![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16739 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.1.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001fda47840 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, openmm._openmm, openmm.app.internal.compiled, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 123)
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"codeSigningMonitor" : 1,
"incident" : "EB3EFFB0-6367-4F2C-BA60-7A32885970E0",
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"procLaunch" : "2025-01-28 15:45:20.9964 +0100",
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"procExitAbsTime" : 7703304480606,
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"codeSigningTeamID" : "LWV8X224YF",
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fault"},"pc":{"value":6854729960},"far":{"value":0}}},{"id":4907690,"frames":[{"imageOffset":8424,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":260}],"threadState":{"x":[{"value":14202171392},{"value":93151},{"value":14201634816},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":14202171392},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6854729960},"far":{"value":0}}},{"id":4916602,"frames":[{"imageOffset":8424,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":260}],"threadState":{"x":[{"value":14317432832},{"value":198215},{"value":14316896256},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":14317432832},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6854729960},"far":{"value":0}}},{"id":4925634,"frames":[{"imageOffset":8424,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":260}],"threadState":{"x":[{"value":14388473856},{"value":154083},{"value":14387937280},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":14388473856},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6854729960},"far":{"value":0}}},{"id":4925635,"frames":[{"imageOffset":8424,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":260}],"threadState":{"x":[{"value":15684759552},{"value":233839},{"value":15684222976},{"value":0},{"value":409604},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":15684759552},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6854729960},"far":{"value":0}}},{"id":4926646,"frames":[{"imageOffset":8424,"symbol":"start_wqthread","symbolLocation":0,"imageIndex":260}],"threadState":{"x":[{"value":14225108992},{"value":0},{"value":14224572416},{"value":0},{"value":278532},{"value":18446744073709551615},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":0},"cpsr":{"value":4096},"fp":{"value":0},"sp":{"value":14225108992},"esr":{"value":0,"description":" Address size fault"},"pc":{"value":6854729960},"far":{"value":0}}}],
"usedImages" : [
[deleted to fit within ticket limits]
],
"sharedCache" : {
"base" : 6850232320,
"size" : 4753735680,
"uuid" : "f66bac4e-1e78-38af-b867-c1cf5daa0302"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=6.1G written=3389K(0%) resident=3389K(0%) swapped_out=0K(0%) unallocated=6.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG image 1312K 59 \nColorSync 592K 31 \nCoreAnimation 4192K 231 \nCoreGraphics 48K 3 \nCoreUI image data 5440K 40 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 4.7G 187 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenCL 21.1M 308 \nOpenCL (reserved) 1664K 49 reserved VM address space (unallocated)\nOpenGL GLSL 384K 4 \nSTACK GUARD 1456K 91 \nStack 221.1M 96 \nStack Guard 56.0M 1 \nVM_ALLOCATE 477.5M 542 \nVM_ALLOCATE (reserved) 544.0M 4 reserved VM address space (unallocated)\n__AUTH 5030K 660 \n__AUTH_CONST 69.6M 907 \n__CTF 824 1 \n__DATA 34.9M 1160 \n__DATA_CONST 35.8M 1169 \n__DATA_DIRTY 2763K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 629.2M 260 \n__OBJC_RW 2354K 1 \n__TEXT 1.3G 1189 \n__TPRO_CONST 272K 2 \ndyld private memory 304K 3 \nmapped file 699.2M 932 \nowned unmapped memory 91.7M 1 \npage table in kernel 3389K 1 \nshared memory 3680K 26 \n=========== ======= ======= \nTOTAL 8.9G 8332 \nTOTAL, minus reserved VM space 8.4G 8332 \n",
