![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 12 months ago
Closed 12 months ago
#16187 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.7.5-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Current thread 0x0000000104b5c580 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in __iter__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mmcif/__init__.py", line 123 in save
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101 in provider_save
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86 in cmd_save
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 62 in display
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138 in show_save_file_dialog
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 127 in
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.mmcif.mmcif_write (total: 54)
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"procLaunch" : "2024-10-23 10:34:44.5366 -0700",
"procRole" : "Foreground",
"version" : 2,
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"modelCode" : "MacBookPro18,4",
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"captureTime" : "2024-10-24 13:05:52.8831 -0700",
"incident" : "6506AFD9-FE0B-4A5F-84F3-340E5FEF8A17",
"bug_type" : "309",
"pid" : 57705,
"procExitAbsTime" : 5374907567463,
"translated" : false,
"cpuType" : "ARM-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
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"wakeTime" : 8231,
"sleepWakeUUID" : "81BA9D90-ABB9-4095-8710-9601566DC8AA",
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"exception" : {"codes":"0x0000000000000002, 0x00000001084da6c0","rawCodes":[2,4434273984],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x00000001084da6c0"},
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"uuid" : "1cb5b95a-41b5-3897-a39d-1305dac761eb",
"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWidgets.framework\/Versions\/A\/QtWidgets",
"name" : "QtWidgets"
},
{
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"arch" : "arm64",
"base" : 5091885056,
"size" : 3047424,
"uuid" : "b2d23268-944f-3492-8cfd-24699ae18bab",
"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so",
"name" : "QtWidgets.abi3.so"
},
{
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"arch" : "arm64",
"base" : 5341446144,
"size" : 622592,
"uuid" : "a07d6b8c-b467-339b-8483-3ba6dc00495e",
"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
"name" : "libqcocoa.dylib"
},
{
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"arch" : "arm64e",
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"size" : 5533696,
"uuid" : "722b2af5-652e-3a7e-8ef8-12671f63a6a7",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
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"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
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"size" : 15441920,
"uuid" : "2c7c9cbb-9199-32e2-93ac-e14539c32a7f",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
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"uuid" : "17982d98-65bc-3327-8526-577ec996453c",
"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.7.1.0"
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"name" : "dyld"
},
{
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"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
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"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
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"source" : "A",
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}
],
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)\nWritable regions: Total=9.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=9.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 1408K 11 \nActivity Tracing 256K 1 \nCG backing stores 4480K 8 \nCG image 2608K 103 \nColorSync 560K 28 \nCoreAnimation 7552K 149 \nCoreGraphics 48K 3 \nCoreUI image data 5584K 49 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 8.1G 1009 \nMALLOC guard page 192K 9 \nMALLOC_MEDIUM (reserved) 392.0M 9 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 608K 38 \nStack 162.9M 39 \nStack Guard 56.0M 1 \nVM_ALLOCATE 308.4M 263 \nVM_ALLOCATE (reserved) 224.0M 3 reserved VM address space (unallocated)\n__AUTH 2632K 316 \n__AUTH_CONST 20.7M 515 \n__CTF 756 1 \n__DATA 24.6M 658 \n__DATA_CONST 27.8M 665 \n__DATA_DIRTY 1822K 221 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 607.5M 149 \n__OBJC_CONST 3703K 287 \n__OBJC_RO 83.0M 1 \n__OBJC_RW 3168K 1 \n__TEXT 724.3M 683 \n__UNICODE 592K 1 \ndyld private memory 1216K 3 \nmapped file 235.2M 64 \nshared memory 3184K 23 \n=========== ======= ======= \nTOTAL 11.3G 5323 \nTOTAL, minus reserved VM space 10.3G 5323 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "5fc94383418129005b4e9ae0",
"factorPackIds" : {
},
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},
{
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}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/PhosphoPDB_SSCorrection/T209A/T209A_cryosparc_P9_J25_006_volume_map_sharp.mrc
Opened T209A_cryosparc_P9_J25_006_volume_map_sharp.mrc as #1, grid size
600,600,600, pixel 0.835, shown at level 0.128, step 4, values float32
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/PhosphoPDB_SSCorrection/T209A/T209A_coot_1_intefaceSCcheck_fitted_edited_real_space_refined_011_split_real_space_refined_027_SSEDIT_real_space_refined_029.pdb
Chain information for
T209A_coot_1_intefaceSCcheck_fitted_edited_real_space_refined_011_split_real_space_refined_027_SSEDIT_real_space_refined_029.pdb
#2
---
Chain | Description
A AB B BB C CB D DB E EB F FB G GB H HB I IB J JB K KB L LB M MB N NB O OB P
PB Q QB R RB S SB T TB U UB V VB W WB | No description available
a ab b bb c cb d db e eb f fb g gb | No description available
> hide atoms
> show cartoons
> hide #!1 models
> select /AB
882 atoms, 888 bonds, 1 pseudobond, 116 residues, 2 models selected
