![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 months ago
Closed 3 months ago
#18414 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.3-arm64-arm-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 0x00000001fad9db40 (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, openmm._openmm, openmm.app.internal.compiled, chimerax.map._map, chimerax.surface._surface, 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.segment._segment, PIL._imagingmath, chimerax.mlp._mlp, chimerax.coulombic._esp (total: 66)
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{
"uptime" : 87000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 1625,
"osVersion" : {
"train" : "macOS 13.3",
"build" : "22E252",
"releaseType" : "User"
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"captureTime" : "2025-08-12 01:56:12.2641 -0400",
"incident" : "CE5E1F72-264C-46E0-AADB-8CC00514CF17",
"pid" : 20560,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-08-11 13:34:30.1832 -0400",
"procStartAbsTime" : 1541690887438,
"procExitAbsTime" : 2096325967489,
"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":"21890E9C-117D-5281-82C5-80ECB6857070","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "3F2A61ED-7900-03CB-C0A7-D0D27485D281",
"throttleTimeout" : 2147483647,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 268,
"sleepWakeUUID" : "C42A8F69-D7FE-4D78-9CFA-FB59F592991F",
"sip" : "enabled",
"vmRegionInfo" : "0x7f28309994a8 is not in any region. Bytes after previous region: 34256400782505 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO (reserved) 600038000000-600040000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x00007f28309994a8","rawCodes":[1,139810590790824],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00007f28309994a8"},
"vmregioninfo" : "0x7f28309994a8 is not in any region. Bytes after previous region: 34256400782505 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO (reserved) 600038000000-600040000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)\n---> \n UNUSED SPACE AT END",
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"faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1_v03-RON2.cxs"
Opened CS_J2730_003_map_sharp_zflip_resam.mrc as #1, grid size 600,600,600,
pixel 0.823, shown at level 0.118, step 1, values float32
Opened composite_J2546-J2730-J2902-J2614 copy.mrc as #4, grid size
600,600,600, pixel 0.823, shown at level 0.405, step 1, values float32
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #2.2, grid size
600,600,600, pixel 0.823, shown at level 0.968, step 1, values float32
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #6.2, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #8.2, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #9.2, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 0 as #7.1, grid size
600,600,600, pixel 0.823, shown at level 0.395, step 1, values float32
Log from Thu Aug 7 18:38:59 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1_v03-RON2.cxs"
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 as #13.1, grid size
600,600,600, pixel 0.823, shown at level 0.0879, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 1 as #13.2, grid size
600,600,600, pixel 0.823, shown at level 0.0952, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip as #15, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 as #16.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 1 as #16.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 0 as #18.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 1 as #18.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 0 as #19.1, grid size
600,600,600, pixel 0.823, shown at level 0.134, step 1, values float32
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 1 as #19.2, grid size
600,600,600, pixel 0.823, shown at level 0.136, step 1, values float32
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip 0 as #20.1, grid
size 600,600,600, pixel 0.823, shown at level 0.194, step 1, values float32
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip 1 as #20.2, grid
size 600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2386_005_volume_map.mrc as #21, grid size 600,600,600,
pixel 0.823, shown at level 0.0115, step 4, values float32
Opened cryosparc_P4_J2386_005_volume_map.mrc z flip as #22, grid size
600,600,600, pixel 0.823, shown at level 0.0992, step 1, values float32
Opened CS_J2730_003_map_sharp_zflip_resam.mrc as #1, grid size 600,600,600,
pixel 0.823, shown at level 0.118, step 1, values float32
Opened composite_J2546-J2730-J2902-J2614 copy.mrc as #4, grid size
600,600,600, pixel 0.823, shown at step 1, values float32
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #2.2, grid size
600,600,600, pixel 0.823, shown at level 0.968, step 1, values float32
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #6.2, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #8.2, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #9.2, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32
Log from Wed Aug 6 11:59:41 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1_v01.cxs"
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip as #5, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip as #7, grid size
600,600,600, pixel 0.823, shown at level 0.0879, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 as #13.1, grid size
600,600,600, pixel 0.823, shown at level 0.0879, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 1 as #13.2, grid size
600,600,600, pixel 0.823, shown at level 0.0952, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip as #15, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 as #16.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 1 as #16.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 0 as #18.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 1 as #18.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 0 as #19.1, grid size
600,600,600, pixel 0.823, shown at level 0.134, step 1, values float32
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 1 as #19.2, grid size
600,600,600, pixel 0.823, shown at level 0.136, step 1, values float32
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip 0 as #20.1, grid
size 600,600,600, pixel 0.823, shown at level 0.194, step 1, values float32
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip 1 as #20.2, grid
size 600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2386_005_volume_map.mrc as #21, grid size 600,600,600,
pixel 0.823, shown at level 0.0115, step 4, values float32
Opened cryosparc_P4_J2386_005_volume_map.mrc z flip as #22, grid size
600,600,600, pixel 0.823, shown at level 0.0992, step 1, values float32
Opened CS_J2730_003_map_sharp_zflip_resam.mrc as #1, grid size 600,600,600,
pixel 0.823, shown at level 0.118, step 1, values float32
Log from Wed Jul 16 16:11:23 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Tue Jun 3 19:59:46 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Map_model_figs_v02.cxs
Opened cryosparc_P4_J2606_003_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.823, shown at level 0.103, step 1, values float32
Opened cryosparc_P4_J2602_004_volume_map_sharp.mrc as #2, grid size
600,600,600, pixel 0.823, shown at level 0.172, step 1, values float32
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc as #3, grid size
600,600,600, pixel 0.823, shown at level 0.176, step 1, values float32
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip as #5, grid size
600,600,600, pixel 0.823, shown at level 0.194, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc as #6, grid size 600,600,600,
pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip as #7, grid size
600,600,600, pixel 0.823, shown at level 0.0879, step 1, values float32
Opened cryosparc_P4_J1996_004_volume_map.mrc as #9, grid size 600,600,600,
pixel 0.823, shown at level 0.0652, step 1, values float32
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip as #10, grid size
600,600,600, pixel 0.823, shown at level 0.134, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 as #13.1, grid size
600,600,600, pixel 0.823, shown at level 0.0879, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 1 as #13.2, grid size
600,600,600, pixel 0.823, shown at level 0.0952, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip as #15, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 as #16.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 1 as #16.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 0 as #18.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 1 as #18.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 0 as #19.1, grid size
600,600,600, pixel 0.823, shown at level 0.134, step 1, values float32
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 1 as #19.2, grid size
600,600,600, pixel 0.823, shown at level 0.136, step 1, values float32
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip 0 as #20.1, grid
size 600,600,600, pixel 0.823, shown at level 0.194, step 1, values float32
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip 1 as #20.2, grid
size 600,600,600, pixel 0.823, shown at level 0.194, step 1, values float32
Opened cryosparc_P4_J2386_005_volume_map.mrc as #21, grid size 600,600,600,
pixel 0.823, shown at level 0.0115, step 4, values float32
Opened cryosparc_P4_J2386_005_volume_map.mrc z flip as #22, grid size
600,600,600, pixel 0.823, shown at level 0.0992, step 1, values float32
Opened cryosparc_P4_J2386_005_volume_map.mrc z flip 0 as #23.1, grid size
600,600,600, pixel 0.823, shown at level 0.0992, step 1, values float32
Opened cryosparc_P4_J2386_005_volume_map.mrc z flip 1 as #23.2, grid size
600,600,600, pixel 0.823, shown at level 0.107, step 1, values float32
Log from Sat May 31 21:34:44 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Figs/Figures_v03.cxs
Opened cryosparc_P4_J2606_003_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.823, shown at level 0.103, step 1, values float32
Opened cryosparc_P4_J2602_004_volume_map_sharp.mrc as #2, grid size
600,600,600, pixel 0.823, shown at level 0.172, step 1, values float32
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc as #3, grid size
600,600,600, pixel 0.823, shown at level 0.176, step 1, values float32
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip as #5, grid size
600,600,600, pixel 0.823, shown at level 0.194, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc as #6, grid size 600,600,600,
pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip as #7, grid size
600,600,600, pixel 0.823, shown at level 0.0879, step 1, values float32
Opened cryosparc_P4_J1996_004_volume_map.mrc as #9, grid size 600,600,600,
pixel 0.823, shown at level 0.0652, step 1, values float32
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip as #10, grid size
600,600,600, pixel 0.823, shown at level 0.134, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 as #13.1, grid size
600,600,600, pixel 0.823, shown at level 0.0879, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 1 as #13.2, grid size
600,600,600, pixel 0.823, shown at level 0.0952, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip as #15, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 as #16.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 1 as #16.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 0 as #18.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 1 as #18.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 0 as #19.1, grid size
600,600,600, pixel 0.823, shown at level 0.134, step 1, values float32
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 1 as #19.2, grid size
600,600,600, pixel 0.823, shown at level 0.136, step 1, values float32
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip 0 as #20.1, grid
size 600,600,600, pixel 0.823, shown at level 0.194, step 1, values float32
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip 1 as #20.2, grid
size 600,600,600, pixel 0.823, shown at level 0.194, step 1, values float32
Log from Mon May 26 07:46:14 2025 Startup Messages
---
warning | Registration file '/Users/meserethaile/Library/Application Support/ChimeraX/registration' has expired
note | available bundle cache has not been initialized yet
> ui tool hide "command line interface"
> ui tool show clix
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/meserethaile/Downloads/cryosparc_P4_J2606_003_volume_map_sharp.mrc
Opened cryosparc_P4_J2606_003_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 0.823, shown at level 0.0517, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #1 step 1
> volume #1 level 0.1032
> open
> /Users/meserethaile/Downloads/cryosparc_P4_J2602_004_volume_map_sharp.mrc
Opened cryosparc_P4_J2602_004_volume_map_sharp.mrc as #2, grid size
600,600,600, pixel 0.823, shown at level 0.0141, step 4, values float32
> open
> /Users/meserethaile/Downloads/cryosparc_P4_J2614_003_volume_map_sharp.mrc
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc as #3, grid size
600,600,600, pixel 0.823, shown at level 0.0176, step 4, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #2 step 1
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #3 step 1
> volume #2 level 0.04849
> volume #3 level 0.06161
> volume #2 level 0.1218
> volume #2 level 0.186
> volume #2 level 0.1722
> volume #3 level 0.1757
> open 3zwz fromDatabase pdb format mmcif
3zwz title:
Crystal structure of Plasmodium falciparum AMA1 in complex with a 39aa PfRON2
peptide [more info...]