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"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
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"logWritingSignature" : "8ed83e182804b0cdd27e4b835a821c285423fb33",
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl
> pH6.5/Map/CS_Jobs_LSN_Computer/J183/J183_004_volume_map_sharp.mrc.filepart"
Unrecognized file suffix '.filepart'
> open "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl
> pH6.5/Map/CS_Jobs_LSN_Computer/J183/J183_004_volume_map_sharp.mrc"
Opened J183_004_volume_map_sharp.mrc as #1, grid size 288,288,288, pixel 0.72,
shown at level 0.219, step 2, values float32
> set bgColor white
> open "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl
> pH6.5/Map/CS_Jobs/J29/J29_004_volume_map_sharp.mrc"
Opened J29_004_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 0.731,
shown at level 0.216, step 1, values float32
> volume flip #1 axis z
Opened J183_004_volume_map_sharp.mrc z flip as #3, grid size 288,288,288,
pixel 0.72, shown at step 1, values float32
> volume #2 color #ff9300
> volume #2 color #ff7e79
> volume #2 color #0096ff
> volume #2 color #0433ff
> volume #2 color #76d6ff
> volume #2 color #0096ff
> ui mousemode right "translate selected models"
> select add #3
2 models selected
> select subtract #3
Nothing selected
> color #2 #0096ffff models
> hide #!3 models
> show #!3 models
> select add #2
2 models selected
> view matrix models #2,1,0,0,-40.053,0,1,0,-41.743,0,0,1,8.3809
> hide #!3 models
> show #!1 models
> select add #1
4 models selected
> select subtract #2
2 models selected
> view matrix models #1,1,0,0,-0.24923,0,1,0,0.05149,0,0,1,-1.3934
> view matrix models #1,1,0,0,-1.5195,0,1,0,-1.6505,0,0,1,-1.4552
> view matrix models #1,1,0,0,12.006,0,1,0,17.03,0,0,1,-2.7959
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.14178,0.97938,-0.14394,42.904,0.97101,0.10933,-0.21255,31.875,-0.19243,-0.16991,-0.96649,240.85
> view matrix models
> #1,-0.94561,0.32488,-0.016346,179.72,0.32506,0.94564,-0.010153,-9.6302,0.012159,-0.014914,-0.99981,207.32
> ui tool show "Side View"
> close #1
> open "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl
> pH6.5/Doppio/job16/edited_coot/test_refined_edited_ISOLDE_4-coot-5.pdb"
Chain information for test_refined_edited_ISOLDE_4-coot-5.pdb #1
---
Chain | Description
A | No description available
> select add #1
5519 atoms, 5594 bonds, 1 pseudobond, 330 residues, 3 models selected
> close #1
> close #3
> open "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl
> pH6.5/Doppio/job16/edited_coot/test_refined_edited_ISOLDE_4-coot-4.pdb"
Chain information for test_refined_edited_ISOLDE_4-coot-4.pdb #1
---
Chain | Description
A | No description available
> close #2
> open "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl
> pH6.5/Map/CS_Jobs/J29/J29_004_volume_map_sharp.mrc"
Opened J29_004_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 0.731,
shown at level 0.216, step 1, values float32
Drag select of 1 residues, 2 J29_004_volume_map_sharp.mrc
> view matrix models
> #1,0.99915,-0.015001,0.038398,-2.3153,0.013039,0.99862,0.050869,-6.1317,-0.039108,-0.050325,0.99797,8.5737,#2,0.99915,-0.015001,0.038398,-2.3153,0.013039,0.99862,0.050869,-6.1317,-0.039108,-0.050325,0.99797,8.5737
> select add #2
11 atoms, 1 residue, 4 models selected
> select add #1
5552 atoms, 5628 bonds, 332 residues, 4 models selected
> select subtract #1
3 models selected
> select add #1
5552 atoms, 5628 bonds, 332 residues, 4 models selected
> select subtract #2
5552 atoms, 5628 bonds, 332 residues, 1 model selected
> select subtract #1
Nothing selected
> ui tool show "Fit in Map"
> select 266-240
Expected an objects specifier or a keyword
> select 266-240
Expected an objects specifier or a keyword
> sel: 240-266
Unknown command: sel: 240-266
> sel:240-266
Unknown command: sel:240-266
> select : 240-266
419 atoms, 419 bonds, 27 residues, 1 model selected
Opened test_refined_edited_ISOLDE_4-coot-4.pdb map 5 as #3, grid size
