![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Last modified 15 months ago
#16021 closed defect
Crash on Mac waking from sleep — at Version 1
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.6.1-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 0x0000000204a8e240 (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.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.chem_group._chem_group, chimerax.atom_search.ast, chimerax.coulombic._esp, chimerax.mlp._mlp, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree (total: 63)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,1",
"coalitionID" : 166650,
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"build" : "23G93",
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"captureTime" : "2024-09-25 20:22:03.7500 +0100",
"codeSigningMonitor" : 1,
"incident" : "8CDB7D00-EED0-41DA-A6B2-781A24C4B2F8",
"pid" : 88455,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-09-25 11:29:54.5205 +0100",
"procStartAbsTime" : 24079284145589,
"procExitAbsTime" : 24577915846215,
"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":"EDD8B610-D200-5890-8C1B-29D609195B52","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "ECED8795-F73E-B1B9-01B1-947CFD465E40",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 1,
"sleepWakeUUID" : "86C7C461-B75B-4121-A4E7-A7DC84BC428A",
"sip" : "enabled",
"vmRegionInfo" : "0x3deb4ade88f8 is not in any region. Bytes after previous region: 67599746369785 Bytes before following region: 37472333559560\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00003deb4ade88f8","rawCodes":[1,68080782706936],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00003deb4ade88f8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":88455},
"vmregioninfo" : "0x3deb4ade88f8 is not in any region. Bytes after previous region: 67599746369785 Bytes before following region: 37472333559560\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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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/sean/Documents/Projects/GOLPH3 paper/Briggs Kat
> Collaboration/GOLPH3 3kn1.pdb"
GOLPH3 3kn1.pdb title:
Crystal structure of golgi phosphoprotein 3 N-term truncation variant [more
info...]
Chain information for GOLPH3 3kn1.pdb #1
---
Chain | Description | UniProt
A | golgi phosphoprotein 3 | GOLP3_HUMAN 52-298
Non-standard residues in GOLPH3 3kn1.pdb #1
---
SO4 — sulfate ion
5 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select sulfate
30 atoms, 24 bonds, 6 residues, 1 model selected
> hide sel atoms
> select clear
Alignment identifier is 1/A
> select clear
> select /A:59-297
1895 atoms, 1926 bonds, 239 residues, 1 model selected
> hide sel atoms
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
/A ARG 59
/A ARG 112
/A GLN 211
/A ARG 231
/A LYS 266
/A LYS 282
/A ASN 284
/A THR 297
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for GOLPH3 3kn1.pdb_A SES surface #1.1: minimum, -23.22, mean
-2.15, maximum 13.32
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> select ::name="HOH"
9 atoms, 9 residues, 1 model selected
> hide sel atoms
> select clear
> set bgColor white
> set bgColor black
> save /Users/sean/Desktop/image1.png supersample 3
> set bgColor white
> save /Users/sean/Desktop/image2.png supersample 3
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting full
> save /Users/sean/Desktop/image3.png supersample 3
> lighting soft
> save /Users/sean/Desktop/image4.png supersample 3
> lighting simple
> save /Users/sean/Desktop/image5.png supersample 3
> lighting flat
> save /Users/sean/Desktop/image6.png supersample 3
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> save /Users/sean/Desktop/image7.png supersample 3
> lighting soft
> save /Users/sean/Desktop/image8.png supersample 3
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting full
> lighting shadows false
> save /Users/sean/Desktop/image9.png supersample 3
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> mlp
Map values for surface "GOLPH3 3kn1.pdb_A SES surface": minimum -27.57, mean
-4.444, maximum 36.64
To also show corresponding color key, enter the above mlp command and add key
true
> save /Users/sean/Desktop/image10.png supersample 3
> lighting simple
> save /Users/sean/Desktop/image11.png supersample 3
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting full
> lighting shadows false
> save /Users/sean/Desktop/image12.png supersample 3
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting soft
> lighting full
> lighting flat
> coulombic
Coulombic values for GOLPH3 3kn1.pdb_A SES surface #1.1: minimum, -23.22, mean
-2.15, maximum 13.32
To also show corresponding color key, enter the above coulombic command and
add key true
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Unsupported scale factor (0.000000) detected on Display1
> hide surfaces
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> save /Users/sean/Desktop/image1.png supersample 3
> graphics silhouettes true
> save /Users/sean/Desktop/image2.png supersample 3
> select ::name="GLN"
77 atoms, 68 bonds, 9 residues, 1 model selected
> show sel atoms
> undo
> show sel atoms
> hide sel atoms
> select ::name="GLU"
171 atoms, 153 bonds, 19 residues, 1 model selected
> show sel atoms
> select ::name="ASP"
112 atoms, 98 bonds, 14 residues, 1 model selected
> show sel atoms
> select clear
> save /Users/sean/Desktop/image3.png supersample 3
> graphics silhouettes false
> save /Users/sean/Desktop/image4.png supersample 3
> select /A:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:154