Chain information for 3zwz #4
---
Chain | Description | UniProt
A | APICAL MEMBRANE ANTIGEN 1, AMA1 | Q7KQK5_PLAF7 103-441
B | RHOPTRY NECK PROTEIN 2 | Q8IKV6_PLAF7 2021-2059
Non-standard residues in 3zwz #4
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
> select add #4
2892 atoms, 2731 bonds, 1 pseudobond, 564 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,150.77,0,1,0,-101.07,0,0,1,505.95
> view matrix models #4,1,0,0,256.23,0,1,0,273.07,0,0,1,143.04
> view matrix models #4,1,0,0,222.62,0,1,0,292.97,0,0,1,161.57
> volume flip #3
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip as #5, grid size
600,600,600, pixel 0.823, shown at step 1, values float32
> view matrix models #4,1,0,0,259.12,0,1,0,329.33,0,0,1,277.73
> view matrix models #4,1,0,0,254.66,0,1,0,319.52,0,0,1,298.54
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.0052801,0.089762,0.99595,237.42,0.92241,0.38418,-0.039516,314.48,-0.38617,0.91888,-0.080769,325.77
> view matrix models
> #4,-0.64059,-0.42716,0.63811,246.1,-0.0063165,0.8339,0.55188,307.43,-0.76786,0.3495,-0.53688,335.13
> view matrix models
> #4,0.17142,-0.9826,0.071492,252.99,-0.21167,0.03414,0.97674,296.72,-0.96219,-0.18256,-0.20214,327.12
> view matrix models
> #4,-0.060486,-0.99228,-0.10831,257.6,-0.30748,-0.084709,0.94778,297.35,-0.94963,0.09063,-0.29998,329.93
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.060486,-0.99228,-0.10831,253.1,-0.30748,-0.084709,0.94778,301.11,-0.94963,0.09063,-0.29998,332.09
> 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 #4 inMap #5
Fit molecule 3zwz (#4) to map cryosparc_P4_J2614_003_volume_map_sharp.mrc z
flip (#5) using 2892 atoms
average map value = 0.07416, steps = 208
shifted from previous position = 26.6
rotated from previous position = 9.94 degrees
atoms outside contour = 2377, contour level = 0.17568
Position of 3zwz (#4) relative to cryosparc_P4_J2614_003_volume_map_sharp.mrc
z flip (#5) coordinates:
Matrix rotation and translation
0.05293533 -0.99853692 0.01103978 231.31013513
-0.35796158 -0.00865367 0.93369621 287.44663572
-0.93223460 -0.05337734 -0.35789594 320.36343888
Axis -0.65450719 0.62546490 0.42475169
Axis point 0.00000000 341.34388986 171.06253126
Rotation angle (degrees) 131.05681941
Shift along axis 164.46854871
> select subtract #4
Nothing selected
> hide #!4 models
> volume #5 level 0.2183
> show #!4 models
> select add #4
2892 atoms, 2731 bonds, 1 pseudobond, 564 residues, 2 models selected
> view matrix models
> #4,0.052935,-0.99854,0.01104,229.69,-0.35796,-0.0086537,0.9337,285.99,-0.93223,-0.053377,-0.3579,323.84
> view matrix models
> #4,0.052935,-0.99854,0.01104,228.73,-0.35796,-0.0086537,0.9337,285.96,-0.93223,-0.053377,-0.3579,323.53
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.0547,-0.98937,0.13473,226.63,-0.33782,0.14531,0.92993,286.43,-0.93962,0.0053534,-0.34218,323.42
> view matrix models
> #4,0.39287,-0.91501,-0.091711,229.84,-0.61421,-0.33531,0.71436,290.68,-0.6844,-0.22432,-0.69374,329.13
> view matrix models
> #4,0.25263,-0.9345,0.25078,223.38,-0.44053,0.11967,0.88973,287.62,-0.86146,-0.33525,-0.38144,322.8
> view matrix models
> #4,0.38852,-0.91614,0.098708,226.06,-0.44983,-0.095083,0.88804,287.03,-0.80418,-0.38942,-0.44904,323.79
> view matrix models
> #4,0.51294,-0.85793,-0.029166,228.46,-0.35492,-0.24289,0.90279,285.86,-0.78162,-0.45273,-0.42908,323.08
> view matrix models
> #4,0.5206,-0.85156,-0.061848,229.15,-0.25126,-0.22203,0.94211,284.66,-0.81599,-0.47492,-0.32955,321.02
> view matrix models
> #4,0.71686,-0.68356,0.13731,224.61,-0.28789,-0.11083,0.95123,284.96,-0.63501,-0.72143,-0.27624,318.38
> fitmap #4 inMap #5
Fit molecule 3zwz (#4) to map cryosparc_P4_J2614_003_volume_map_sharp.mrc z
flip (#5) using 2892 atoms
average map value = 0.1527, steps = 188
shifted from previous position = 3.62
rotated from previous position = 34.8 degrees
atoms outside contour = 2079, contour level = 0.2183
Position of 3zwz (#4) relative to cryosparc_P4_J2614_003_volume_map_sharp.mrc
z flip (#5) coordinates:
Matrix rotation and translation
0.27882958 -0.95722043 -0.07735055 228.32568023
-0.45677008 -0.20304060 0.86610369 287.32033700
-0.84475745 -0.20616391 -0.49384338 324.58692754
Axis -0.76027814 0.54412042 0.35483816
Axis point 0.00000000 304.01666654 152.06635633
Rotation angle (degrees) 135.15582083
Shift along axis 97.92166563
> fitmap #4 inMap #5
Fit molecule 3zwz (#4) to map cryosparc_P4_J2614_003_volume_map_sharp.mrc z
flip (#5) using 2892 atoms
average map value = 0.1527, steps = 44
shifted from previous position = 0.00249
rotated from previous position = 0.00333 degrees
atoms outside contour = 2080, contour level = 0.2183
Position of 3zwz (#4) relative to cryosparc_P4_J2614_003_volume_map_sharp.mrc
z flip (#5) coordinates:
Matrix rotation and translation
0.27881318 -0.95722143 -0.07739731 228.32597888
-0.45673538 -0.20306577 0.86611609 287.32176523
-0.84478163 -0.20613450 -0.49381431 324.58774291
Axis -0.76027285 0.54410925 0.35486663
Axis point 0.00000000 304.01462600 152.07234351
Rotation angle (degrees) 135.15632817
Shift along axis 97.92974526
> volume #5 level 0.1672
> volume #5 color #b2af69
> volume #5 color #b2af6980
> select subtract #4
Nothing selected
> color #4 #906f90ff
> color #4 #907190ff
> select add #4
2892 atoms, 2731 bonds, 1 pseudobond, 564 residues, 2 models selected
> hide (#!4 & sel) target a
> volume #5 color #b2af4e80
> volume #5 color #97af4e80
> volume #5 color #974d4e80
> select subtract #4
Nothing selected
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain /B
Alignment identifier is 4/B
> select clear
> select /B:2023-2058
259 atoms, 263 bonds, 36 residues, 1 model selected
> color sel yellow
> open /Users/meserethaile/Downloads/cryosparc_P4_J2546_009_volume_map.mrc
Opened cryosparc_P4_J2546_009_volume_map.mrc as #6, grid size 600,600,600,
pixel 0.823, shown at level 0.0188, step 4, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #6 step 1
> volume #6 level 0.1093
> volume #6 level 0.166
> view matrix models
> #4,0.36407,-0.87396,0.32196,219.7,-0.92177,-0.28861,0.25892,301.94,-0.13336,-0.39103,-0.91066,330.01
> view matrix models
> #4,0.16705,-0.86529,0.47262,217.32,-0.94349,-0.0011332,0.3314,301.37,-0.28622,-0.50127,-0.81658,328.28
> view matrix models
> #4,0.07023,-0.98771,0.13961,224.45,-0.51618,0.083782,0.85237,288.75,-0.8536,-0.13193,-0.50395,325.07
> fitmap #4 inMap #5
Fit molecule 3zwz (#4) to map cryosparc_P4_J2614_003_volume_map_sharp.mrc z
flip (#5) using 2892 atoms
average map value = 0.1527, steps = 92
shifted from previous position = 0.44
rotated from previous position = 17.4 degrees
atoms outside contour = 1601, contour level = 0.16716
Position of 3zwz (#4) relative to cryosparc_P4_J2614_003_volume_map_sharp.mrc
z flip (#5) coordinates:
Matrix rotation and translation
0.27889580 -0.95720965 -0.07724516 228.32390022
-0.45685548 -0.20300112 0.86606790 287.31926264
-0.84468941 -0.20625282 -0.49392264 324.58696998
Axis -0.76030148 0.54413664 0.35476328
Axis point 0.00000000 304.01942783 152.05049424
Rotation angle (degrees) 135.15474655
Shift along axis 97.89747611
> fitmap #4 inMap #5
Fit molecule 3zwz (#4) to map cryosparc_P4_J2614_003_volume_map_sharp.mrc z
flip (#5) using 2892 atoms
average map value = 0.1527, steps = 40
shifted from previous position = 0.0056
rotated from previous position = 0.0178 degrees
atoms outside contour = 1600, contour level = 0.16716
Position of 3zwz (#4) relative to cryosparc_P4_J2614_003_volume_map_sharp.mrc
z flip (#5) coordinates:
Matrix rotation and translation
0.27870107 -0.95724887 -0.07746165 228.32828427
-0.45674437 -0.20306688 0.86611109 287.31956721
-0.84481376 -0.20600591 -0.49381299 324.59072368
Axis -0.76023879 0.54412983 0.35490803
Axis point 0.00000000 304.01305348 152.09214800
Rotation angle (degrees) 135.16087469
Shift along axis 97.95498318
> select add #4
2892 atoms, 2731 bonds, 1 pseudobond, 564 residues, 2 models selected
> select subtract #4
Nothing selected
> volume #5 color #974d6b80
> volume flip #6
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip as #7, grid size
600,600,600, pixel 0.823, shown at step 1, values float32
> volume #7 color #974d6b80
> select add #7
2 models selected
> volume #7 level 0.1394
> volume #5 level 0.2524
> select subtract #7
Nothing selected
> lighting shadows true
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> set bgColor white
> volume #5 level 0.1899
> volume #5 level 0.187
> volume #7 level 0.1394
> open
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Models/J1332_R2seq_coot.pdb
Chain information for J1332_R2seq_coot.pdb #8
---
Chain | Description
A | No description available
> fitmap #8 inMap #7
Fit molecule J1332_R2seq_coot.pdb (#8) to map
cryosparc_P4_J2546_009_volume_map.mrc z flip (#7) using 9230 atoms
average map value = 0.2458, steps = 72
shifted from previous position = 3.27