43,50,87, pixel 1.67, shown at level 0.0888, step 1, values float32
Opened test_refined_edited_ISOLDE_4-coot-4.pdb map 5 as #4, grid size
43,50,87, pixel 1.67, shown at level 0.0888, step 1, values float32
> fitmap #1 inMap #2 resolution 5 moveWholeMolecules false
Fit map test_refined_edited_ISOLDE_4-coot-4.pdb map 5 in map
J29_004_volume_map_sharp.mrc using 12228 points
correlation = 0.894, correlation about mean = 0.6943, overlap = 808.4
steps = 44, shift = 0.0897, angle = 0.131 degrees
Position of test_refined_edited_ISOLDE_4-coot-4.pdb map 5 (#4) relative to
J29_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999804 -0.00193185 -0.00043150 0.14694904
0.00193235 0.99999748 0.00114485 -0.23057858
0.00042928 -0.00114568 0.99999925 0.10258373
Axis -0.50079531 -0.18819878 0.84485814
Axis point 113.94387319 90.58999761 0.00000000
Rotation angle (degrees) 0.13102948
Shift along axis 0.05647192
Average map value = 0.1985 for 5552 atoms, 3404 outside contour
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
> select add #1
5552 atoms, 5628 bonds, 332 residues, 1 model selected
> select subtract #1
Nothing selected
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 5 residues in model #1 to IUPAC-IUB
standards.
Opened test_refined_edited_ISOLDE_4-coot-4.pdb map 5 as #3, grid size
45,50,87, pixel 1.67, shown at level 0.0888, step 1, values float32
Chain information for test_refined_edited_ISOLDE_4-coot-4.pdb
---
Chain | Description
1.2/A | No description available
> clipper associate #2 toModel #1
Opened J29_004_volume_map_sharp.mrc as #1.1.1.1, grid size 256,256,256, pixel
0.731, shown at step 1, values float32
> view matrix models
> #1.2,0.98105,-0.062145,-0.18354,26.128,-0.076075,0.74762,-0.65975,97.232,0.17822,0.66121,0.72873,-49.946
> undo
> ui mousemode right select
> volume #1.1.1.1 color #0433ff
> volume #1.1.1.1 color #0433ffe5
> volume #1.1.1.1 color #0433ffe6
> select add #1.2
5552 atoms, 5628 bonds, 332 residues, 10 models selected
> select add #1.2
5552 atoms, 5628 bonds, 332 residues, 10 models selected
> select add #1.2
5552 atoms, 5628 bonds, 332 residues, 10 models selected
> select add #1.2
5552 atoms, 5628 bonds, 332 residues, 10 models selected
> select add #1
5552 atoms, 5628 bonds, 332 residues, 17 models selected
> select add #1
5552 atoms, 5628 bonds, 332 residues, 17 models selected
> select add #1
5552 atoms, 5628 bonds, 332 residues, 17 models selected
> select subtract #1.3
5552 atoms, 5628 bonds, 332 residues, 16 models selected
> select add #1.2
5552 atoms, 5628 bonds, 332 residues, 16 models selected
> select clear
Drag select of 1 atoms, 1 bonds
> volume #!1.1.1.1 style surface
> transparency #1.1.1.1.2 0
> volume #1.1.1.1 color #0433ff24
> volume #1.1.1.1 level 0.2145
Drag select of 1 atoms
> show sel cartoons
> hide sel atoms
> show sel cartoons
> hide sel atoms
> show sel cartoons
> style sel stick
Changed 1 atom style
> hide sel cartoons
> show sel cartoons
> select add #1.2
5552 atoms, 5628 bonds, 332 residues, 10 models selected
> select add #1.2
5552 atoms, 5628 bonds, 332 residues, 10 models selected
> hide sel atoms
> show sel cartoons
> select clear
> select add #1.2
5552 atoms, 5628 bonds, 332 residues, 10 models selected
> select add #1.2
5552 atoms, 5628 bonds, 332 residues, 10 models selected
> select add #1
5552 atoms, 5628 bonds, 332 residues, 17 models selected
> select add #1
5552 atoms, 5628 bonds, 332 residues, 17 models selected
> select add #1
5552 atoms, 5628 bonds, 332 residues, 17 models selected
> select add #1
5552 atoms, 5628 bonds, 332 residues, 17 models selected
> select subtract #1.1
5552 atoms, 5628 bonds, 332 residues, 12 models selected
> select add #1.2
5552 atoms, 5628 bonds, 332 residues, 12 models selected
Drag select of 2 residues
> select : 240-266
419 atoms, 419 bonds, 27 residues, 1 model selected
> select : 240-266
419 atoms, 419 bonds, 27 residues, 1 model selected
> isolde release torsions #1.2&sel
> isolde release torsions #1.2 backbone false
> close #1.2
Deleting atomic symmetry model...