> setattr #2/A:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/AB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/B:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/BB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/C:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/CB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/D:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/DB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/EB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/E:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/F:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/FB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/G:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/GB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/H:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/HB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/I:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/IB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/J:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/JB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/KB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/K:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/L:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/LB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/MB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/M:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/N:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/NB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/OB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/O:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/P:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/PB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/Q:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/QB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/RB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/R:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/S:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/SB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/T:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/TB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/UB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/U:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/V:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/VB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/WB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/W:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/X:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 0 items
> save "/Users/elizabethbond/OneDrive -
> UCSF/PhosphoPDB_SSCorrection/T209A/ChimeraX/T209A_SS.pdb" relModel #2
> close #2
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/PhosphoPDB_SSCorrection/T175E/T175E-coot-1_real_space_refined_009_real_space_refined_011.pdb
Chain information for
T175E-coot-1_real_space_refined_009_real_space_refined_011.pdb #2
---
Chain | Description
A AB I IB L LB M MB R RB S SB T TB | No description available
B BB C CB D DB E EB F FB G GB H HB J JB K KB N NB O OB | No description
available
P PB Q QB | No description available
a ab b bb c cb d db e eb f fb g gb h hb i ib j jb | No description available
> close #1
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/PhosphoPDB_SSCorrection/T175E/T175E_cryosparc_P29_J61_004_volume_map_sharp.mrc
Opened T175E_cryosparc_P29_J61_004_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 1.33, shown at level 0.397, step 2, values float32
> hide atoms
> show cartoons
> select /A
886 atoms, 892 bonds, 1 pseudobond, 116 residues, 2 models selected
> select clear
> setattr #2/A:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/AB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/B:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/BB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/CB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/C:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/D:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/DB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/EB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/E:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/F:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/FB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/GB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/G:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/H:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/HB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/IB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/I:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/J:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/JB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/KB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/K:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/L:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/LB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/MB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/M:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/N:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/NB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/OB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/O:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/P:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 15 items
> setattr #2/PB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/QB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/Q:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/R:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/RB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/SB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/S:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/T:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/TB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/UB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 0 items