rotated from previous position = 2.51 degrees
atoms outside contour = 2295, contour level = 0.13942
Position of J1332_R2seq_coot.pdb (#8) relative to
cryosparc_P4_J2546_009_volume_map.mrc z flip (#7) coordinates:
Matrix rotation and translation
0.99955761 -0.02952277 -0.00360310 7.28628788
0.02939182 0.99905011 -0.03217133 2.98774955
0.00454947 0.03205119 0.99947587 -7.84771483
Axis 0.73369975 -0.09313775 0.67306021
Axis point -0.00000000 241.74080827 85.11189816
Rotation angle (degrees) 2.50842052
Shift along axis -0.21430926
> volume #5 level 0.2108
> save
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Figs/Figures_v01.cxs
> volume #5 level 0.1752
> volume #5 level 0.1942
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "Hide Dust"
> surface dust #5 size 4.94
> volume #7 level 0.1136
> surface dust #7 size 4.94
> volume #7 level 0.08787
> surface dust #7 size 4.91
> surface dust #7 size 7.26
> open "/Users/meserethaile/Desktop/HoLab/Lab Meeting
> PPTs/Figs/250519_figs/cryosparc_P4_J1996_004_volume_map.mrc"
Opened cryosparc_P4_J1996_004_volume_map.mrc as #9, grid size 600,600,600,
pixel 0.823, shown at level 0.0124, step 4, values float32
> volume #9 step 1
> volume #9 level 0.06524
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> volume flip #9
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip as #10, grid size
600,600,600, pixel 0.823, shown at step 1, values float32
> volume #10 level 0.1445
> surface dust #10 size 4.94
> volume #10 level 0.1638
> volume #10 color #974d6b80
> volume #10 level 0.1339
> surface dust #10 size 5.11
> surface dust #10 size 13.92
> hide #!4 models
> hide #!8 models
> show #!8 models
> color #8 #9d8420ff
> open
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Models/J1332_R4seq_coot.pdb
Chain information for J1332_R4seq_coot.pdb #11
---
Chain | Description
A | No description available
> open
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Models/J1332_R5seq_coot.pdb
Chain information for J1332_R5seq_coot.pdb #12
---
Chain | Description
A | No description available
> hide #!12 models
> show #!12 models
> color #12 #7d6f86ff
> color #11 #90a583ff
> hide #!10 models
> hide #!7 models
> hide #!5 models
> color #11 #1f2041ff
> color #11 #94b9afff
> show #!4 models
> color #4 #edbfb7ff
> color #4 #273c2cff
> color #4 #114b5fff
> color #4 #f79d84ff
> color #4 #002e2cff
> show #!10 models
> hide #!10 models
> show #!7 models
> hide #!7 models
> save
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Figs/Figures_v01.cxs
> show #!10 models
> hide #!10 models
> show #!7 models
> ui tool show "Surface Color"
> ui tool show "Surface Zone"
> surface zone #7 nearAtoms #8 distance 4.94
[Repeated 1 time(s)]
> surface zone #7 nearAtoms #8 distance 5.09
> surface zone #7 nearAtoms #8 distance 2.84
[Repeated 1 time(s)]
> ui tool show "Segment Map"
> ui tool show "Color Zone"
> color zone #7 near #8 distance 4.94
> volume splitbyzone #7
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 as #13.1, grid size
600,600,600, pixel 0.823, shown at level 0.0879, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 1 as #13.2, grid size
600,600,600, pixel 0.823, shown at level 0.0879, step 1, values float32
> volume #13.2 level 0.1012
> surface dust #13.2 size 4.94
> volume #13.2 level 0.09233
> color zone #7 near #11 distance 4.94
[Repeated 1 time(s)]
> color zone #7 near #12 distance 4.94
[Repeated 2 time(s)]
> color zone #7 near #12 distance 4.88
> color zone #7 near #12 distance 6.23
[Repeated 1 time(s)]
> help help:user/tools/colorzone.html
> color zone #5 near #4 distance 4.94
> show #!5 models
> color zone #5 near #4 distance 5.15
> color zone #5 near #4 distance 5.23
> hide #!4 models
> show #!7 models
> color zone #7 near #11 distance 6.23
[Repeated 1 time(s)]
> color zone #7 near #12 distance 6.23
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> color zone #7 near #12 distance 6.23
> color zone #7 near #12 distance 5.82
[Repeated 1 time(s)]
> color single #7
> color zone #7 near #12 distance 5.82
> color zone #10 near #12 distance 4.94
> show #!10 models
> volume splitbyzone #10
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 0 as #14.1, grid size
600,600,600, pixel 0.823, shown at level 0.134, step 1, values float32
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 1 as #14.2, grid size
600,600,600, pixel 0.823, shown at level 0.134, step 1, values float32
> close #14.2
> close #14.1
> hide #!8 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!10 models
> hide #!10 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> volume flip #6
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip as #15, grid size
600,600,600, pixel 0.823, shown at step 1, values float32
> color zone #15 near #12 distance 4.94
> color zone #15 near #12 distance 4.96
> color zone #15 near #12 distance 5.9
> volume splitbyzone #15
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 as #16.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 1 as #16.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
> color zone #16.1 near #11 distance 4.94
> color zone #16.1 near #11 distance 4.7
> color zone #16.1 near #11 distance 6.39
> color zone #16.1 near #11 distance 6.48
> color zone #16.1 near #11 distance 6.82
> color zone #16.1 near #11 distance 6.91
> color zone #16.1 near #11 distance 5.55
> color zone #16.1 near #11 distance 5.63
> color zone #16.1 near #11 distance 2.78
[Repeated 2 time(s)]
> volume splitbyzone #16.1
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 0 as #17.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 1 as #17.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
> close #17.2
> close #17.1
> color zone #16.1 near #11 distance 2.75
> color zone #16.1 near #11 distance 3.78
> color zone #16.1 near #11 distance 3.83
> color zone #16.1 near #11 distance 4.47
> volume splitbyzone #16.1
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 0 as #18.1, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
Opened cryosparc_P4_J2546_009_volume_map.mrc z flip 0 1 as #18.2, grid size
600,600,600, pixel 0.823, shown at level 0.166, step 1, values float32
> volume #13.2 level 0.09516
> color zone #10 near #12 distance 4.94
> color zone #10 near #12 distance 5.01
> color zone #10 near #12 distance 32.15
> color zone #10 near #12 distance 34.28
> color zone #10 near #12 distance 28.65
> color zone #10 near #12 distance 26.87
> volume splitbyzone #10
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 0 as #19.1, grid size
600,600,600, pixel 0.823, shown at level 0.134, step 1, values float32
Opened cryosparc_P4_J1996_004_volume_map.mrc z flip 1 as #19.2, grid size
600,600,600, pixel 0.823, shown at level 0.134, step 1, values float32
> volume #19.2 level 0.1306
> volume #19.2 level 0.1355
> ui tool show "Hide Dust"
> surface dust #19.2 size 4.94
> surface dust #19.2 size 5.15
> surface dust #19.2 size 12.08
> save
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Figs/Figures_v02.cxs
> lighting flat
> show #!4 models
> hide #!4 models
> lighting full
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> color zone #5 near #4 distance 5.23
> show #!5 models
> color zone #5 near #4 distance 5.41
> color zone #5 near #4 distance 14.34
> color zone #5 near #4 distance 15.49
> color zone #5 near #4 distance 9.52
> color zone #5 near #4 distance 9.27
> color zone #5 near #4 distance 8.48
> hide #!13.2 models
> show #!13.2 models
> hide #!13.2 models
> show #!13.2 models
> hide #!13.2 models
> show #!13.2 models
> hide #!13.2 models
> show #!13.2 models
> hide #!13.2 models
> volume splitbyzone #5
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip 0 as #20.1, grid
size 600,600,600, pixel 0.823, shown at level 0.194, step 1, values float32
Opened cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip 1 as #20.2, grid
size 600,600,600, pixel 0.823, shown at level 0.194, step 1, values float32
> surface dust #20.2 size 4.94
> save
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Figs/Figures_v02.cxs
——— End of log from Mon May 26 07:46:14 2025 ———
opened ChimeraX session
> hide #!19.2 models
> show #!19.2 models
> color #19.2 #f1a805ff models
> color #19.2 #e0ac70ff models
> color #19.2 #d8a768ff models
> hide #!16.2 models
> show #!16.2 models
> color #16.2 #d8a768ff models
> hide #!13.2 models
> show #!13.2 models
> color #13.2 #9d7982ff models
> hide #!20.2 models
> show #!20.2 models
> hide #!20.2 models
> open /Users/meserethaile/Downloads/cryosparc_P4_J2386_005_volume_map.mrc
Opened cryosparc_P4_J2386_005_volume_map.mrc as #21, grid size 600,600,600,
pixel 0.823, shown at level 0.0115, step 4, values float32
> ui tool show CliX
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select down
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> volume flip #21
Opened cryosparc_P4_J2386_005_volume_map.mrc z flip as #22, grid size