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:154,159
18 atoms, 16 bonds, 2 residues, 1 model selected
> select /A:83,154,159
26 atoms, 23 bonds, 3 residues, 1 model selected
> select /A:83,154,159,273
34 atoms, 30 bonds, 4 residues, 1 model selected
> select /A:83,154,159,273,275
42 atoms, 37 bonds, 5 residues, 1 model selected
> select /A:83,154,159,273,275,277
51 atoms, 45 bonds, 6 residues, 1 model selected
> select /A:83,154,159,273,275,277,279
60 atoms, 53 bonds, 7 residues, 1 model selected
> select /A:73,83,154,159,273,275,277,279
68 atoms, 60 bonds, 8 residues, 1 model selected
> select /A:73,75,83,154,159,273,275,277,279
77 atoms, 68 bonds, 9 residues, 1 model selected
> select /A:73,75,83,154,159,250,273,275,277,279
86 atoms, 76 bonds, 10 residues, 1 model selected
> select /A:73,75,83,154,159,247,250,273,275,277,279
94 atoms, 83 bonds, 11 residues, 1 model selected
> select /A:73,75,83,154,159,247,250,258-259,273,275,277,279
111 atoms, 99 bonds, 13 residues, 1 model selected
> select /A:73,75,83,154,159,247,250,258-259,262,273,275,277,279
119 atoms, 106 bonds, 14 residues, 1 model selected
> select ~sel
1815 atoms, 1818 bonds, 240 residues, 1 model selected
> hide sel atoms
> select clear
> save /Users/sean/Desktop/image5.png supersample 3
> graphics silhouettes true
> save /Users/sean/Desktop/image6.png supersample 3
> close #1
> open "/Users/sean/Documents/Projects/GOLPH3 paper/Briggs Kat
> Collaboration/20240406_leaf_fitting_v26.cxs" format session
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.187, step 1, values float32
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00645, step 1, values float32
opened ChimeraX session
> hide #!25 models
> show #!25 models
> hide #!34 models
> show #!33 models
> hide #!32 models
> show #!32 models
> hide #!33 models
> ui tool show "Side View"
> show #!31 models
> hide #!31 models
> show #!31 models
> hide #!31 models
> hide #32.1 models
> show #32.1 models
> hide #32.2 models
> show #32.2 models
> hide #!25 models
> show #!25 models
> show #!33 models
> hide #!33 models
> show #!34 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!34 models
> set bgColor white
> hide #39 models
> show #39 models
> hide #39 models
> hide #28 models
> show #28 models
> hide #26.3 models
> hide #!29 models
> show #!29 models
> hide #28 models
> show #28 models
> hide #!26.2 models
> show #!26.2 models
> hide #!26.2 models
> save /Users/sean/Desktop/image1.png supersample 3
> hide #!30 models
> show #!30 models
> hide #27.2 models
> show #27.2 models
> hide #27.2 models
> show #27.2 models
> hide #32.1 models
> show #32.1 models
> hide #32.2 models
> show #32.2 models
> hide #38 models
> show #38 models
> hide #38 models
> show #38 models
> hide #38 models
> show #38 models
> ui tool show "Side View"
> view
> close
> open "/Users/sean/Documents/Projects/GOLPH3 paper/Briggs Kat
> Collaboration/20240406_leaf_fitting_v26.cxs" format session
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.187, step 1, values float32
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00645, step 1, values float32
opened ChimeraX session
> show #!3 models
> hide #!3 models
> show #!3 models
Unsupported scale factor (0.000000) detected on Display1
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/sean/Documents/Projects/GOLPH3 paper/Briggs Kat
> Collaboration/20240808_COPI_leaf_AF3_for_figs_v7_with_files.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset1.mrc as #58, grid size
292,292,292, pixel 1.71, shown at level 0.005, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #60, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #62, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
Log from Wed Sep 25 22:56:27 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v7.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset1.mrc as #58, grid size
292,292,292, pixel 1.71, shown at level 0.005, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #60, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #62, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
Log from Fri Aug 9 13:21:55 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240806_COPI_leaf_AF3_for_figs_v2.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.008, step 1, values float32
Opened emd_3720_2017_leaf.map as #56, grid size 128,128,128, pixel 1.78, shown
at level 0.155, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc as #58, grid size 292,292,292,
pixel 1.71, shown at level 0.005, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc copy as #61, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
Log from Tue Aug 6 15:17:45 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240715_leaf_fitting_AF3_only_v4.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00585, step 1, values float32
Log from Wed Jul 24 16:40:43 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3
> /fold_20240711_copi_golph3/20240711_leaf_fitting_alphafold_withGolph3AF3_v2.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00736, step 1, values float32
Log from Sat Jul 13 09:14:12 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604
> /fold_2024_06_04_12_31/20240710_leaf_fitting_alphafold_only_withAF3_v5.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00736, step 1, values float32
Log from Fri Jul 12 14:16:12 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604
> /fold_2024_06_04_12_31/20240710_leaf_fitting_alphafold_only_withAF3_v4.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00465, step 1, values float32