> show #!1 models
> hide #!1 models
> save "/Users/elizabethbond/OneDrive -
> UCSF/PhosphoPDB_SSCorrection/T175E/ChimeraX/T175E_SS.pdb" relModel #2
> close #2
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/PhosphoPDB_SSCorrection/T175A/T175A_mod72_coot_0_real_space_refined_006_real_space_refined_009.pdb
Chain information for
T175A_mod72_coot_0_real_space_refined_006_real_space_refined_009.pdb #2
---
Chain | Description
A AB B BB D DB F FB G GB I IB J JB K KB L LB M MB N NB O OB P PB Q QB R RB |
No description available
C CB E EB H HB S SB | No description available
T TB | No description available
a ab b bb c cb d db e eb f fb g gb h hb i ib j jb | No description available
> close #1
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/PhosphoPDB_SSCorrection/T175A/T175A_cryosparc_P10_J12_004_volume_map_sharp.mrc
Opened T175A_cryosparc_P10_J12_004_volume_map_sharp.mrc as #1, grid size
600,600,600, pixel 0.835, shown at level 0.0916, step 4, values float32
> hide #!1 models
> hide atoms
> show cartoons
> select /A
873 atoms, 879 bonds, 1 pseudobond, 115 residues, 2 models selected
> select clear
> setattr #2/A:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/AB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/B:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/BB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/CB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/C:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/D:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/DB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/EB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/E:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/F:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/FB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/GB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/G:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/H:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/HB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/IB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/I:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/J:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/JB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/KB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/K:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/L:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/LB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/MB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/M:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/N:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/NB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/OB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/O:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/P:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/Q:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/QB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/PB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/RB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/R:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/S:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/SB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/TB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/T:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 15 items
> setattr #2/U:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 0 items
> save "/Users/elizabethbond/OneDrive -
> UCSF/PhosphoPDB_SSCorrection/T175A/ChimeraX/T175A_SS.pdb" relModel #2
> close #2
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/PhosphoPDB_SSCorrection/S56A/S56A_fit_real_space_refined_003_real_space_refined_005.pdb
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb #2
---
Chain | Description
A I K | No description available
AB EB HB J KB L LB M MB RB S TB | No description available
B BB C CB D DB E F FB G GB H JB N NB O OB | No description available
IB SB T | No description available
P PB | No description available
Q QB | No description available
R | No description available
a ab b bb c cb d db e eb f fb g gb h hb i ib j jb | No description available
> close #1
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/PhosphoPDB_SSCorrection/S56A/S56A_cryosparc_P7_J15_005_volume_map_sharp.mrc
Opened S56A_cryosparc_P7_J15_005_volume_map_sharp.mrc as #1, grid size
600,600,600, pixel 0.835, shown at level 0.101, step 4, values float32
> hide #!1 models
> hide atoms
> show cartoons
> setattr #2/A:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> select /A
893 atoms, 899 bonds, 1 pseudobond, 117 residues, 2 models selected
> select clear
> setattr #2/AB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/B:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/BB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/CB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/C:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/D:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/DB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/EB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/E:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/F:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/FB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/GB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/G:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/H:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/HB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/IB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/I:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/J:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/JB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/KB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/K:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/L:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/LB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/MB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/M:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/N:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/NB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/OB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/O:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/P:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 15 items