Deleting atomic symmetry model...
> open "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl
> pH6.5/Doppio/job16/edited_coot/test_refined_edited_ISOLDE_4-coot-4.pdb"
Chain information for test_refined_edited_ISOLDE_4-coot-4.pdb #2
---
Chain | Description
A | No description available
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 5 residues in model #2 to IUPAC-IUB
standards.
Chain information for test_refined_edited_ISOLDE_4-coot-4.pdb
---
Chain | Description
2.2/A | No description available
Deleting atomic symmetry model...
> select clear
> volume #1.1.1.1 level 0.1375
> isolde restrain distances #2.2
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Please select a single atom!
> select all
5552 atoms, 5628 bonds, 332 residues, 21 models selected
Please select a single atom!
> isolde sim start /A
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 12 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:153
ISOLDE: started sim
> isolde pepflip /A:153
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:152
ISOLDE: started sim
> isolde pepflip /A:152
> isolde cisflip /A:152
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:153
ISOLDE: started sim
> isolde pepflip /A:153
Deleting atomic symmetry model...
Deleting atomic symmetry model...
> isolde pepflip /A:153
> isolde cisflip /A:153
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:152
ISOLDE: started sim
Deleting atomic symmetry model...
> isolde pepflip /A:152
> isolde cisflip /A:152
> isolde pepflip /A:152
> isolde pepflip /A:153
> isolde cisflip /A:153
> isolde pepflip /A:152
> isolde cisflip /A:152
> isolde pepflip /A:152
> isolde cisflip /A:152
> isolde pepflip /A:153
Unable to flip peptide bond after 50 rounds. Giving up.
> isolde cisflip /A:152
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:197
ISOLDE: started sim
> isolde pepflip /A:197
> isolde cisflip /A:197
Deleting atomic symmetry model...
> isolde pepflip /A:197
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:196
ISOLDE: started sim
> isolde pepflip /A:196
> isolde pepflip #!2.2/A:196
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde stepto next
Deleting atomic symmetry model...
> isolde stepto prev
> isolde sim start /A:196
ISOLDE: started sim
> isolde pepflip /A:196
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl
> pH6.5/Doppio/job16/edited_coot/test_refined_edited_ISOLDE_4-coot-6.pdb"
> close
Deleting atomic symmetry model...
> open "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl pH6.5/Doppio/job26/refined.mmcif"
> "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl pH6.5/Doppio/job26/refined_expanded.mmcif"
> "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl pH6.5/Doppio/job26/sharpened_weighted.mrc"
Summary of feedback from opening /Users/jessicakleiz/Library/Mobile
Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
collection_CryoARM_VIB_SsCl pH6.5/Doppio/job26/refined.mmcif
---
warning | Unknown polymer entity '1' on line 27
Summary of feedback from opening /Users/jessicakleiz/Library/Mobile
Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
collection_CryoARM_VIB_SsCl pH6.5/Doppio/job26/refined_expanded.mmcif
---
warning | Unknown polymer entity '1' on line 27
Chain information for refined.mmcif #1
---
Chain | Description
A | No description available
Chain information for refined_expanded.mmcif #2
---
Chain | Description
A B C D E | No description available
Opened sharpened_weighted.mrc as #3, grid size 90,90,90, pixel 2.08, shown at
level 1.51, step 1, values float32
> open "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl
> pH6.5/Map/CS_Jobs/J29/J29_004_volume_map_sharp.mrc"
Opened J29_004_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 0.731,
shown at level 0.216, step 1, values float32
> volume #4 level 0.2306
> color #2 #011993ff
> color #2 #0433ffff
> color #1 #ff2f92ff
> color byhetero
> style stick
Changed 16734 atom styles
> style stick
Changed 16734 atom styles
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> volume #4 level 0.1836
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> ui tool show "Side View"
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
> ui tool show "Ramachandran Plot"
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 10 residues in model #2 to IUPAC-IUB
standards.