Log from Wed Jul 10 18:08:13 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/alphafold 3 /GT 20240604
> /fold_2024_06_04_12_31/20240710_leaf_fitting_alphafold_only_withAF3_v2.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00465, step 1, values float32
Log from Wed Jul 10 17:31:38 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240710_leaf_fitting_alphafold_only_fitting.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00404, step 1, values float32
Log from Wed Jul 10 16:36:09 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240710_leaf_fitting_alphafold_only_fitting.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00404, step 1, values float32
Log from Wed Jul 10 16:07:37 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240709_leaf_fitting_v39_labelled.cxs"
Opened relion_locres_filtered_20240326_GT.mrc as #1, grid size 292,292,292,
pixel 1.71, shown at level 0.00473, step 1, values float32
Log from Tue Jul 9 17:02:08 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240708_leaf_fitting_v36_labelled.cxs"
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.12, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00463, step 1, values float32
Log from Mon Jul 8 16:31:05 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240522_leaf_fitting_v32_labelled.cxs"
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.12, step 1, values float32
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00733, step 1, values float32
Log from Mon Jun 3 13:56:09 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera
> sessions/20240521_leaf_fitting_v31_mutations_interactions_labeled.cxs"
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.12, step 1, values float32
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00733, step 1, values float32
Log from Tue May 21 23:56:29 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240406_leaf_fitting_v25.cxs"
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.187, step 1, values float32
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00645, step 1, values float32
Log from Mon Apr 15 16:36:47 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240406_leaf_fitting_v21.cxs"
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.187, step 1, values float32
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00645, step 1, values float32
Log from Mon Apr 15 15:35:58 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240328_leaf_fitting_v17.cxs"
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.187, step 1, values float32
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00645, step 1, values float32
Opened cryosparc_P126_J1413_005_volume_map.mrc as #35, grid size 480,480,480,
pixel 0.953, shown at level 0.136, step 1, values float32
Opened cryosparc_P126_J1449_008_volume_map_sharp.mrc as #36, grid size
480,480,480, pixel 0.953, shown at level 0.227, step 1, values float32
Log from Fri Mar 29 15:25:34 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Chimera sessions/20240326_leaf_fitting_v13.cxs"
Opened emdb 3720 as #2, grid size 128,128,128, pixel 1.78, shown at level
0.153, step 1, values float32
Opened postprocess_20231221.mrc as #1, grid size 156,156,156, pixel 2.55,
shown at level 0.0037, step 1, values float32
Opened COPI_golph_linkage1_postprocess.mrc as #13, grid size 128,128,128,
pixel 3.4, shown at level 0.368, step 1, values float32
Opened emd_2986_2015_linkage1.map as #14, grid size 200,200,200, pixel 2.02,
shown at level 2.05, step 1, values float32
Opened emd_3722_2017_linkage1.map as #15, grid size 212,212,212, pixel 1.78,
shown at level 0.0358, step 1, values float32
Opened COPI_golph_linkage2_postprocess.mrc as #16, grid size 150,150,150,
pixel 3.4, shown at level 0.475, step 1, values float32
Opened emd_2987_2015_linkage2.map as #17, grid size 200,200,200, pixel 2.02,
shown at level 1.91, step 1, values float32
Opened emd_3723_2017_linkage2.map as #18, grid size 212,212,212, pixel 1.78,
shown at level 0.0556, step 1, values float32
Opened COPI_golph_linkage3_postprocess.mrc as #19, grid size 160,160,160,
pixel 3.4, shown at level 0.54, step 1, values float32
Opened emd_2988_2015_linkage3.map as #20, grid size 200,200,200, pixel 2.02,
shown at level 1.01, step 1, values float32
Opened COPI_golph_linkage4_postprocess.mrc as #21, grid size 160,160,160,
pixel 3.4, shown at level 0.5, step 1, values float32
Opened emd_2989_2015_linkage4.map as #22, grid size 200,200,200, pixel 2.02,
shown at level 1.74, step 1, values float32
Opened emd_3724_2017_linkage4.map as #23, grid size 212,212,212, pixel 1.78,
shown at level 0.0393, step 1, values float32
Opened relion_locres_filtered_20240325_GT.mrc as #33, grid size 292,292,292,
pixel 1.71, shown at level 0.0083, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc as #34, grid size 292,292,292,
pixel 1.71, shown at level 0.00747, step 1, values float32
Log from Tue Mar 26 13:48:19 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
[deleted to fit within ticket limits]
> ui tool show "Color Zone"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> color zone #58 near #38 distance 10.26
> hide #!1 models
> select subtract #58
Nothing selected
> color zone #58 near #38 distance 10.93
> color zone #58 near #38 distance 4.35
> color zone #58 near #38 distance 5.21
> color zone #58 near #38 distance 5.14
> color zone #58 near #39 distance 5.14
> volume splitbyzone #58
Opened relion_locres_filtered_20240326_GT.mrc 0 as #59.1, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
Opened relion_locres_filtered_20240326_GT.mrc 1 as #59.2, grid size
292,292,292, pixel 1.71, shown at level 0.008, step 1, values float32