> setattr #2/PB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/QB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/Q:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/R:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/RB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/SB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/S:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/T:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/TB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/UB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 0 items
> setattr #2/U:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 0 items
> setattr #2/V:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 0 items
> setattr #2/P:142-150,173-185,202-218,229-233,258-269 res ss_type 1
Assigning ss_type attribute to 49 items
> setattr #2/PB:142-150,173-185,202-218,229-233,258-269 res ss_type 1
Assigning ss_type attribute to 56 items
> setattr #2/PB:142-150,173-185,202-218,229-233,244-255 res ss_type 1
Assigning ss_type attribute to 49 items
> setattr #2/P:142-150,173-185,202-218,229-233,244-255 res ss_type 1
Assigning ss_type attribute to 56 items
> setattr #2/P:142-150,173-185,202-218,229-233,258-269 res ss_type 1
Assigning ss_type attribute to 49 items
> setattr #2/P:142-150,173-185,202-218,229-233,258-262 res ss_type 1
Assigning ss_type attribute to 49 items
> select /P
917 atoms, 924 bonds, 121 residues, 1 model selected
> delete sel
> select /PB
917 atoms, 923 bonds, 1 pseudobond, 121 residues, 2 models selected
> combine sel
> show #!1 models
> color #1 #b2b2b28b models
> volume #1 step 1
> volume #1 level 0.4703
> volume #1 level 0.2533
> select add #2
51852 atoms, 52206 bonds, 39 pseudobonds, 6887 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #3
51852 atoms, 52206 bonds, 39 pseudobonds, 6887 residues, 2 models selected
> select subtract #3
Nothing selected
> select add #3
51852 atoms, 52206 bonds, 39 pseudobonds, 6887 residues, 2 models selected
> select subtract #3
Nothing selected
> combine #2/P
No structures specified
> combine #2/PB
> select add #4
51852 atoms, 52206 bonds, 39 pseudobonds, 6887 residues, 2 models selected
> select subtract #4
Nothing selected
> close #3
> select add #4
51852 atoms, 52206 bonds, 39 pseudobonds, 6887 residues, 2 models selected
> select subtract #4
Nothing selected
> close #4
> select PB
Expected an objects specifier or a keyword
> split #2
Split S56A_fit_real_space_refined_003_real_space_refined_005.pdb (#2) into 59
models
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb A #2.1
---
Chain | Description
A | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb AB #2.2
---
Chain | Description
AB | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb B #2.3
---
Chain | Description
B | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb BB #2.4
---
Chain | Description
BB | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb C #2.5
---
Chain | Description
C | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb CB #2.6
---
Chain | Description
CB | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb D #2.7
---
Chain | Description
D | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb DB #2.8
---
Chain | Description
DB | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb E #2.9
---
Chain | Description
E | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb EB #2.10
---
Chain | Description
EB | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb F #2.11
---
Chain | Description
F | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb FB #2.12
---
Chain | Description
FB | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb G #2.13
---
Chain | Description
G | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb GB #2.14
---
Chain | Description
GB | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb H #2.15
---
Chain | Description
H | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb HB #2.16
---
Chain | Description
HB | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb I #2.17
---
Chain | Description
I | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb IB #2.18
---
Chain | Description
IB | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb J #2.19
---
Chain | Description
J | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb JB #2.20
---
Chain | Description
JB | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb K #2.21
---
Chain | Description
K | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb KB #2.22
---
Chain | Description
KB | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb L #2.23
---
Chain | Description
L | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb LB #2.24
---
Chain | Description
LB | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb M #2.25
---
Chain | Description
M | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb MB #2.26
---
Chain | Description
MB | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb N #2.27
---
Chain | Description
N | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb NB #2.28
---
Chain | Description
NB | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb O #2.29
---
Chain | Description
O | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb OB #2.30
---
Chain | Description
OB | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb PB #2.31
---
Chain | Description
PB | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb Q #2.32
---
Chain | Description
Q | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb QB #2.33
---
Chain | Description
