> surface (#!1 & sel)
> select x/y
Expected an objects specifier or a keyword
> select /x/y
3444 atoms, 3860 bonds, 168 residues, 2 models selected
> show #!2 models
> show #!3 models
> select /x/y
3444 atoms, 3860 bonds, 168 residues, 2 models selected
> surface hidePatches (#!1-2 & sel)
> show sel cartoons
> select /2
8610 atoms, 8740 bonds, 3 pseudobonds, 1087 residues, 6 models selected
> ui tool show "Color Actions"
> color (#!1-3 & sel) #00ff77ff
> select /4
7678 atoms, 7776 bonds, 6 pseudobonds, 987 residues, 5 models selected
> color (#!1-3 & sel) #b7ff9dff
> select /6
7441 atoms, 7546 bonds, 3 pseudobonds, 957 residues, 5 models selected
> color (#!1-3 & sel) #246b05ff
> select /7
7654 atoms, 7753 bonds, 3 pseudobonds, 989 residues, 5 models selected
> color (#!1-3 & sel) #6b8e23ff
> select /3
7253 atoms, 7339 bonds, 6 pseudobonds, 931 residues, 6 models selected
> color (#!1-3 & sel) #7fff00ff
> select /5
7552 atoms, 7644 bonds, 5 pseudobonds, 975 residues, 6 models selected
> color (#!1-3 & sel) #228b22ff
> hide #!2 models
> show #!2 models
> select /3
7253 atoms, 7339 bonds, 6 pseudobonds, 931 residues, 6 models selected
> surface hidePatches (#!1-3 & sel)
> select
> /3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467
4631 atoms, 4624 bonds, 3 pseudobonds, 636 residues, 5 models selected
> show sel cartoons
> transparency (#!1-3 & sel) 70
> select clear
> hide cartoons
> show cartoons
> hide #!2 models
> hide #!3 models
> select /3
7253 atoms, 7339 bonds, 6 pseudobonds, 931 residues, 6 models selected
> hide sel & #!1 cartoons
> show #!2 models
> hide #!1 models
> select /3
7253 atoms, 7339 bonds, 6 pseudobonds, 931 residues, 6 models selected
> hide sel & #!2 cartoons
> show #!3 models
> hide #!2 models
> hide sel & #!3 cartoons
> select /4/7
15332 atoms, 15529 bonds, 9 pseudobonds, 1976 residues, 6 models selected
> surface (#!3 & sel)
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> select #1/5
2565 atoms, 2596 bonds, 2 pseudobonds, 330 residues, 2 models selected
> surface hidePatches (#!1 & sel)
> hide sel cartoons
> hide #!1 models
> show #!3 models
> select #3/5
2428 atoms, 2458 bonds, 1 pseudobond, 315 residues, 2 models selected
> select #3/5
2428 atoms, 2458 bonds, 1 pseudobond, 315 residues, 2 models selected
> select #3/7
2623 atoms, 2657 bonds, 1 pseudobond, 339 residues, 2 models selected
> surface hidePatches (#!3 & sel)
> hide sel cartoons
> select #3/3/6
5010 atoms, 5076 bonds, 1 pseudobond, 646 residues, 2 models selected
> surface hidePatches (#!3 & sel)
> select #3/3/6/4
7728 atoms, 7831 bonds, 1 pseudobond, 994 residues, 2 models selected
> surface hidePatches (#!3 & sel)
> hide sel cartoons
> show #!1 models
> hide #!3 models
> select #1/3/6/4
7306 atoms, 7400 bonds, 7 pseudobonds, 938 residues, 2 models selected
> surface hidePatches (#!1 & sel)
> hide sel cartoons
> select #1/3/6/4/7
9903 atoms, 10031 bonds, 7 pseudobonds, 1274 residues, 2 models selected
> surface hidePatches (#!1 & sel)
> hide sel cartoons
> select #1/2/5
5440 atoms, 5515 bonds, 3 pseudobonds, 693 residues, 2 models selected
> surface (#!1 & sel)
> show sel cartoons
> select clear
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> select #2/3/6/4/7
9772 atoms, 9895 bonds, 9 pseudobonds, 1257 residues, 2 models selected
> surface hidePatches (#!2 & sel)
> hide sel cartoons
> show #!1 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> save /Users/butryna/Desktop/image1.png supersample 3
> lighting full
> lighting soft
> lighting simple
> lighting full
===== Log before crash end =====
Log:
Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-22.5.11
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
OS Loader Version: 580.140.1~8
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 1 hour, 14 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
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: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
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-ISOLDE: 1.7.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
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: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
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
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
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: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
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: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 14 months ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset |
comment:2 by , 14 months ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Graphics hardware encountered an error and was reset → Graphics crash, macOS 14.6.1, Intel Iris Plus Graphics |
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Apple Intel graphics driver crash.