> hide #!59.2 models
> show #!59.2 models
> hide #!59.1 models
> show #!59.1 models
> hide #!59.2 models
> show #!59.2 models
> color zone #58 near #38 distance 5.14
[Repeated 1 time(s)]
> color zone #59.1 near #38 distance 10.26
[Repeated 1 time(s)]
> color zone #59.1 near #41 distance 9.26
> color zone #59.1 near #41 distance 9.16
> color zone #59.1 near #41 distance 9.06
> color zone #59.1 near #41 distance 8.96
> color zone #59.1 near #41 distance 8.86
> color zone #59.1 near #41 distance 8.76
> color zone #59.1 near #41 distance 8.66
> color zone #59.1 near #41 distance 8.56
> color zone #59.1 near #41 distance 8.46
> color zone #59.1 near #41 distance 8.36
> color zone #59.1 near #41 distance 8.26
> color zone #59.1 near #41 distance 8.16
> color zone #59.1 near #41 distance 8.06
> color zone #59.1 near #41 distance 7.96
> color zone #59.1 near #38 distance 7.96
> help help:user/tools/colorzone.html
> close #59.1
> close #59
> show #!58 models
> color zone #58 near #38 distance 5.14
> color zone #58 near #39 distance 5.14
> combine #38 #39 #41 #42 #43 #44 #45 #46 #47 #48 #49 #50 #51 #52 #53 #54 #55
Remapping chain ID 'D' in 20240711_copi_golph3_alpha_I592-G900.cif #39 to 'E'
Remapping chain ID 'F' in 20240711_copi_golph3_betaprime_L587-D905.cif #42 to
'G'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_S711-L953.cif #43 to 'H'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_H311-E659.cif #44 to 'I'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_M1-H311_K660-A710.cif #45
to 'J'
Remapping chain ID 'G' in 20240711_copi_golph3_delta_M1-S273.cif #46 to 'K'
Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_K300-F448.cif #47 to 'L'
Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_M1-P299.cif #48 to 'M'
Remapping chain ID 'H' in 20240711_copi_golph3_gammm1_T449-R609.cif #49 to 'N'
Remapping chain ID 'I' in 20240711_copi_golph3_zeta1.cif #50 to 'O'
Remapping chain ID 'B' in 20240711_copi_golph3_third_Arf1.cif #53 to 'P'
Remapping chain ID 'A' in 20240711_copi_golph3_golph3_.cif #55 to 'Q'
> hide #!59 models
> show #!59 models
> hide #55 models
> hide #!54 models
> hide #53 models
> hide #52 models
> hide #51 models
> hide #50 models
> hide #!49 models
> hide #48 models
> hide #47 models
> hide #!46 models
> hide #!45 models
> hide #!44 models
> hide #!43 models
> hide #42 models
> hide #41 models
> hide #39 models
> hide #38 models
> hide #!58 models
> color zone #58 near #59 distance 5.14
> show #!58 models
> hide #!59 models
> color zone #58 near #59 distance 4.97
> color zone #58 near #59 distance 4.45
> surface dust #58 size 17.1
> color zone #58 near #59 distance 4.31
> color zone #58 near #59 distance 4.7
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #58 step 1
> volume #58 level 0.005
> color zone #58 near #59 distance 5.19
> set bgColor white
> save /Users/becca/Desktop/image1.png supersample 3
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> volume #58 level 0.008
> save /Users/becca/Desktop/image1.png supersample 3
> volume #58 level 0.005
> color zone #58 near #59 distance 5.43
> color zone #58 near #59 distance 6.99
> save /Users/becca/Desktop/image1.png supersample 3
> volume #58 level 0.008
> save /Users/becca/Desktop/image1.png supersample 3
> hide #!58 models
> show #!59 models
> rename #59 combined_model_COPI_GOLPH3
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240806_COPI_leaf_AF3_for_figs_v1.cxs"
> show #!1 models
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240806_COPI_leaf_AF3_for_figs_v1.cxs"
> hide #!59 models
> show #!58 models
> hide #!1 models
> volume #58 level 0.005
> ui mousemode right "map eraser"
> volume erase #58 center 281.84,261.87,305.71 radius 22.725
Opened relion_locres_filtered_20240326_GT.mrc copy as #61, grid size
292,292,292, pixel 1.71, shown at step 1, values float32
> surface dust #61 size 17.1
> color zone #61 near #59 distance 10.26
> color zone #61 near #59 distance 10.16
> color zone #61 near #59 distance 6.84
> save /Users/becca/Desktop/image1.png supersample 3
> volume #61 level 0.008
> save /Users/becca/Desktop/image2.png supersample 3
> volume #61 level 0.005
> save /Users/becca/Desktop/image3.png supersample 3
> volume #61 level 0.008
> save /Users/becca/Desktop/image4.png supersample 3
> color zone #61 near #59 distance 4.76
> color zone #61 near #59 distance 4.4
> color zone #61 near #59 distance 5.99
> save /Users/becca/Desktop/image5.png supersample 3
> hide #!61 models
> show #!1 models
> color #1 #a9a9a9a0 models
> hide #!1 models
> color #1 #a9a9a9a1 models
> show #!1 models
> show #!57 models
> hide #!57 models
> show #!59 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> ui mousemode right select
> select #59/O:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #59/O:74
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #59/O:72
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
> style sel stick
Changed 6 atom styles
> show #!1 models
> hide #!1 models
> select #59/O:108
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select #59/O:107
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select #59/O:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #59/O:108
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #59/O:108
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #59/O:109
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select #59/O:106
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 11 atom styles
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #59/Q:223
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> select clear