QB | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb R #2.34
---
Chain | Description
R | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb RB #2.35
---
Chain | Description
RB | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb S #2.36
---
Chain | Description
S | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb SB #2.37
---
Chain | Description
SB | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb T #2.38
---
Chain | Description
T | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb TB #2.39
---
Chain | Description
TB | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb a #2.40
---
Chain | Description
a | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb ab #2.41
---
Chain | Description
ab | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb b #2.42
---
Chain | Description
b | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb bb #2.43
---
Chain | Description
bb | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb c #2.44
---
Chain | Description
c | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb cb #2.45
---
Chain | Description
cb | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb d #2.46
---
Chain | Description
d | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb db #2.47
---
Chain | Description
db | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb e #2.48
---
Chain | Description
e | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb eb #2.49
---
Chain | Description
eb | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb f #2.50
---
Chain | Description
f | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb fb #2.51
---
Chain | Description
fb | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb g #2.52
---
Chain | Description
g | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb gb #2.53
---
Chain | Description
gb | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb h #2.54
---
Chain | Description
h | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb hb #2.55
---
Chain | Description
hb | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb i #2.56
---
Chain | Description
i | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb ib #2.57
---
Chain | Description
ib | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb j #2.58
---
Chain | Description
j | No description available
Chain information for
S56A_fit_real_space_refined_003_real_space_refined_005.pdb jb #2.59
---
Chain | Description
jb | No description available
> select #2/PB
917 atoms, 923 bonds, 1 pseudobond, 121 residues, 2 models selected
> combine sel
> select add #2
51852 atoms, 52206 bonds, 39 pseudobonds, 6887 residues, 99 models selected
> select subtract #2
Nothing selected
> hide #!2 models
> show #!2 models
> select add #3
917 atoms, 923 bonds, 1 pseudobond, 121 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.24945,-0.8457,0.47177,420.62,-0.70687,0.492,0.50821,181.42,-0.6619,-0.2067,-0.72053,684.52
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.24945,-0.8457,0.47177,404.5,-0.70687,0.492,0.50821,172.81,-0.6619,-0.2067,-0.72053,684.28
> fitmap #3 inMap #1
Fit molecule copy of
S56A_fit_real_space_refined_003_real_space_refined_005.pdb PB (#3) to map
S56A_cryosparc_P7_J15_005_volume_map_sharp.mrc (#1) using 917 atoms
average map value = 0.2113, steps = 136
shifted from previous position = 3.04
rotated from previous position = 19.9 degrees
atoms outside contour = 572, contour level = 0.25331
Position of copy of S56A_fit_real_space_refined_003_real_space_refined_005.pdb
PB (#3) relative to S56A_cryosparc_P7_J15_005_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.44754802 -0.63101544 0.63365629 340.05667174
-0.64740780 0.71743827 0.25718762 156.64640841
-0.61689863 -0.29513021 -0.72961239 705.96088138
Axis -0.40398000 0.91468924 -0.01198981
Axis point 357.11211401 0.00000000 280.77287391
Rotation angle (degrees) 136.87474792
Shift along axis -2.55764427
> view matrix models
> #3,-0.44755,-0.63102,0.63366,344.28,-0.64741,0.71744,0.25719,156.5,-0.6169,-0.29513,-0.72961,711.69
> view matrix models
> #3,-0.44755,-0.63102,0.63366,342.5,-0.64741,0.71744,0.25719,156.8,-0.6169,-0.29513,-0.72961,706.71
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.71264,-0.69584,0.089176,571.9,-0.49391,0.58793,0.64062,56.34,-0.4982,0.41249,-0.76266,472.47
> view matrix models
> #3,-0.78865,-0.61154,0.063718,570.85,-0.41268,0.60331,0.68243,21.373,-0.45577,0.5119,-0.72817,422.93
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.78865,-0.61154,0.063718,571.07,-0.41268,0.60331,0.68243,22.976,-0.45577,0.5119,-0.72817,419.43
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.51749,-0.85518,0.029601,591.37,-0.75172,0.47086,0.46174,202.26,-0.40881,0.21669,-0.88652,541.42
> fitmap #3 inMap #1
Fit molecule copy of
S56A_fit_real_space_refined_003_real_space_refined_005.pdb PB (#3) to map
S56A_cryosparc_P7_J15_005_volume_map_sharp.mrc (#1) using 917 atoms
average map value = 0.3993, steps = 164
shifted from previous position = 2.7
rotated from previous position = 33.8 degrees
atoms outside contour = 288, contour level = 0.25331
Position of copy of S56A_fit_real_space_refined_003_real_space_refined_005.pdb
PB (#3) relative to S56A_cryosparc_P7_J15_005_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.66738007 -0.64802086 -0.36697796 671.81491196
-0.64794854 0.26235419 0.71507551 175.56515408
-0.36710564 0.71500997 -0.59497412 298.91587913
Axis -0.40781387 0.79446595 0.45001300
Axis point 380.97541267 0.00000000 99.71786364
Rotation angle (degrees) 179.99539603
Shift along axis 0.02112909
> combine #2-3
Remapping chain ID 'PB' in copy of
S56A_fit_real_space_refined_003_real_space_refined_005.pdb PB #3 to 'PC'
> hide #!3 models
> hide #!2 models
> save "/Users/elizabethbond/OneDrive -
> UCSF/PhosphoPDB_SSCorrection/S56A/ChimeraX/S56A_SS.pdb" models #4 relModel
> #4
> close #4
> close #3
> close #2
> close #1
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/PhosphoPDB_SSCorrection/RsbX/RsbX_cryosparc_P19_J60_004_volume_map_sharp.mrc