600,600,600, pixel 0.823, shown at step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #22 level 0.09923
> 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 #22 near #4 distance 4.94
> color zone #22 near #4 distance 5.04
> color zone #22 near #4 distance 9.82
> color zone #22 near #4 distance 9.49
> volume splitbyzone #22
Opened cryosparc_P4_J2386_005_volume_map.mrc z flip 0 as #23.1, grid size
600,600,600, pixel 0.823, shown at level 0.0992, step 1, values float32
Opened cryosparc_P4_J2386_005_volume_map.mrc z flip 1 as #23.2, grid size
600,600,600, pixel 0.823, shown at level 0.0992, step 1, values float32
> color #23.2 #5e718bff models
> hide #!18.2 models
> show #!18.2 models
> color #18.2 #c2754cff models
> volume #23.2 level 0.1074
> hide #11 models
> hide #!12 models
> color #18.2 #99a99aff models
> lighting flat
> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Cart01.png width
> 1320 height 877 supersample 3 transparentBackground true
> turn x -90
> save /Users/meserethaile/Desktop/image18.png supersample 3
> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Cart02.png width
> 1320 height 877 supersample 3 transparentBackground true
> turn x 90
> turn y 180
> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Cart03.png width
> 1320 height 877 supersample 3 transparentBackground true
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting soft
> lighting simple
> lighting flat
> lighting full
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
[Repeated 1 time(s)]
> lighting shadows false
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Fig01.png width
> 1320 height 877 supersample 3 transparentBackground true
> turn y -180
> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Fig02.png width
> 1320 height 877 supersample 3 transparentBackground true
> turn x -90
> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Fig03.png width
> 1320 height 877 supersample 3 transparentBackground true
> show #!4 models
> hide #!4 models
> show #!12 models
> show #11 models
> color #12 #d8a768ff
> color #11 #99a99aff
> color #8 #9d7982ff
> show #!8 models
> hide #!18.2 models
> hide #!19.2 models
> hide #!16.2 models
> hide #!13.2 models
> hide #!23.2 models
> show #!23.2 models
> hide #!23.2 models
> ui tool show "Side View"
> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Fig04.png width
> 1320 height 877 supersample 3 transparentBackground true
> turn x 90
> show #!4 models
> color #4 grey
> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Fig05.png width
> 1320 height 877 supersample 3 transparentBackground true
> save
> /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Map_model_figs_v02.cxs
——— End of log from Sat May 31 21:34:44 2025 ———
opened ChimeraX session
> hide #11 models
> show #11 models
> color #11 #7da99aff
> color #11 #7ca99aff
> color #11 #78a99aff
> color #11 #70a99aff
> color #11 #6da99aff
> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./newgreen1.png
> width 1984 height 1296 supersample 3
> ui tool show CliX
> turn x -90
> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./newgreen2.png
> width 1984 height 1237 supersample 3
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> ui tool show "Side View"
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./newgreen3.png
> width 1984 height 1237 supersample 3
> turn x 90
> lighting shadows true
> lighting shadows false
> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./newgreen4.png
> width 1984 height 1237 supersample 3
[Repeated 1 time(s)]
> color #4 #bfbfbfff
> color #4 grey
> color #4 #acacacff
> color #4 #aaaaaaff
> color #4 #abababff
> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./newgrey1.png
> width 1984 height 1237 supersample 3
> hide #11 models
> hide #!12 models
> show #!19.2 models
> show #!16.2 models
> show #!18.2 models
> show #11 models
> color #11 #9c9c9cff
> color #18.2 #a3dfceff models
> hide #11 models
> show #11 models
> color #11 #a3dfceff
> hide #11 models
> show #11 models
> hide #11 models
> save
> /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Map_model_figs_v03_newcolors.cxs
> hide #!16.2 models
> hide #!19.2 models
> show #!12 models
> show #11 models
> hide #!18.2 models
> color #11 #99a99aff
> color #11 #67a99aff
> color #11 #5ea99aff
> color #11 #60a99aff
> color #11 #61a99aff
> color #11 #65a99aff
> color #11 #66a99aff
> color #11 #69a99aff
> color #11 #68a99aff
> color #11 #64a99aff
> hide #11 models
> color #18.2 #64a99aff models
> show #!18.2 models
> show #!13.2 models
> show #!16.2 models
> hide #!12 models
> show #!23.2 models
> hide #!4 models
> show #!19.2 models
> hide #!19.2 models
> show #!19.2 models
> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./mapnew1.png
> width 1984 height 1237 supersample 3
> turn x -90
> hide #!8 models
> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./mapnew2png.png
> width 1984 height 1237 supersample 3
> turn x 90
> save /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./mapnew1.png
> width 1984 height 1237 supersample 3
> save
> /Users/meserethaile/Desktop/HoLab/Grants/May2025/Figs./Map_model_figs_v03_newcolors.cxs
——— End of log from Tue Jun 3 19:59:46 2025 ———
opened ChimeraX session
> open
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Models/July2025/AMA1-RON_coot17-branch2a.pdb
Summary of feedback from opening
/Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Models/July2025/AMA1-RON_coot17-branch2a.pdb
---
warning | PDB SEQRES record for chain B is incomplete. Ignoring input sequence records as basis for sequence.
Chain information for AMA1-RON_coot17-branch2a.pdb #24
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> close #24
> close #1
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> close #2
> show #!3 models
> hide #!3 models
> close #3
> close #4
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> close #6
> show #!7 models
> hide #!7 models
> close #9
> show #!10 models
> hide #!10 models
> close #10
> show #!12 models
> hide #!12 models
> show #11 models
> hide #11 models
> show #!8 models
> hide #!8 models
> hide #!23.2 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!16.2 models
> show #!16.2 models
> hide #!16.2 models
> show #!16.2 models
> open
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Models/June2025/CS_J2730_003_map_sharp_zflip_resam.mrc
Opened CS_J2730_003_map_sharp_zflip_resam.mrc as #1, grid size 600,600,600,
pixel 0.823, shown at level 0.00632, step 4, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #1 step 1
> close #23
> volume #1 level 0.07624
> volume #1 level 0.07974
> hide #!19.2 models
> ui tool show "Hide Dust"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
[Repeated 1 time(s)]
> surface dust #1 size 4.94
> volume #1 level 0.09722
> color #22 #d8a768ff models
> show #!22 models
> hide #!22 models
> color #1 #d8a768ff models
> volume #1 level 0.1532
> volume #1 level 0.1182
> show #!5 models
> hide #!5 models
> show #!5 models
> open
> /Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Models/July2025/AMA1-RON_coot17-2a.pdb
Summary of feedback from opening
/Users/meserethaile/Desktop/AMA1-RON2/DataProcessing/Models/July2025/AMA1-RON_coot17-2a.pdb
---
warning | PDB SEQRES record for chain B is incomplete. Ignoring input sequence records as basis for sequence.
Chain information for AMA1-RON_coot17-2a.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> show #!2 target m
> hide #!20 models
> hide #!19 models
> hide #!18.2 models
> hide #!18 models
> hide #17 models
> hide #!16.2 models
> hide #!16 models
> hide #14 models
> hide #!13.2 models
> hide #!13 models
> hide #!5 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #11 models
> hide #11 models
> show #!18.2 models
> hide #!18.2 models
> show #!5 models
> ui tool show "Color Zone"
Drag select of 2464 residues, 6 pseudobonds
> select up
20536 atoms, 20917 bonds, 6 pseudobonds, 2508 residues, 2 models selected
> select up
21149 atoms, 21545 bonds, 6 pseudobonds, 2592 residues, 2 models selected
> select up
24379 atoms, 24851 bonds, 7 pseudobonds, 2993 residues, 2 models selected
> select down
21149 atoms, 21545 bonds, 6 pseudobonds, 2592 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> save
> /Users/meserethaile/Desktop/AMA1-RON2/Manuscript/Figures_v01/AMA1-RON_coot17-2a-AMA1.pdb
> models #2
> color zone #5 near #2 distance 8.37
> color zone #5 near #2 distance 8.51
> color zone #5 near #2 distance 9.49
> color single #5
> color zone #5 near #2 distance 9.49
> color zone #5 near #2 distance 9.38
> color zone #5 near #2 distance 764.89
> color zone #5 near #2 distance 823
> color zone #5 near #2 distance 6.11
> hide #!18 models
> hide #!5 models
> show #!5 models
> volume #20.2 level 0.09497
> volume #20.2 level 0.1661
> hide #!20.2 models
> volume #5 level 0.1657
> color zone #5 near #2 distance 6.11
> 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.