> select #59/Q:224
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #59/Q:225
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> select #59/Q:259
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> select #59/Q:263
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #59/Q:225
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #59/Q:226
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> select clear
> select #59/Q:225
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #59/Q:226@CB
1 atom, 1 residue, 1 model selected
> select #59/Q:226@CA
1 atom, 1 residue, 1 model selected
> select #59/Q:226
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #59/O:107@NZ
1 atom, 1 residue, 1 model selected
> select #59/Q:259
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #59/O:106@CG
1 atom, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #59/O:106
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #59/O:108@CB
1 atom, 1 residue, 1 model selected
> hide sel atoms
> undo
> select #59/O:107
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #59/O:108
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #59/Q:263
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!1 models
> select #59/M:12
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #59/M:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:3
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #59/M:2
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
[Repeated 1 time(s)]
> select #59/M:3
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #59/M:2
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #59/M:3
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #59/M:4
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #59/M:5
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:16
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #59/M:6
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> select #59/M:7
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:8
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1
2 models selected
> select #59/M:9
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1
2 models selected
> select #1
2 models selected
> select clear
> select #1
2 models selected
> select clear
> select #59/M:10
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select clear
> select #59/M:11
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:12
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:13
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:14
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:15
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/M:16
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #59/K:255
4 atoms, 3 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:254
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:253
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:252
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:251
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:250
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:249
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:248
7 atoms, 6 bonds, 1 residue, 1 model selected
> delete sel
> select #59/K:247
9 atoms, 8 bonds, 1 residue, 1 model selected
> delete sel
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240806_COPI_leaf_AF3_for_figs_v2.cxs"
> show #!61 models
> hide #!1 models
> color zone #61 near #59 distance 5.86
> color zone #61 near #59 distance 5.55
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240806_COPI_leaf_AF3_for_figs_v2.cxs"
——— End of log from Tue Aug 6 15:17:45 2024 ———
opened ChimeraX session
> hide #!61 models
> show #!61 models
> hide #!59 models
> show #!59 models
> hide #!61 models
> show #!58 models
> hide #!58 models
> show #!58 models
> show #!61 models
> hide #!61 models
> show #!61 models
> hide #!61 models
> show #!56 models
> hide #!56 models
> show #!57 models
> close #61
> combine #1
No structures specified
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/relion_locres_filtered_20240326_GT.mrc"
Opened relion_locres_filtered_20240326_GT.mrc as #60, grid size 292,292,292,
pixel 1.71, shown at level 0.00473, step 2, values float32
> select add #60
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #60,1,0,0,94.293,0,1,0,59.794,0,0,1,17.203
> view matrix models #60,1,0,0,87.011,0,1,0,46.591,0,0,1,75.712
> view matrix models #60,1,0,0,62.484,0,1,0,72.607,0,0,1,72.836
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> fitmap #60 inMap #1
Fit map relion_locres_filtered_20240326_GT.mrc in map
relion_locres_filtered_20240326_GT.mrc using 30918 points
correlation = 1, correlation about mean = 1, overlap = 3.365
steps = 92, shift = 5.1, angle = 0.971 degrees
Position of relion_locres_filtered_20240326_GT.mrc (#60) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99999999 0.00004012 -0.00014956 0.04461249
-0.00004012 1.00000000 0.00001176 -0.00027160
0.00014956 -0.00001176 0.99999999 -0.04335390
Axis -0.07572659 -0.96307673 -0.25835770
Axis point 275.92599265 0.00000000 302.35452588
Rotation angle (degrees) 0.00889794
Shift along axis 0.00808403
> select subtract #60
Nothing selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #60 step 1
> volume #60 level 0.005
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v5.cxs"
> color #24 #98fcffff
> color #24 label_red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #24 alphav1
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color name label_red #E32723
Color 'label_red' is opaque: rgb(89%, 15.3%, 13.7%) hex: #e32723