Opened RsbX_cryosparc_P19_J60_004_volume_map_sharp.mrc as #1, grid size
600,600,600, pixel 0.865, shown at level 0.103, step 4, values float32
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/PhosphoPDB_SSCorrection/RsbX/RSX_chainReassign_real_space_refined_001_real_space_refined_002_real_space_refined_005.pdb
Chain information for
RSX_chainReassign_real_space_refined_001_real_space_refined_002_real_space_refined_005.pdb
#2
---
Chain | Description
A AB B BB C CB D DB F FB G GB GC GD H HB I IB IC ID J JB K KB L LB N NB | No
description available
a ab b bb d db e eb f fb g gb h hb i ib j jb k kb l lb m mb n nb o ob p pb q
qb | No description available
> volume #1 step 1
> volume #1 level 0.2156
> hide atoms
> show cartoons
> setattr #2/A:142-150,173-185,202-218,229-233,258-262 res ss_type 1
Assigning ss_type attribute to 44 items
> setattr #2/AB:142-150,173-185,202-218,229-233,258-262 res ss_type 1
Assigning ss_type attribute to 44 items
> setattr #2/B:142-150,173-185,202-218,229-233,258-262 res ss_type 1
Assigning ss_type attribute to 44 items
> setattr #2/BB:142-150,173-185,202-218,229-233,258-262 res ss_type 1
Assigning ss_type attribute to 44 items
> setattr #2/CB:142-150,173-185,202-218,229-233,258-262 res ss_type 1
Assigning ss_type attribute to 44 items
> setattr #2/C:142-150,173-185,202-218,229-233,258-262 res ss_type 1
Assigning ss_type attribute to 44 items
> setattr #2/A:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> select /A
884 atoms, 890 bonds, 1 pseudobond, 116 residues, 2 models selected
> setattr #2/B:142-150 res ss_type 0
Assigning ss_type attribute to 4 items
> setattr #2/A:142-150 res ss_type 0
Assigning ss_type attribute to 4 items
> setattr #2/AB:142-150 res ss_type 0
Assigning ss_type attribute to 4 items
> setattr #2/B:142-150 res ss_type 0
Assigning ss_type attribute to 4 items
> setattr #2/BB:142-150 res ss_type 0
Assigning ss_type attribute to 4 items
> setattr #2/CB:142-150 res ss_type 0
Assigning ss_type attribute to 4 items
> setattr #2/CB:142-150 res ss_type 0
Assigning ss_type attribute to 4 items
> setattr #2/A:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/AB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/B:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/BB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/CB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/C:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> select /D
884 atoms, 890 bonds, 1 pseudobond, 116 residues, 2 models selected
> view sel
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/phenixStressosome/T209E_LocalRes/RealSpaceRefine_14/T209E_SS_correct_real_space_refined_014.pdb
Chain information for T209E_SS_correct_real_space_refined_014.pdb #3
---
Chain | Description
A AB B BB C CB D DB E EB F FB G GB H HB I IB J JB K KB L LB M MB N NB O OB |
No description available
a ab b bb c cb d db e eb f fb g gb h hb i ib j jb k kb l lb m mb n nb o ob |
No description available
> hide sel atoms
> select add #2
52640 atoms, 53000 bonds, 29 pseudobonds, 7024 residues, 2 models selected
> select subtract #2
Nothing selected
> hide #!2 models
> hide #!3 atoms
> show #!3 cartoons
> view #3
> hide #!3 models
> show #!2 models
> select /D
1761 atoms, 1773 bonds, 2 pseudobonds, 231 residues, 4 models selected
> setattr #2/D:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/DB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/EB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 0 items
> setattr #2/E:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 0 items
> setattr #2/E:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 0 items
> select #2/E
Nothing selected
> select #2/F
884 atoms, 890 bonds, 1 pseudobond, 116 residues, 2 models selected
> setattr #2/F:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/FB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/GB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/G:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/H:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/HB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/IB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/I:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/J:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/JB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/KB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/K:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/L:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/LB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/MB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 0 items
> setattr #2/M:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 0 items
> setattr #2/N:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/NB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 18 items
> setattr #2/OB:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 0 items
> setattr #2/O:152-154,161-163,190-192,223-225,253-255,272-274 res ss_type 2
Assigning ss_type attribute to 0 items
> close #3
> ui tool show "Change Chain IDs"
> select /N
884 atoms, 890 bonds, 1 pseudobond, 116 residues, 2 models selected
> changechains sel E
Chain IDs of 116 residues changed
> select /NB
884 atoms, 890 bonds, 1 pseudobond, 116 residues, 2 models selected
> changechains sel EB
Chain IDs of 116 residues changed
> select clear
> save "/Users/elizabethbond/OneDrive -
> UCSF/PhosphoPDB_SSCorrection/RsbX/ChimeraX/RSX_SS.pdb" relModel #2
> close #1-2
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/phenixStressosome/T209E_LocalRes/RealSpaceRefine_14/T209E_SS_correct_real_space_refined_014.cif
Summary of feedback from opening
/Users/elizabethbond/Library/CloudStorage/OneDrive-
UCSF/phenixStressosome/T209E_LocalRes/RealSpaceRefine_14/T209E_SS_correct_real_space_refined_014.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 2477
Missing entity information. Treating each chain as a separate entity.