Chain information for refined_expanded.mmcif
---
Chain | Description
2.2/A 2.2/B 2.2/C 2.2/D 2.2/E | No description available
ISOLDE: created disulfide bonds between the following residues:
A131-A145; A69-A115; D69-D115; E131-E145; B131-B145; D131-D145; C69-C115;
E69-E115; C131-C145; B69-B115
Computing secondary structure
> ui tool show "Ramachandran Plot"
> clipper associate #4 toModel #2
Opened J29_004_volume_map_sharp.mrc as #2.1.1.1, grid size 256,256,256, pixel
0.731, shown at step 1, values float32
> ui tool show "Ramachandran Plot"
> close
> open "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl
> pH6.5/Map/CS_Jobs/J29/J29_004_volume_map_sharp.mrc"
Opened J29_004_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 0.731,
shown at level 0.216, step 1, values float32
> open "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl pH6.5/Doppio/job26/refined_expanded.pdb"
Chain information for refined_expanded.pdb #2
---
Chain | Description
A B C D E | No description available
> style stick
Changed 13945 atom styles
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 10 residues in model #2 to IUPAC-IUB
standards.
Chain information for refined_expanded.pdb
---
Chain | Description
2.2/A 2.2/B 2.2/C 2.2/D 2.2/E | No description available
ISOLDE: created disulfide bonds between the following residues:
B131-B145; B69-B115; E69-E115; D131-D145; C131-C145; D69-D115; E131-E145;
C69-C115
Computing secondary structure
> clipper associate #1 toModel #2
Opened J29_004_volume_map_sharp.mrc as #2.1.1.1, grid size 256,256,256, pixel
0.731, shown at step 1, values float32
> hide #!2.2 models
> show #!2.2 models
> volume style surface
> volume #2.1.1.1 color #2b772c
> volume #2.1.1.1 color #2b772c4b
> ui tool show "Ramachandran Plot"
> volume #2.1.1.1 level 0.1359
> isolde sim start /C:226/D:288
Sim termination reason: None
ISOLDE: stopped sim
> addh #2.2
Summary of feedback from adding hydrogens to refined_expanded.pdb #2.2
---
warnings | Not adding hydrogens to /A ARG 21 CB because it is missing heavy-atom bond partners
Not adding hydrogens to /A GLU 76 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B ARG 21 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B GLU 76 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /C ARG 21 CB because it is missing heavy-atom bond
partners
5 messages similar to the above omitted
notes | Termini for refined_expanded.pdb (#2.2) chain A determined from SEQRES records
Termini for refined_expanded.pdb (#2.2) chain B determined from SEQRES records
Termini for refined_expanded.pdb (#2.2) chain C determined from SEQRES records
Termini for refined_expanded.pdb (#2.2) chain D determined from SEQRES records
Termini for refined_expanded.pdb (#2.2) chain E determined from SEQRES records
Chain-initial residues that are actual N termini: /A ILE 4, /B ILE 4, /C ILE
4, /D ILE 4, /E ILE 4
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A LEU 335, /B LEU 335, /C LEU
335, /D LEU 335, /E LEU 335
Chain-final residues that are not actual C termini:
1230 hydrogen bonds
13815 hydrogens added
> isolde restrain distances #2.2
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde sim start /C:223-229/D:285-291
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:288/E:226
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #!2.2/E:226
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:226/B:288
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /D:226/E:288
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:226/C:288
ISOLDE: started sim
> volume #2.1.1.1 level 0.114
> volume #2.1.1.1 level 0.1234
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:269/E:177
ISOLDE: started sim
> isolde pepflip /A:269
> isolde cisflip /A:269
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:269
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /B:177/C:269
ISOLDE: started sim
> volume #2.1.1.1 level 0.06526
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /C:269
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:177/B:269
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 5 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.2271
> isolde sim start /D:177/E:269
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 4 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /C:177/D:269
ISOLDE: started sim
> isolde pepflip /D:269
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /D:269
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /D:53/E:93
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /B:53/C:93
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /C:53/D:93
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:53/B:93
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:93/E:53
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:169/B:194
ISOLDE: started sim
> volume #2.1.1.1 level 0.1876
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:169/B:194
ISOLDE: started sim
> close #2.2.9
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:169/C:194
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:194/E:169
ISOLDE: started sim