> color name label_purple #6C4896
Color 'label_purple' is opaque: rgb(42.4%, 28.2%, 58.8%) hex: #6c4896
> color name arf1v2 #EB70A8
Color 'arf1v2' is opaque: rgb(92.2%, 43.9%, 65.9%) hex: #eb70a8
> color name alphav1 #5786F5
Color 'alphav1' is opaque: rgb(34.1%, 52.5%, 96.1%) hex: #5786f5
> color name alphav2 #2A4B9B
Color 'alphav2' is opaque: rgb(16.5%, 29.4%, 60.8%) hex: #2a4b9b
> color name betapv1 #53EAF3
Color 'betapv1' is opaque: rgb(32.5%, 91.8%, 95.3%) hex: #53eaf3
> color name betapv2 #759ED9
Color 'betapv2' is opaque: rgb(45.9%, 62%, 85.1%) hex: #759ed9
> color name betav1 #37863D
Color 'betav1' is opaque: rgb(21.6%, 52.5%, 23.9%) hex: #37863d
> color name betav2 #207B35
Color 'betav2' is opaque: rgb(12.5%, 48.2%, 20.8%) hex: #207b35
> color name deltav1 #CE8041
Color 'deltav1' is opaque: rgb(80.8%, 50.2%, 25.5%) hex: #ce8041
> color name deltav2 #E97408
Color 'deltav2' is opaque: rgb(91.4%, 45.5%, 3.14%) hex: #e97408
> color name epsilonv1 #F06969
Color 'epsilonv1' is opaque: rgb(94.1%, 41.2%, 41.2%) hex: #f06969
> color name gammav1 #2AFF3C
Color 'gammav1' is opaque: rgb(16.5%, 100%, 23.5%) hex: #2aff3c
> color name gammav2 #61B230
Color 'gammav2' is opaque: rgb(38%, 69.8%, 18.8%) hex: #61b230
> color name zetav1 #E0C819
Color 'zetav1' is opaque: rgb(87.8%, 78.4%, 9.8%) hex: #e0c819
> color name zetav2 #EFE30C
Color 'zetav2' is opaque: rgb(93.7%, 89%, 4.71%) hex: #efe30c
> color name arf1v1 #FF76AF
Color 'arf1v1' is opaque: rgb(100%, 46.3%, 68.6%) hex: #ff76af
> color #24 label_red
> color #60 white models
> color #56 white models
> hide #!57 models
> hide #!58 models
> hide #!59 models
> color #38 alphav1
> show #38 models
> hide #!60 models
> show #39 models
> show #41 models
> show #42 models
> show #!43 models
> show #!44 models
> show #!45 models
> show #!46 models
> show #48 models
> show #47 models
> show #!49 models
> show #50 models
> show #51 models
> show #52 models
> show #53 models
> show #!54 models
> color #39 alphav1
> color #41 betapv1
> color #42 betapv1
> color #43 betav1
> color #44 betav1
> color #45 betav1
> color #46 deltav1
> color #47 gammav1
> color #47 gammav2
> color #48 gammav2
> color #49 gammav2
> color #43 betav2
> color #44 betav2
> color #45 betav2
> color #50 zetav1
> color #51 arf1v1
> color #52 arf1v1
> color #53 arf1v1
> color #47 #acacacff
> color #47 gammav2
> color #47 #61db30ff
> color #47 #61c730ff
> color #47 #58c730ff
> color #47 #58de30ff
> color name gammav3 #58DE30
Color 'gammav3' is opaque: rgb(34.5%, 87.1%, 18.8%) hex: #58de30
> color #48 gammav3
> color #49 gammav3
> color #51 arf1v2
> color #52 arf1v2
> color #53 arf1v2
> color #38 alphav1
> color #38 alphav2
> color #39 alphav2
> color #54 label_purple
> color #55 label_purple
> show #55 models
> color #11 #801effff
> color #11 #801ed1ff
> color name label_purplev2 #7F1ED1
Color 'label_purplev2' is opaque: rgb(49.8%, 11.8%, 82%) hex: #7f1ed1
> color #54 label_purplev2
> color #55 label_purplev2
> combine #38 #39 #40 #41 #42 #43 #44 #45 #46 #47 #48 #49 #50 #51 #52 #53 #54
> #55
Remapping chain ID 'D' in 20240711_copi_golph3_alpha_I592-G900.cif #39 to 'E'
Remapping chain ID 'D' in fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif
#40 to 'I'
Remapping chain ID 'E' in fold_hs_copa_b1_b2_d_e_g1_z1_golph3_1_47_model_0.cif
#40 to 'J'
Remapping chain ID 'F' in 20240711_copi_golph3_betaprime_M1-S586.cif #41 to
'K'
Remapping chain ID 'F' in 20240711_copi_golph3_betaprime_L587-D905.cif #42 to
'L'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_S711-L953.cif #43 to 'M'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_H311-E659.cif #44 to 'N'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_M1-H311_K660-A710.cif #45
to 'O'
Remapping chain ID 'G' in 20240711_copi_golph3_delta_M1-S273.cif #46 to 'P'
Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_K300-F448.cif #47 to 'Q'
Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_M1-P299.cif #48 to 'R'
Remapping chain ID 'H' in 20240711_copi_golph3_gammm1_T449-R609.cif #49 to 'S'
Remapping chain ID 'I' in 20240711_copi_golph3_zeta1.cif #50 to 'T'
Remapping chain ID 'B' in 20240711_copi_golph3_beta_Arf1_.cif #51 to 'U'
Remapping chain ID 'C' in 20240711_copi_golph3_gamma_Arf1_.cif #52 to 'V'
Remapping chain ID 'B' in 20240711_copi_golph3_third_Arf1.cif #53 to 'W'
Remapping chain ID 'A' in 20240711_copi_golph3_golph3_M1-.cif #54 to 'X'
Remapping chain ID 'A' in 20240711_copi_golph3_golph3_.cif #55 to 'Y'
> hide #38 models
> hide #39 models
> hide #41 models
> hide #42 models
> hide #!43 models
> hide #!44 models
> hide #!45 models
> hide #!46 models
> hide #47 models
> hide #48 models
> hide #!49 models
> hide #50 models
> hide #51 models
> hide #52 models
> hide #53 models
> hide #!54 models
> hide #55 models
> rename #59 combined_model_COPI_GOLPH3_colorset1
> rename #58 relion_locres_filtered_20240326_GT_colorset1.mrc
> ui tool show "Color Zone"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> show #!60 models
> color zone #60 near #61 distance 10.26
> color zone #60 near #61 distance 10.73
> color zone #60 near #61 distance 4.91
> volume #60 level 0.01316
> close #61
> combine #38 #39 #41 #42 #43 #44 #45 #46 #47 #48 #49 #50 #51 #52 #53 #54 #55
Remapping chain ID 'D' in 20240711_copi_golph3_alpha_I592-G900.cif #39 to 'E'
Remapping chain ID 'F' in 20240711_copi_golph3_betaprime_L587-D905.cif #42 to
'G'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_S711-L953.cif #43 to 'H'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_H311-E659.cif #44 to 'I'
Remapping chain ID 'E' in 20240711_copi_golph3_beta_M1-H311_K660-A710.cif #45