> fitmap #2 inMap #5
Fit molecule AMA1-RON_coot17-2a.pdb (#2) to map
cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip (#5) using 3230 atoms
average map value = 0.1745, steps = 92
shifted from previous position = 4.59
rotated from previous position = 4.84 degrees
atoms outside contour = 1589, contour level = 0.16572
Position of AMA1-RON_coot17-2a.pdb (#2) relative to
cryosparc_P4_J2614_003_volume_map_sharp.mrc z flip (#5) coordinates:
Matrix rotation and translation
0.99722033 -0.05751848 0.04736287 1.36165169
0.05934502 0.99750995 -0.03810588 -2.20762168
-0.04505314 0.04081071 0.99815064 2.71122437
Axis 0.46807268 0.54814092 0.69314465
Axis point 49.71397994 10.63849155 0.00000000
Rotation angle (degrees) 4.83574496
Shift along axis 1.30653483
> color single #5
> color zone #5 near #2 distance 6.11
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> open /Users/meserethaile/Downloads/cryosparc_P4_J3019_019_volume_map.mrc
Opened cryosparc_P4_J3019_019_volume_map.mrc as #3, grid size 600,600,600,
pixel 0.823, shown at level 0.00748, step 4, values float32
> hide #!3 models
> close #3
> save
> /Users/meserethaile/Desktop/AMA1-RON2/Manuscript/Figures_v01/Fig1_v02.cxs
——— End of log from Wed Jul 16 16:11:23 2025 ———
opened ChimeraX session
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> open "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb"
Chain information for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> open "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/composite_J2546-J2730-J2902-J2614 copy.mrc"
Opened composite_J2546-J2730-J2902-J2614 copy.mrc as #4, grid size
600,600,600, pixel 0.823, shown at level 0.162, step 4, values float32
> show #!15 models
> hide #!15 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #4 step 1
> volume #4 level 0.7613
> volume #4 level 0.8394
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> show #!3 models
> ui tool show CliX
> split #3 chains
Split AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb (#3) into 4 models
Chain information for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb A
#3.1
---
Chain | Description
A | No description available
Chain information for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb B
#3.2
---
Chain | Description
B | No description available
Chain information for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb C
#3.3
---
Chain | Description
C | No description available
Chain information for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb D
#3.4
---
Chain | Description
D | No description available
> hide #!4 models
> select add #3.4
3230 atoms, 3313 bonds, 1 pseudobond, 401 residues, 2 models selected
> select subtract #3.4
Nothing selected
> hide #!3.4 models
> hide #!3.3 models
> hide #3.2 models
> hide #!3.1 models
> show #!3.1 models
> close #2
> hide #!3 models
> show #!3 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> color #3.1 #9d7982ff
> show #3.2 models
> hide #3.2 models
> show #3.2 models
> color #3.2 #64a99aff
> show #!3.3 models
> color #3.3 #f1a805ff
> color #3.3 #d8a768ff
> show #!3.4 models
> color #3.4 #6699ffff
> color #3.4 #788ba9ff
> ui tool show "Side View"
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1_v01.cxs"
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1-1.png" width 1686 height 1098 supersample 3
> close #11#8,12
> show #!4 models
> hide #!4 models
> show #!4 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "Color Zone"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color zone #4 near #3.1 distance 4.94
> color zone #4 near #3.1 distance 5.1
> color zone #4 near #3.1 distance 7.23
> color zone #4 near #3.1 distance 7.3
> color zone #4 near #3.1 distance 5.87
> color zone #4 near #3.1 distance 5
[Repeated 1 time(s)]
> volume splitbyzone #4
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 0 as #2.1, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #2.2, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32
> hide #!2.1 models
> volume #2.2 level 0.9678
> color zone #4 near #3.2 distance 5
> show #!2.1 models
> hide #!2.2 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!2.1 models
> hide #!2 models
> show #!4 models
> volume splitbyzone #4
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 0 as #6.1, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #6.2, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32
> color zone #4 near #3.3 distance 5
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!6.1 models
> hide #!6 models
> show #!6 models
> color zone #4 near #3.3 distance 5.16
> color zone #4 near #3.3 distance 5.67
> color zone #4 near #3.3 distance 5.77
> color zone #4 near #3.3 distance 6.78
> color zone #4 near #3.3 distance 6.84
> color zone #4 near #3.3 distance 6.52
> hide #!3.4 models
> hide #3.2 models
> hide #!3.1 models
> hide #!3 models
> show #!3.1 models
> hide #!3.1 models
> hide #!6 models
> hide #!6.2 models
> color single #4
> color zone #4 near #3.3 distance 6.52
> color zone #4 near #3.3 distance 7
[Repeated 1 time(s)]
> volume splitbyzone #4
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 0 as #8.1, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #8.2, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32
> hide #!8.1 models
> hide #!8 models
> hide #!3.3 models
> color zone #4 near #3.4 distance 7
> show #!4 models
> color zone #4 near #3.4 distance 6
[Repeated 1 time(s)]
> color zone #4 near #3.4 distance 5
[Repeated 3 time(s)]
> volume splitbyzone #4
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 0 as #9.1, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #9.2, grid size
600,600,600, pixel 0.823, shown at level 0.839, step 1, values float32
> hide #!9.1 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> close #8.1
> close #9.1
> close #6.1
> show #!8 models
> show #!7 models
> hide #!7 models
> close #7
> show #!6.2 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> hide #4.1 models
> show #!4 models
> show #!2.2 models
> close #2.1
> show #4.1 models
> hide #4.1 models
> hide #!4 models
> close #5
> ui tool show "Hide Dust"
> surface dust #2.2 size 4.94
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> surface dust #6.2 size 4.94
> surface dust #8.2 size 4.94
> surface dust #9.2 size 4.94
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1-1.png" width 1470 height 1098 supersample 3
> hide #!9.2 models
> hide #!8.2 models
> hide #!6.2 models
> hide #!2.2 models
> show #!3.1 models
> show #3.2 models
> show #!3.3 models
> show #!3.4 models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1-2.png" width 1470 height 1098 supersample 3
> hide #!3 models
> show #!3 models
> turn x -90
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1-2-1.png" width 1470 height 1098 supersample 3
> show #!6.2 models
> hide #!3.4 models
> hide #!3.3 models
> hide #3.2 models
> hide #!3.1 models
> hide #!3 models
> show #!8.2 models
> show #!9.2 models
> show #!2.2 models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1-1-1.png" width 1470 height 1098 supersample 3
> turn y -90
> turn y 90
> turn x 90
> turn y 180
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1-3-1.png" width 1470 height 1098 supersample 3
> hide #!2.2 models
> show #!3.4 models
> show #!3.3 models
> show #3.2 models
> show #!3.1 models
> hide #!6.2 models
> hide #!8.2 models
> hide #!9.2 models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1-3.png" width 1470 height 1098 supersample 3
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1_v01.cxs"
——— End of log from Wed Aug 6 11:59:41 2025 ———
opened ChimeraX session
> close #14,17#13,15-16,18-22
> show #!9.2 models
> hide #!9.2 models
> show #!9.2 models
> hide #!9.2 models
> hide #!3.3 models
> hide #3.2 models
> hide #!3.4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #4 change surface color #6699ff
> hide #!3.1 models
> hide #!4 models
> show #!4 models
> show #4.1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> color #4 grey models
> color #4 #404040ff models
> color #4 grey models
> volume #4 level 0.3966
> 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.