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:194
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /D:169/E:194
ISOLDE: started sim
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
> volume #2.1.1.1 level 0.1895
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl
> pH6.5/Doppio/job26/edited_ISOLDE/refined_expanded_ISOLDE-1.pdb"
> isolde sim start /C:169/D:194
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:243/E:237
ISOLDE: started sim
> volume #2.1.1.1 level 0.1704
> volume #2.1.1.1 level 0.15
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /B:237/C:243
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:25/E:8
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /C:8/D:25
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /D:8/E:25
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /B:8/C:25
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:8/B:25
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /C:262/D:261
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:262/B:261
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:197
ISOLDE: started sim
> isolde pepflip /A:197
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:197
ISOLDE: started sim
> isolde pepflip /A:196
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:197
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:196
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /C:158
ISOLDE: started sim
> isolde pepflip /C:158
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:152
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:149-155
ISOLDE: started sim
> isolde pepflip /B:153
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /D:152
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:196
ISOLDE: started sim
> isolde pepflip /B:197
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:197
ISOLDE: started sim
> isolde pepflip /B:197
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:266
ISOLDE: started sim
> isolde pepflip /B:266
> isolde pepflip #!2.2/B:266
> isolde stepto next
> isolde stepto prev
> isolde stepto next
> isolde pepflip /B:267
> isolde stepto prev
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /B:266
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.09923
> isolde sim start /B:197
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:197
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:42-43
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /B:9,71
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:93/E:53
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /C:53/D:93
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:324,328
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:42-43
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /C:48
ISOLDE: started sim
> isolde pepflip /C:48
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 4 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /E:152
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:266
ISOLDE: started sim
> isolde pepflip /A:266
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /D:236
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /C:152
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:152
ISOLDE: started sim
> isolde pepflip /A:153
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:249
ISOLDE: started sim
> isolde pepflip /A:249
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde pepflip /A:248
ISOLDE: started sim
> isolde pepflip /A:248
> isolde pepflip /A:249
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:249
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /A:98
ISOLDE: started sim
> isolde pepflip /A:98
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /C:98
ISOLDE: started sim
> isolde pepflip /C:98
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /D:98
ISOLDE: started sim
> isolde pepflip /D:98
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /D:142
ISOLDE: started sim
> isolde pepflip /D:142
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /E:98
ISOLDE: started sim
> isolde pepflip /E:98
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:98
ISOLDE: started sim
> isolde pepflip /B:98
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /E:142
ISOLDE: started sim
> isolde pepflip /E:142
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl
> pH6.5/Doppio/job26/edited_ISOLDE/refined_expanded_ISOLDE-2.pdb"
> isolde sim start /B:142
ISOLDE: started sim
> isolde pepflip /B:142
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /C:142
ISOLDE: started sim
> isolde pepflip /C:142
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:142
ISOLDE: started sim
> isolde pepflip /A:142
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:142
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:48
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /E:48
ISOLDE: started sim
> isolde pepflip /E:48
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /D:266
ISOLDE: started sim
> isolde pepflip /D:266
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /C:47-48
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl
> pH6.5/Doppio/job26/edited_ISOLDE/refined_expanded_ISOLDE-3.pdb"
> select 5
Expected an objects specifier or a keyword
> select 5
Expected an objects specifier or a keyword
> select residues 5
Invalid "residues" argument: Expected true or false (or 1 or 0)
> select resiue 5
Expected an objects specifier or a keyword
> ui tool show "Ramachandran Plot"
> isolde sim start /A:239
ISOLDE: started sim
> isolde pepflip /A:239
> volume #2.1.1.1 level 0.134
> isolde pepflip /A:239
> isolde pepflip /A:240
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:239
ISOLDE: started sim
> isolde pepflip /A:239
> isolde cisflip /A:239
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:239
ISOLDE: started sim
> isolde sim pause
> isolde sim resume
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /C:239
ISOLDE: started sim
> isolde pepflip /C:239
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /D:239
ISOLDE: started sim
> isolde pepflip /D:239
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /D:239
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /E:239
ISOLDE: started sim
> isolde pepflip /E:239
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde pepflip /E:239
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:239
ISOLDE: started sim
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:236-242
ISOLDE: started sim
> isolde pepflip /B:239
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.1497
> isolde sim start /B:239
ISOLDE: started sim
> isolde pepflip /B:238
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl
> pH6.5/Doppio/job26/edited_ISOLDE/refined_expanded_ISOLDE-4.pdb"
> isolde sim start /A:239
ISOLDE: started sim
> isolde pepflip /A:239
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #!2.2/A:239
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:5
ISOLDE: started sim
> isolde pepflip /A:5
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /B:5
ISOLDE: started sim
> isolde pepflip /B:5
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /C:5
ISOLDE: started sim
> isolde pepflip /C:5
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /E:5
ISOLDE: started sim
> isolde pepflip /E:5
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /D:5
ISOLDE: started sim
> isolde pepflip /D:5
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl
> pH6.5/Doppio/job26/edited_ISOLDE/refined_expanded_ISOLDE-5.pdb"
> isolde sim start /D:266
ISOLDE: started sim
> isolde pepflip /D:266
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /B:215/C:269
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /A:269/E:215
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> save "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl
> pH6.5/Doppio/job26/edited_ISOLDE/refined_expanded_ISOLDE-6.pdb"
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl
> pH6.5/Doppio/job37_Gemmi_inputjob34/refined_gemmi_processed.cif-
> coot-0_piece_cut.pdb"
Chain information for refined_gemmi_processed.cif-coot-0_piece_cut.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> set bgColor white
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> color #1 #0433ffff
> color #1 #2b772cff
> open "/Users/jessicakleiz/Library/Mobile
> Documents/com~apple~CloudDocs/LSN/SsCl/Processing_Full data
> collection_CryoARM_VIB_SsCl
> pH6.5/Map/CS_Jobs/J29/J29_004_volume_map_sharp.mrc"
Opened J29_004_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 0.731,
shown at level 0.216, step 1, values float32
> volume #2 level 0.1638
> transparency 50
> volume #2 level 0.132
> volume #2 level 0.1559
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1 to IUPAC-IUB
standards.
Chain information for refined_gemmi_processed.cif-coot-0_piece_cut.pdb
---
Chain | Description
1.2/A | No description available
ISOLDE: created disulfide bonds between the following residues:
A131-A145; A69-A115
> clipper associate #2 toModel #1
Opened J29_004_volume_map_sharp.mrc as #1.1.1.1, grid size 256,256,256, pixel
0.731, shown at step 1, values float32
> volume style surface
> transparency 50
> volume #1.1.1.1 color #2b772c
> volume #1.1.1.1 color #2b772c2a
> volume #1.1.1.1 level 0.2123
> volume #1.1.1.1 color #2b772c63
> select add #1.2
2725 atoms, 2798 bonds, 1 pseudobond, 324 residues, 10 models selected
> select add #1.2
2725 atoms, 2798 bonds, 1 pseudobond, 324 residues, 10 models selected
> ui tool show "Ramachandran Plot"
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,4
Model Number: Z15G0040EFN/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 GB
System Firmware Version: 11881.41.5
OS Loader Version: 11881.41.5
Software:
System Software Overview:
System Version: macOS 15.1.1 (24B91)
Kernel Version: Darwin 24.1.0
Time since boot: 15 days, 29 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG HDR 4K:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
ChimeraX-Clipper: 0.24.0
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: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.9
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 9 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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