to 'J'
Remapping chain ID 'G' in 20240711_copi_golph3_delta_M1-S273.cif #46 to 'K'
Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_K300-F448.cif #47 to 'L'
Remapping chain ID 'H' in 20240711_copi_golph3_gamma1_M1-P299.cif #48 to 'M'
Remapping chain ID 'H' in 20240711_copi_golph3_gammm1_T449-R609.cif #49 to 'N'
Remapping chain ID 'I' in 20240711_copi_golph3_zeta1.cif #50 to 'O'
Remapping chain ID 'B' in 20240711_copi_golph3_third_Arf1.cif #53 to 'P'
Remapping chain ID 'A' in 20240711_copi_golph3_golph3_.cif #55 to 'Q'
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color zone #60 near #61 distance 4.91
> hide #!60 models
> ui mousemode right select
> select #61/K:255
4 atoms, 3 bonds, 1 residue, 1 model selected
> delete sel
> select #61/K:254
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #61/K:252
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #61/K:253
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select clear
> select #61/K:252
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete sel
> select #61/K:251
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete sel
> select #61/K:250
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #61/K:249
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete sel
> select #61/K:248
7 atoms, 6 bonds, 1 residue, 1 model selected
> delete sel
> show #!60 models
> color single #60
> color zone #60 near #61 distance 4.91
> volume #60 level 0.008979
> color zone #60 near #61 distance 4.85
> color zone #60 near #61 distance 6.64
> color #1 #ebebebff models
> color #1 #d6d6d6ff models
> volume #60 level 0.008
> hide #!61 models
> rename #61 combine_model_COPI_GOLPH3_colorset2
> rename #60 relion_locres_filtered_20240326_GT_colorset2.mrc
> save /Users/becca/Desktop/image1.png supersample 3
> color #1 #d6d6d6cc models
> color #1 #d6d6d69a models
> color #1 #d6d6d699 models
> show #!1 models
> hide #!60 models
> show #!61 models
> save /Users/becca/Desktop/image2.png supersample 3
> save /Users/becca/Desktop/image3.png supersample 3
> hide #!61 models
> show #!60 models
> hide #!1 models
> save /Users/becca/Desktop/image4.png supersample 3
> color #60 #ffffffb9 models
> color #60 #ffffffb7 models
> color zone #60 near #61 distance 6.64
> color #60 #ffffffb8 models
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v6.cxs"
> hide #!60 models
> show #!61 models
> color #61/chain Q label_purple
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #61/chainQ label_purple
> color #61/chainP label_purple
> color #61/chainP blue
> color #61/P blue
> undo
> color #61/Q label_purple
> color #61/R label_purple
> color #61/p label_purple
> undo
> color #61/o label_purple
> undo
> color #61/a label_purple
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/relion_locres_filtered_20240326_GT.mrc"
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #62, grid size
292,292,292, pixel 1.71, shown at level 0.00473, step 2, values float32
> color #62 white models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #62 step 1
> volume #62 level 0.008
> select add #62
2 models selected
> show #!60 models
> ui mousemode right "translate selected models"
> view matrix models #62,1,0,0,82.731,0,1,0,56.524,0,0,1,33.509
> view matrix models #62,1,0,0,79.094,0,1,0,68.742,0,0,1,76.061
> view matrix models #62,1,0,0,75.329,0,1,0,66.28,0,0,1,82.958
> view matrix models #62,1,0,0,62.569,0,1,0,73.325,0,0,1,77.393
> fitmap #62 inMap #1
Fit map relion_locres_filtered_20240326_GT_colorset2.mrc in map
relion_locres_filtered_20240326_GT.mrc using 67258 points
correlation = 1, correlation about mean = 1, overlap = 21.45
steps = 52, shift = 2.4, angle = 0.977 degrees
Position of relion_locres_filtered_20240326_GT_colorset2.mrc (#62) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 -0.00001875 -0.00002627 0.01893074
0.00001875 1.00000000 -0.00002003 -0.00224731
0.00002628 0.00002003 1.00000000 0.00132667
Axis 0.52718994 -0.69167549 0.49361502
Axis point 178.51353821 0.00000000 475.91658522
Rotation angle (degrees) 0.00217651
Shift along axis 0.01218937
> select subtract #62
Nothing selected
> color zone #62 near #61 distance 10.26
> hide #!60 models
> hide #!61 models
> surface dust #62 size 17.1
> show #!60 models
> surface dust #60 size 17.1
> surface dust #62 size 17.1
> hide #!62 models
> hide #!60 models
> show #!62 models
> save /Users/becca/Desktop/image5.png supersample 3
> hide #!62 models
> show #!61 models
> show #!1 models
> save /Users/becca/Desktop/image6.png supersample 3
> hide #!1 models
> show #!1 models
> save /Users/becca/Desktop/image7.png supersample 3
> hide #!1 models
> hide #!61 models
> show #!62 models
> save /Users/becca/Desktop/image8.png supersample 3
> save /Users/becca/Desktop/image9.png supersample 3
> hide #!62 models
> show #!61 models
> show #!1 models
> save /Users/becca/Desktop/image10.png supersample 3
> hide #!1 models
> color #61/b gammav2
> color #61/c gammav2
> color #61/d gammav2
> color #61/e gammav2
> color #61/f gammav2
> color #61/g gammav2
> color #61/f betapv2
> color #61/g betapv2
> color #61/h gammav2
> color #61/i gammav2
> color #61/j gammav2
> color #61/k gammav2
> color #61/l gammav2
> color #61/m gammav2
> color #61/n gammav2
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and resources/COPI-Golph3
> dataset/Structure files/relion_locres_filtered_20240326_GT.mrc"
Opened relion_locres_filtered_20240326_GT_colorset2.mrc as #63, grid size
292,292,292, pixel 1.71, shown at level 0.00473, step 2, values float32
> color #63 white models
> select add #63
2 models selected