> open "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb"
Chain information for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> color zone #4 near #5 distance 4.94
> color zone #4 near #5 distance 5.05
> color zone #4 near #5 distance 7.87
> color zone #4 near #5 distance 11.07
> color zone #4 near #5 distance 11.71
> color zone #4 near #5 distance 20.07
> color zone #4 near #5 distance 12.39
> color zone #4 near #5 distance 24.93
> color zone #4 near #5 distance 20.85
> color zone #4 near #5 distance 39.26
> color zone #4 near #5 distance 39
> color zone #4 near #5 distance 3
> color zone #4 near #5 distance 1
> color zone #4 near #5 distance 18
> color zone #4 near #5 distance 189
> color zone #4 near #5 distance 18
> color zone #4 near #5 distance 1
> color zone #4 near #5 distance 19
> color zone #4 near #5 distance 1
> color zone #4 near #5 distance 17
> volume #4 level 0.4677
> volume #4 level 0.5388
> color zone #4 near #5 distance 1
> color zone #4 near #5 distance 12
> color zone #4 near #5 distance 1
> color zone #4 near #5 distance 8
> color zone #4 near #5 distance 6
> ui tool show "Hide Dust"
> surface dust #4 size 4.94
> surface dust #4 size 4.93
> surface dust #4 size 2.98
> volume #4 level 0.4045
> color zone #4 near #5 distance 7
> color zone #4 near #5 distance 9
> volume splitbyzone #4
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 0 as #7.1, grid size
600,600,600, pixel 0.823, shown at level 0.405, step 1, values float32
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 1 as #7.2, grid size
600,600,600, pixel 0.823, shown at level 0.405, step 1, values float32
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 2 as #7.3, grid size
600,600,600, pixel 0.823, shown at level 0.405, step 1, values float32
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 3 as #7.4, grid size
600,600,600, pixel 0.823, shown at level 0.405, step 1, values float32
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 4 as #7.5, grid size
600,600,600, pixel 0.823, shown at level 0.405, step 1, values float32
> hide #!7.1 models
> show #!7.1 models
> hide #!7.1 models
> show #!7.1 models
> close #7.2-5
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!7.1 models
> show #!7.1 models
> volume #7.1 level 0.4377
> surface dust #7.1 size 4.94
> volume #7.1 level 0.3952
> surface dust #7.1 size 4.97
> surface dust #7.1 size 7.19
> hide #!5 models
> ui tool show "Map Eraser"
> volume erase #7.1 center 241.98,202.77,305.6 radius 20.333
> volume erase #7.1 center 280.23,164.5,268.59 radius 20.333
> volume erase #7.1 center 217.03,293.11,207.92 radius 20.333
> hide #!7.1 models
> show #!7.1 models
> color #7.1 #bfbfbfff models
> color #7.1 #404040ff models
> color #7.1 grey models
> color #7.1 #80808080 models
> volume erase #7.1 center 198.09,236.21,234.68 radius 20.246
> volume erase #7.1 center 197.72,249.34,219 radius 20.246
> show #3.2 models
> show #!3.3 models
> show #!3.4 models
> show #!3.1 models
> ui tool show "Side View"
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1_v03-RON2.cxs"
> hide #!3.4 models
> hide #3.2 models
> hide #!3.3 models
> hide #!7.1 models
> ui tool show CliX
> setattr m autochain false
Assigning autochain attribute to 29 items
Traceback (most recent call last):
File "/Users/meserethaile/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/clix/widgets/cli_widget.py", line 514, in event
done = self._keypress_event(event)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/meserethaile/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/clix/widgets/cli_widget.py", line 388, in _keypress_event
done = self._event_return(event)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/meserethaile/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/clix/widgets/cli_widget.py", line 493, in _event_return
self.run_command()
File "/Users/meserethaile/Library/Application
Support/ChimeraX/1.8/lib/python/site-
packages/chimerax/clix/widgets/cli_widget.py", line 72, in run_command
run(self._session, line)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/setattr.py", line 148, in set_attr
if attr_name not in type_attrs(class_):
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 69, in type_attrs
attrs.extend(t._attr_registration.reg_attr_info.keys())
^^^^^^^^^^^^^^^^^^^^
AttributeError: type object 'Volume' has no attribute '_attr_registration'
AttributeError: type object 'Volume' has no attribute '_attr_registration'
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 69, in type_attrs
attrs.extend(t._attr_registration.reg_attr_info.keys())
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> setattr #3.1 autochain false
Missing or invalid "attrValue" argument: Expected a text string
> select clear
[Repeated 1 time(s)]
> hide #!3.1 atoms
> hide #!3.1 cartoons
> show #!3.1 cartoons
> ui tool show "Selection Inspector"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> setattr =sel p display false
Assigning display attribute to 1 item
> select clear
[Repeated 6 time(s)]
> ui tool show "Selection Inspector"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> setattr =sel p display false
Assigning display attribute to 1 item
> show #3.2 models
> hide #3.2 models
> show #3.2 models
> hide #3.2 models
> hide #!3.1 models
> select add #3.1
10058 atoms, 10274 bonds, 2 pseudobonds, 1228 residues, 2 models selected
> select subtract #3.1
Nothing selected
> show #!7.1 models
> vop gaussian #7.1 sdev 2.47
Opened composite_J2546-J2730-J2902-J2614 copy.mrc 0 gaussian as #10, grid size
600,600,600, pixel 0.823, shown at step 1, values float32
> close #10
> show #!7.1 models
> hide #!7.1 models
> show #!3.1 models
> show #3.2 models
> hide #3.2 models
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> lighting full
> lighting simple
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows false
> graphics silhouettes true
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting full
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting simple
> view orient
Drag select of 366 residues
> select up
3848 atoms, 3927 bonds, 461 residues, 1 model selected
> select up
10058 atoms, 10274 bonds, 1228 residues, 1 model selected
> select down
3848 atoms, 3927 bonds, 461 residues, 1 model selected
> select clear
Drag select of 578 residues
> select up
5000 atoms, 5106 bonds, 604 residues, 1 model selected
> select down
4794 atoms, 578 residues, 1 model selected
> select add #3.1/A:1176
4805 atoms, 11 bonds, 579 residues, 1 model selected
> select add #3.1/A:1175
4813 atoms, 18 bonds, 580 residues, 1 model selected
> color sel 550C18
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select clear
Alignment identifier is 3.1/A
Alignment identifier is 3.2/B
Alignment identifier is 3.3/C
Alignment identifier is 3.4/D
Alignment identifier is 5/A
Alignment identifier is 5/B
Alignment identifier is 5/C
Alignment identifier is 5/D
> select #3.1/A:821
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/A:821-1217
2738 atoms, 2799 bonds, 1 pseudobond, 331 residues, 2 models selected
> select #3.1/A:1237-1238
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #3.1/A:821-1238
2903 atoms, 2966 bonds, 1 pseudobond, 352 residues, 2 models selected
> select #3.1/A:1349
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/A:821-1349
3822 atoms, 3909 bonds, 1 pseudobond, 463 residues, 2 models selected
> select #3.1/A:1489
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3.1/A:821-1489
4641 atoms, 4742 bonds, 2 pseudobonds, 560 residues, 2 models selected
> select
> #3.1/A:828-846,926-930,934-946,951-964,973-996,1009-1020,1034-1039,1048-1066,1073-1086,1089-1094,1098-1100,1108-1112,1117-1131,1133-1137,1147-1153,1156-1166,1185-1187,1198-1227,1239-1250,1264-1266,1279-1307,1312-1318,1325-1332,1345-1347,1358-1366,1415-1450,1454-1459,1461-1472,1476-1487,1493-1503,1507-1512,1521-1531,1534-1551,1555-1563,1570-1575,1581-1585,1595-1601,1606-1621,1623-1647,1658-1686,1689-1707,1711-1715,1717-1732,1750-1765,1785-1800,1806-1826,1829-1831,1850-1852,1855-1887,1890-1898,1902-1907,1913-1915,1917-1921,1925-1933,1936-1944,1949-1966,1970-1978,1980-2027,2056-2058,2063-2068,2070-2072,2075-2078,2080-2082,2085-2098,2100-2123,2127-2155
6847 atoms, 6923 bonds, 825 residues, 1 model selected
> select #3.1/A:1492
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.1/A:821-1492
4663 atoms, 4765 bonds, 2 pseudobonds, 563 residues, 2 models selected
> select #3.1/A:1507-1508
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #3.1/A:1507-1513
55 atoms, 55 bonds, 7 residues, 1 model selected
> select #3.1/A:1503
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/A:1494-1503
93 atoms, 94 bonds, 10 residues, 1 model selected
> select #3.1/A:1492
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.1/A:821-1492
4663 atoms, 4765 bonds, 2 pseudobonds, 563 residues, 2 models selected
> select #3.1/A:1578
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.1/A:1578
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #3.1
10058 atoms, 10274 bonds, 2 pseudobonds, 1228 residues, 2 models selected
> select subtract #3.1
Nothing selected
> select add #3
24900 atoms, 25398 bonds, 7 pseudobonds, 3059 residues, 8 models selected
> select subtract #3
Nothing selected
> show #!7.1 models
> hide #!7.1 models
> coulombic #!3.1
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb A_A
SES surface #3.1.2: minimum, -19.16, mean 2.07, maximum 27.66
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic #!3.1
Coulombic values for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb A_A
SES surface #3.1.2: minimum, -19.16, mean 2.07, maximum 27.66
To also show corresponding color key, enter the above coulombic command and
add key true
> show #!3.1 atoms
[Repeated 1 time(s)]
> color #!3.1 bychain
> color #!3.1 byhetero
[Repeated 1 time(s)]
> color #!3.1 bychain
> hide #!3.1 cartoons
> show #!3.1 cartoons
> hide #!3.1 surfaces
> hide #!3.1 atoms
> show #!3.1 cartoons
> color #3.1 #9d7982ff
> select clear
> select #3.1/A:1411
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3.1/A:1493
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.1/A:1493-1831
2795 atoms, 2847 bonds, 339 residues, 1 model selected
> select #3.1/A:1493-1494
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #3.1/A:1493-1863
3055 atoms, 3113 bonds, 371 residues, 1 model selected
> select #3.1/A:1948
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3.1/A:1493-1948
3738 atoms, 3815 bonds, 456 residues, 1 model selected
> select #3.1/A:1968-1969
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #3.1/A:1493-1969
3903 atoms, 3982 bonds, 477 residues, 1 model selected
> select #3.1/A:2027-2028
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #3.1/A:1992-2028
295 atoms, 297 bonds, 37 residues, 1 model selected
> select #3.1/A:1978-1979
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #3.1/A:1493-1979
3993 atoms, 4076 bonds, 487 residues, 1 model selected
> select