> view matrix models #63,1,0,0,75.253,0,1,0,55.49,0,0,1,11.12
> view matrix models #63,1,0,0,90.631,0,1,0,59.745,0,0,1,63.045
> view matrix models #63,1,0,0,68.515,0,1,0,55.118,0,0,1,78.162
> view matrix models #63,1,0,0,66.634,0,1,0,67.567,0,0,1,67.24
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #63 step 1
> volume #63 level 0.008
> fitmap #63 inMap #1
Fit map relion_locres_filtered_20240326_GT_colorset2.mrc in map
relion_locres_filtered_20240326_GT.mrc using 67258 points
correlation = 0.5415, correlation about mean = 0.1363, overlap = 7.061
steps = 116, shift = 7.07, angle = 5.74 degrees
Position of relion_locres_filtered_20240326_GT_colorset2.mrc (#63) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99362306 0.08167924 -0.07772850 -0.92565197
-0.08058175 0.99660031 0.01715800 10.92285128
0.07886570 -0.01078508 0.99682691 -23.17442071
Axis -0.12297538 -0.68915930 -0.71409839
Axis point 213.07603457 14.21459699 0.00000000
Rotation angle (degrees) 6.52360209
Shift along axis 9.13506435
> show #!1 models
> view matrix models
> #63,0.99499,0.069158,-0.072244,60.427,-0.06889,0.99761,0.0061881,84.855,0.072498,-0.0011802,0.99737,52.494
> view matrix models
> #63,0.99499,0.069158,-0.072244,61.276,-0.06889,0.99761,0.0061881,84.838,0.072498,-0.0011802,0.99737,55.066
> show #!60 models
> hide #!60 models
> show #!60 models
> hide #!60 models
> show #!60 models
> hide #!60 models
> hide #!61 models
> fitmap #63 inMap #1
Fit map relion_locres_filtered_20240326_GT_colorset2.mrc in map
relion_locres_filtered_20240326_GT.mrc using 67258 points
correlation = 0.5415, correlation about mean = 0.1362, overlap = 7.06
steps = 64, shift = 3.65, angle = 0.0144 degrees
Position of relion_locres_filtered_20240326_GT_colorset2.mrc (#63) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
0.99360075 0.08181777 -0.07786785 -0.90541724
-0.08073064 0.99659074 0.01701358 11.00212074
0.07899439 -0.01061838 0.99681851 -23.23121300
Axis -0.12141808 -0.68927119 -0.71425687
Axis point 213.54257878 14.23471065 0.00000000
Rotation angle (degrees) 6.53375156
Shift along axis 9.11954274
> view matrix models
> #63,0.99497,0.069297,-0.072381,72.42,-0.069041,0.9976,0.006042,87.797,0.072626,-0.0010144,0.99736,54.674
> fitmap #63 inMap #1
Fit map relion_locres_filtered_20240326_GT_colorset2.mrc in map
relion_locres_filtered_20240326_GT.mrc using 67258 points
correlation = 1, correlation about mean = 1, overlap = 21.46
steps = 152, shift = 9.34, angle = 6.54 degrees
Position of relion_locres_filtered_20240326_GT_colorset2.mrc (#63) relative to
relion_locres_filtered_20240326_GT.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 -0.00003458 0.00000150 0.00697228
0.00003458 1.00000000 -0.00002441 0.00466924
-0.00000150 0.00002441 1.00000000 -0.01150830
Axis 0.57631042 0.03541164 0.81646330
Axis point -140.35346721 288.49393815 0.00000000
Rotation angle (degrees) 0.00242674
Shift along axis -0.00521256
> select subtract #63
Nothing selected
> hide #!1 models
> show #!62 models
> hide #!62 models
> show #!60 models
> hide #!60 models
> show #!61 models
> hide #!61 models
> color zone #63 near #61 distance 10.26
> color zone #63 near #61 distance 10.66
> color zone #63 near #61 distance 8.31
> surface dust #63 size 17.1
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> save /Users/becca/Desktop/image1.png supersample 3
> hide #!63 models
> show #!61 models
> show #!1 models
> save /Users/becca/Desktop/image2.png supersample 3
> save /Users/becca/Desktop/image3.png supersample 3
> hide #!1 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!61 models
> show #!63 models
> save /Users/becca/Desktop/image4.png supersample 3
> save /Users/becca/Desktop/image5.png supersample 3
> hide #!63 models
> show #!62 models
> hide #!62 models
> show #!62 models
> hide #!62 models
> show #!61 models
> show #!1 models
> save /Users/becca/Desktop/image6.png supersample 3
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/Files from
> csparc/cryosparc_P126_J2191_class_02_final_volume.mrc"
Opened cryosparc_P126_J2191_class_02_final_volume.mrc as #64, grid size
180,180,180, pixel 2.42, shown at level 0.333, step 1, values float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/Files from
> csparc/cryosparc_P126_J2191_class_01_final_volume.mrc"
Opened cryosparc_P126_J2191_class_01_final_volume.mrc as #65, grid size
180,180,180, pixel 2.42, shown at level 0.333, step 1, values float32
> open "/Users/becca/Desktop/Postdoc/COPI notebooks and
> resources/Processing/Files from
> csparc/cryosparc_P126_J2191_class_00_final_volume.mrc"
Opened cryosparc_P126_J2191_class_00_final_volume.mrc as #66, grid size
180,180,180, pixel 2.42, shown at level 0.337, step 1, values float32
> close #66
> close #65
> close #64
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v7.cxs"
——— End of log from Fri Aug 9 13:21:55 2024 ———
opened ChimeraX session
> save "/Users/becca/Desktop/Postdoc/Grants and paper drafts/Golph3
> paper/Chimera sessions/20240808_COPI_leaf_AF3_for_figs_v7_with_files.cxs"
> includeMaps true
——— End of log from Wed Sep 25 22:56:27 2024 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
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: MacBookPro18,1
Model Number: Z14V000GPB/A
Chip: Unknown
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 29 days, 9 hours, 10 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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 (1)
comment:1 by , 15 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
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Reported by Sean Munro