> #3.1/A:828-846,926-930,934-946,951-964,973-996,1009-1020,1034-1039,1048-1066,1073-1086,1089-1094,1098-1100,1108-1112,1117-1131,1133-1137,1147-1153,1156-1166,1185-1187,1198-1227,1239-1250,1264-1266,1279-1307,1312-1318,1325-1332,1345-1347,1358-1366,1415-1450,1454-1459,1461-1472,1476-1487,1493-1503,1507-1512,1521-1531,1534-1551,1555-1563,1570-1575,1581-1585,1595-1601,1606-1621,1623-1647,1658-1686,1689-1707,1711-1715,1717-1732,1750-1765,1785-1800,1806-1826,1829-1831,1850-1852,1855-1887,1890-1898,1902-1907,1913-1915,1917-1921,1925-1933,1936-1944,1949-1966,1970-1978,1980-2027,2056-2058,2063-2068,2070-2072,2075-2078,2080-2082,2085-2098,2100-2123,2127-2155
6847 atoms, 6923 bonds, 825 residues, 1 model selected
> select #3.1/A:2059-2060
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #3.1/A:2059-2061
19 atoms, 18 bonds, 3 residues, 1 model selected
> mlp sel
Map values for surface "AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface": minimum -28.48, mean -4.09, maximum 23.02
To also show corresponding color key, enter the above mlp command and add key
true
> select clear
> mlp #!3.1
Map values for surface "AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface": minimum -28.48, mean -4.09, maximum 23.02
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic #!3.1
Coulombic values for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb A_A
SES surface #3.1.2: minimum, -19.16, mean 2.07, maximum 27.66
To also show corresponding color key, enter the above coulombic command and
add key true
> rainbow #!3.1
> mlp #!3.1
Map values for surface "AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface": minimum -28.48, mean -4.09, maximum 23.02
To also show corresponding color key, enter the above mlp command and add key
true
> rainbow #!3.1
> mlp #!3.1
Map values for surface "AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface": minimum -28.48, mean -4.09, maximum 23.02
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!3.1 surfaces
> select add #3.1
10058 atoms, 10274 bonds, 2 pseudobonds, 1228 residues, 2 models selected
> color #3.1 #d8a768ff
> color #3.1 #9d7982ff
> select subtract #3.1
1 model selected
> select add #3.1
10058 atoms, 10274 bonds, 2 pseudobonds, 1228 residues, 2 models selected
> select subtract #3.1
1 model selected
> select
> #3.1/A:828-846,926-930,934-946,951-964,973-996,1009-1020,1034-1039,1048-1066,1073-1086,1089-1094,1098-1100,1108-1112,1117-1131,1133-1137,1147-1153,1156-1166,1185-1187,1198-1227,1239-1250,1264-1266,1279-1307,1312-1318,1325-1332,1345-1347,1358-1366,1415-1450,1454-1459,1461-1472,1476-1487,1493-1503,1507-1512,1521-1531,1534-1551,1555-1563,1570-1575,1581-1585,1595-1601,1606-1621,1623-1647,1658-1686,1689-1707,1711-1715,1717-1732,1750-1765,1785-1800,1806-1826,1829-1831,1850-1852,1855-1887,1890-1898,1902-1907,1913-1915,1917-1921,1925-1933,1936-1944,1949-1966,1970-1978,1980-2027,2056-2058,2063-2068,2070-2072,2075-2078,2080-2082,2085-2098,2100-2123,2127-2155
6847 atoms, 6923 bonds, 825 residues, 1 model selected
> select #3.1/A:1980
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3.1/A:1980-2027
391 atoms, 400 bonds, 48 residues, 1 model selected
> select #3.1/A:2092
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
106 atoms, 108 bonds, 14 residues, 2 models selected
> select up
6076 atoms, 6202 bonds, 747 residues, 2 models selected
> select down
106 atoms, 108 bonds, 14 residues, 2 models selected
> select add #3.1/A:2081
118 atoms, 120 bonds, 15 residues, 2 models selected
> select add #3.1/A:2083
129 atoms, 131 bonds, 16 residues, 2 models selected
> select up
149 atoms, 154 bonds, 19 residues, 2 models selected
> select add #3.1/A:2077
155 atoms, 159 bonds, 20 residues, 2 models selected
> select add #3.1/A:2079
159 atoms, 162 bonds, 21 residues, 2 models selected
> select up
183 atoms, 189 bonds, 24 residues, 2 models selected
> show #!7.1 models
> hide #!7.1 models
> show #!7.1 models
> hide #!7.1 models
> show #!7.1 models
> hide #!7.1 models
> show #!3.4 models
> hide #!3.4 models
> show #!7.1 models
> coulombic sel
Coulombic values for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb A_A
SES surface #3.1.2: minimum, -19.16, mean 2.07, maximum 27.66
To also show corresponding color key, enter the above coulombic command and
add key true
> select #3.1/A:2118
8 atoms, 7 bonds, 1 residue, 1 model selected
> select
> #3.1/A:828-846,926-930,934-946,951-964,973-996,1009-1020,1034-1039,1048-1066,1073-1086,1089-1094,1098-1100,1108-1112,1117-1131,1133-1137,1147-1153,1156-1166,1185-1187,1198-1227,1239-1250,1264-1266,1279-1307,1312-1318,1325-1332,1345-1347,1358-1366,1415-1450,1454-1459,1461-1472,1476-1487,1493-1503,1507-1512,1521-1531,1534-1551,1555-1563,1570-1575,1581-1585,1595-1601,1606-1621,1623-1647,1658-1686,1689-1707,1711-1715,1717-1732,1750-1765,1785-1800,1806-1826,1829-1831,1850-1852,1855-1887,1890-1898,1902-1907,1913-1915,1917-1921,1925-1933,1936-1944,1949-1966,1970-1978,1980-2027,2056-2058,2063-2068,2070-2072,2075-2078,2080-2082,2085-2098,2100-2123,2127-2155
6847 atoms, 6923 bonds, 825 residues, 1 model selected
> select #3.1/A:2123
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/A:2100-2123
206 atoms, 210 bonds, 24 residues, 1 model selected
> select #3.1/A:1763
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/A 949-1272
Expected a keyword
> select #3.1/949-1272
Nothing selected
> select #3.1:949-1272
2654 atoms, 2714 bonds, 324 residues, 1 model selected
> select #3.1:1857-2062
1639 atoms, 1678 bonds, 206 residues, 1 model selected
> hide #!7.1 models
> hide sel surfaces
> select clear
> hide #!3.1 surfaces
> mlp #!3.1
Map values for surface "AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface": minimum -28.48, mean -4.09, maximum 23.02
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!3.1 surfaces
> select #3.1/A:1761
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3.1/A:2101
15 atoms, 13 bonds, 2 residues, 2 models selected
> select up
341 atoms, 347 bonds, 40 residues, 2 models selected
> mlp sel
Map values for surface "AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface": minimum -28.48, mean -4.09, maximum 23.02
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel key true
Map values for surface "AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface": minimum -28.48, mean -4.09, maximum 23.02
> key lipophilicity :-20 :0 :20 showTool true
> ui mousemode right "color key"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #3.1/A:2077
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #3.1/A:2064
12 atoms, 10 bonds, 2 residues, 2 models selected
> select add #3.1/A:2072
19 atoms, 16 bonds, 3 residues, 2 models selected
> select add #3.1/A:2070
30 atoms, 27 bonds, 4 residues, 2 models selected
> select add #3.1/A:2074
38 atoms, 34 bonds, 5 residues, 2 models selected
> select up
109 atoms, 109 bonds, 15 residues, 2 models selected
> select up
6076 atoms, 6202 bonds, 747 residues, 2 models selected
> select down
109 atoms, 109 bonds, 15 residues, 2 models selected
> select add #3.1/A:2069
116 atoms, 115 bonds, 16 residues, 2 models selected
> mlp sel
Map values for surface "AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface": minimum -28.48, mean -4.09, maximum 23.02
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> select clear
> select #3.1/A:2028
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/A:2061
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #3.1/A:2028
14 atoms, 12 bonds, 2 residues, 2 models selected
> select up
86 atoms, 85 bonds, 14 residues, 2 models selected
> select clear
Drag select of 26 residues
> select up
220 atoms, 224 bonds, 31 residues, 2 models selected
> select up
6076 atoms, 6202 bonds, 747 residues, 2 models selected
> select down
220 atoms, 224 bonds, 31 residues, 2 models selected
> select add #3.1/A:2059
226 atoms, 229 bonds, 32 residues, 2 models selected
> select add #3.1/A:2060
233 atoms, 235 bonds, 33 residues, 2 models selected
> select add #3.1/A:2061
239 atoms, 240 bonds, 34 residues, 2 models selected
> ui mousemode right "map eraser"
> mlp sel key true
Map values for surface "AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface": minimum -28.48, mean -4.09, maximum 23.02
> key lipophilicity :-20 :0 :20 showTool true
> ui mousemode right "color key"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> key delete
> ui mousemode right "map eraser"
> select #3.1/A:1850
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3.1/A:1850
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #3.1/A:1802
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/A:1802-1878
624 atoms, 638 bonds, 77 residues, 1 model selected
> show #!3.3 models
> hide #!3.3 models
> show #!3.3 models
> open /Users/meserethaile/Downloads/cryosparc_P4_J3693_004_volume_map.mrc
Opened cryosparc_P4_J3693_004_volume_map.mrc as #10, grid size 600,600,600,
pixel 0.823, shown at level 0.0115, step 4, values float32
> close #10
> hide sel surfaces
> select add #3.1
10058 atoms, 10274 bonds, 2 pseudobonds, 1228 residues, 3 models selected
> hide sel surfaces
> select clear
> show #!7.1 models
> hide #!7.1 models
> show #!7.1 models
> show #!3.4 models
> hide #!7.1 models
> show #!7.1 models
> hide #!7.1 models
> hide #!3.4 models
Drag select of 42 residues
> select up
680 atoms, 694 bonds, 89 residues, 2 models selected
> select down
299 atoms, 42 residues, 2 models selected
Drag select of 56 residues
[Repeated 1 time(s)]
> select #3.1/A:2058-2059
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #3.1/A:2058-2073
112 atoms, 112 bonds, 16 residues, 1 model selected
Drag select of 5 residues
> show sel atoms
> coulombic sel
Coulombic values for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb A_A
SES surface #3.1.2: minimum, -19.16, mean 2.07, maximum 27.66
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> select clear
Drag select of 4 atoms, 20 residues, 2 bonds
> select subtract #3.1/A:2019
140 atoms, 2 bonds, 19 residues, 2 models selected
> select subtract #3.1/A:2020
132 atoms, 2 bonds, 18 residues, 2 models selected
> select subtract #3.1/A:2021
124 atoms, 2 bonds, 17 residues, 2 models selected
> select subtract #3.1/A:2018
118 atoms, 2 bonds, 16 residues, 2 models selected
> show sel atoms
> coulombic sel
Coulombic values for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb A_A
SES surface #3.1.2: minimum, -19.16, mean 2.07, maximum 27.66
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> hide sel atoms
> select clear
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Fig1_v03-RON2.cxs"
——— End of log from Thu Aug 7 18:38:59 2025 ———
opened ChimeraX session
> hide #!3.3 models
> hide #!3.1 models
> ui tool show "Command Line Interface"
> ui tool show CliX
> show #!7.1 models
> hide #!7.1 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> open "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/composite_J2546-J2730-J2902-J2614 copy.mrc"
Opened composite_J2546-J2730-J2902-J2614 copy.mrc as #10, grid size
600,600,600, pixel 0.823, shown at level 0.162, step 4, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #10 step 1
> volume #10 level 0.9566
> volume #10 level 1.009
> show #!6.2 models
> hide #!6.2 models
> show #!6.2 models
> hide #!6.2 models
> show #!9.2 models
> show #!8.2 models
> show #!6.2 models
> hide #!6.2 models
> hide #!8.2 models
> hide #!9.2 models
> view #6.2 #8.2 #9.2 #2.2
No displayed objects specified.
> rock y 15
> rock y 50
> rock y 80
> rock y 15 4
> rock y 15 10
> rock y 15 1
> stop
> rock y 15 4 frames 200
Repeated keyword argument "frames"
> rock y 15 frames 200
> rock y 80 frames 200
> stop
> rock y 80 frames 1000
> stop
> show #!9.2 models
> show #!8.2 models
> show #!2.2 models
> show #!6.2 models
> rock y 30
> stop
> hide #!6.2 models
> hide #!8.2 models
> hide #!9.2 models
> hide #!2.2 models
> rock y 30
> view #2.2
No displayed objects specified.
> stop
> rock y 30
> open #2.2
Unrecognized file suffix '.2'
> stop
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting full
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> volume #10 level 1.048
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /1.png" width 1339 height 769 supersample 3
> transparentBackground true
> show #!2.2 models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /2.png" width 1339 height 769 supersample 3
> transparentBackground true
> show #!6.2 models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /3.png" width 1339 height 769 supersample 3
> transparentBackground true
> show #!8.2 models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /4.png" width 1339 height 769 supersample 3
> transparentBackground true
> show #!9.2 models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /5.png" width 1339 height 769 supersample 3
> transparentBackground true
> turn x -90
> ui tool show "Side View"
> turn x -90
> show #!3.1 models
> show #3.2 models
> hide #3.2 models
> show #!3.3 models
> show #3.2 models
> show #!3.4 models
> hide #!2.2 models
> hide #!10 models
> hide #!9.2 models
> hide #!8.2 models
> hide #!6.2 models
> hide #3.2 models
> hide #!3.3 models
> hide #!3.4 models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /6.png" width 1339 height 769 supersample 3
> show #!2.2 models
> show #!7.1 models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /6.1.png" width 1339 height 769 supersample 3
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /6.1.png" width 1339 height 769 supersample 3
> transparentBackground true
> hide #!7.1 models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /6.2.png" width 1339 height 769 supersample 3
> transparentBackground true
> hide #!2.2 models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /6.3.png" width 1339 height 769 supersample 3
> transparentBackground true
> show #!2.2 models
> hide #!3.1 models
> show #3.2 models
> hide #3.2 models
> show #!9.2 models
> show #!6.2 models
> show #!8.2 models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /6.4.png" width 1339 height 769 supersample 3
> transparentBackground true
> hide #!8.2 models
> hide #!9.2 models
> hide #!6.2 models
> hide #!2.2 models
> show #3.2 models
> select #3.2:740-899
1283 atoms, 1297 bonds, 160 residues, 1 model selected
> transparency sel 40
> transparency #3.1 sel 40
Missing or invalid "percent" argument: Expected a number
> transparency 40 #3.1 sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select clear
> color #3.2:740-899 #72c1af
> transparency 30 #3.2:740-899
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #3.2:740-899 #72c1af
> transparency 30 #3.2/740-899
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color #3.2:740-899 #72c1af
> transparency 30 cartoons #3.2/740-899
Expected ',' or a keyword
> color #3.2:740-899 #72c1af
> transparency 30 cartoons #3.2/740-899
Expected ',' or a keyword
> colordef domaincol ffcc00
> color name domaincol ffcc00
Missing or invalid "color" argument: Invalid color name or specifier
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color #3.2:740-899 #72c1af
> transparency 30 cartoons #3.2:740-899
Expected ',' or a keyword
> select #3.2:740-899
1283 atoms, 1297 bonds, 160 residues, 1 model selected
> transparency 30 ribbons sel
Expected ',' or a keyword
> colordef domaincol ffcc00
> color name domaincol ffcc00
Missing or invalid "color" argument: Invalid color name or specifier
> namecolor domaincol ffcc00
Unknown command: namecolor domaincol ffcc00
> color #ffcc00 #3:740-899
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select #3.2:740-899
1283 atoms, 1297 bonds, 160 residues, 1 model selected
> color #ffcc00 sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select #3.2:740-899
1283 atoms, 1297 bonds, 160 residues, 1 model selected
> color ribbons #ffcc00 sel
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color ffcc00 #3.2:740-899 target r
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select clear
> show #!6.2 models
> hide #!6.2 models
> show #!6.2 models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /7.png" width 1339 height 718 supersample 3
> transparentBackground true
> hide #!6.2 models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /7.1.png" width 1339 height 718 supersample 3
> transparentBackground true
> show #!2.2 models
> hide #!2.2 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> turn x -90
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /7.2.png" width 1339 height 718 supersample 3
> transparentBackground true
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> color #2.2 #9d798280 models
> show #!3.1 models
> hide #!2.2 models
> hide #!3.1 models
> show #!2.2 models
> color #2.2 #9d7982ff models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /7.3.png" width 1339 height 718 supersample 3
> transparentBackground true
> color #2.2 #9d798280 models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /7.4.png" width 1339 height 718 supersample 3
> transparentBackground true
> hide #!2.2 models
> show #!3.1 models
> select add #3.1
10058 atoms, 10274 bonds, 2 pseudobonds, 1228 residues, 2 models selected
> show sel surfaces
> mlp sel
Map values for surface "AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface": minimum -28.48, mean -4.09, maximum 23.02
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> style sel sphere
Changed 10058 atom styles
> show sel surfaces
> color sel bypolymer
> color sel bychain
> color sel byhetero
> mlp sel
Map values for surface "AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb
A_A SES surface": minimum -28.48, mean -4.09, maximum 23.02
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Coulombic values for AMA1-RON_coot21_recombine_rsr8_isolde_delh copy.pdb A_A
SES surface #3.1.2: minimum, -19.16, mean 2.07, maximum 27.66
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> color #2.2 #9d7982ff models
> color #3.1 #9d7982ff
> select clear
> turn y 50
> turn y -50
> turn y 20
> turn y -20
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /RON4.cxs"
> hide #3.2 models
> hide #!3.1 models
> show #!3.3 models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /8.1.png" width 1339 height 718 supersample 3
> transparentBackground true
> turn y 90
> turn y -90
> turn x 90
> turn x -90
> turn x 40
> turn x 10
> turn x -10
> turn x 10
> turn x 40
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /8.2.png" width 1339 height 718 supersample 3
> transparentBackground true
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> turn x 40
> turn x -40
> show #!3.1 models
> turn x -40
> turn x 40
> turn x -50
> turn x 50
> turn x -70
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /8.3.png" width 1339 height 718 supersample 3
> transparentBackground true
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> turn x 70
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> turn x -70
> turn x 90
> hide #!3.1 models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /8.4.png" width 1339 height 718 supersample 3
> transparentBackground true
> show #!3.1 models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /8.5.png" width 1339 height 718 supersample 3
> transparentBackground true
> show #!2.2 models
> hide #!3.1 models
> show #!8.2 models
> hide #!3.3 models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /8.6.png" width 1339 height 718 supersample 3
> transparentBackground true
> show #!3.3 models
> hide #!2.2 models
> hide #!8.2 models
> save "/Users/meserethaile/Desktop/HoLab/Thesis Project/Meeting
> 2025/Figures/Videos /RON5.cxs"
> show #!3.4 models
> hide #!3.3 models
===== Log before crash end =====
Log:
Startup Messages
---
warning | Registration file '/Users/meserethaile/Library/Application Support/ChimeraX/registration' has expired
note | available bundle cache has not been initialized yet
> ui tool hide "command line interface"
> ui tool show clix
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/meserethaile/Desktop/AMA1-RON2/DataProcessing/Models/August2025/AMA1-RON_coot21_recombine_rsr8_isolde_delh.pdb
> format pdb
Chain information for AMA1-RON_coot21_recombine_rsr8_isolde_delh.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> set bgColor white
Drag select of 216 residues, 1 pseudobonds
> select up
2087 atoms, 2137 bonds, 1 pseudobond, 259 residues, 2 models selected
> select up
3230 atoms, 3313 bonds, 1 pseudobond, 401 residues, 2 models selected
> select up
24900 atoms, 25398 bonds, 7 pseudobonds, 3059 residues, 2 models selected
> select down
3230 atoms, 3313 bonds, 1 pseudobond, 401 residues, 2 models selected
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2
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: Mac14,7
Model Number: Z16R0005ZLL/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 8422.100.650
OS Loader Version: 8422.100.650
Software:
System Software Overview:
System Version: macOS 13.3 (22E252)
Kernel Version: Darwin 22.4.0
Time since boot: 2 days, 7 hours, 13 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP M27fe FHD:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
annotated-types: 0.7.0
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-ArtiaX: 0.5.0
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-Clipper: 0.23.1
ChimeraX-clix: 0.1.9
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-ISOLDE: 1.8
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
geomdl: 5.3.1
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
pandas: 2.2.3
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
pyarrow: 18.0.0
pycollada: 0.8
pydantic: 2.9.2
pydantic-core: 2.23.4
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
starfile: 0.5.10
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 3 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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