Bad residue range for struct_conf "1" near line 150
Bad residue range for struct_conf "2" near line 151
Bad residue range for struct_conf "3" near line 152
Bad residue range for struct_conf "4" near line 153
Bad residue range for struct_conf "5" near line 154
15 messages similar to the above omitted
Invalid residue range for struct_conf "21": invalid chain "CB", near line 170
Invalid residue range for struct_conf "22": invalid chain "CB", near line 171
Invalid residue range for struct_conf "23": invalid chain "CB", near line 172
Invalid residue range for struct_conf "24": invalid chain "CB", near line 173
Bad residue range for struct_conf "25" near line 174
Bad residue range for struct_conf "26" near line 175
Bad residue range for struct_conf "27" near line 176
Bad residue range for struct_conf "28" near line 177
Invalid residue range for struct_conf "29": invalid chain "DB", near line 178
Invalid residue range for struct_conf "30": invalid chain "DB", near line 179
Invalid residue range for struct_conf "31": invalid chain "DB", near line 180
Invalid residue range for struct_conf "32": invalid chain "DB", near line 181
Bad residue range for struct_conf "33" near line 182
Bad residue range for struct_conf "34" near line 183
Bad residue range for struct_conf "35" near line 184
Bad residue range for struct_conf "36" near line 185
Invalid residue range for struct_conf "37": invalid chain "EB", near line 186
Invalid residue range for struct_conf "38": invalid chain "EB", near line 187
Invalid residue range for struct_conf "39": invalid chain "EB", near line 188
Invalid residue range for struct_conf "40": invalid chain "EB", near line 189
Bad residue range for struct_conf "41" near line 190
Bad residue range for struct_conf "42" near line 191
Bad residue range for struct_conf "43" near line 192
Bad residue range for struct_conf "44" near line 193
Invalid residue range for struct_conf "45": invalid chain "FB", near line 194
Invalid residue range for struct_conf "46": invalid chain "FB", near line 195
Invalid residue range for struct_conf "47": invalid chain "FB", near line 196
Invalid residue range for struct_conf "48": invalid chain "FB", near line 197
Bad residue range for struct_conf "49" near line 198
Bad residue range for struct_conf "50" near line 199
Bad residue range for struct_conf "51" near line 200
Bad residue range for struct_conf "52" near line 201
Invalid residue range for struct_conf "53": invalid chain "GB", near line 202
Invalid residue range for struct_conf "54": invalid chain "GB", near line 203
Invalid residue range for struct_conf "55": invalid chain "GB", near line 204
Invalid residue range for struct_conf "56": invalid chain "GB", near line 205
Bad residue range for struct_conf "57" near line 206
Bad residue range for struct_conf "58" near line 207
Bad residue range for struct_conf "59" near line 208
Bad residue range for struct_conf "60" near line 209
Invalid residue range for struct_conf "61": invalid chain "HB", near line 210
Invalid residue range for struct_conf "62": invalid chain "HB", near line 211
Invalid residue range for struct_conf "63": invalid chain "HB", near line 212
Invalid residue range for struct_conf "64": invalid chain "HB", near line 213
Bad residue range for struct_conf "65" near line 214
Bad residue range for struct_conf "66" near line 215
Bad residue range for struct_conf "67" near line 216
Bad residue range for struct_conf "68" near line 217
Invalid residue range for struct_conf "69": invalid chain "IB", near line 218
Invalid residue range for struct_conf "70": invalid chain "IB", near line 219
Invalid residue range for struct_conf "71": invalid chain "IB", near line 220
Invalid residue range for struct_conf "72": invalid chain "IB", near line 221
Bad residue range for struct_conf "73" near line 222
Bad residue range for struct_conf "74" near line 223
Bad residue range for struct_conf "75" near line 224
Bad residue range for struct_conf "76" near line 225
Invalid residue range for struct_conf "77": invalid chain "JB", near line 226
Invalid residue range for struct_conf "78": invalid chain "JB", near line 227
Invalid residue range for struct_conf "79": invalid chain "JB", near line 228
Invalid residue range for struct_conf "80": invalid chain "JB", near line 229
Bad residue range for struct_conf "81" near line 230
Bad residue range for struct_conf "82" near line 231
Bad residue range for struct_conf "83" near line 232
Bad residue range for struct_conf "84" near line 233
Invalid residue range for struct_conf "85": invalid chain "KB", near line 234
Invalid residue range for struct_conf "86": invalid chain "KB", near line 235
Invalid residue range for struct_conf "87": invalid chain "KB", near line 236
Invalid residue range for struct_conf "88": invalid chain "KB", near line 237
Bad residue range for struct_conf "89" near line 238
Bad residue range for struct_conf "90" near line 239
Bad residue range for struct_conf "91" near line 240
Bad residue range for struct_conf "92" near line 241
Invalid residue range for struct_conf "93": invalid chain "LB", near line 242
Invalid residue range for struct_conf "94": invalid chain "LB", near line 243
Invalid residue range for struct_conf "95": invalid chain "LB", near line 244
Invalid residue range for struct_conf "96": invalid chain "LB", near line 245
Bad residue range for struct_conf "97" near line 246
Bad residue range for struct_conf "98" near line 247
Bad residue range for struct_conf "99" near line 248
Bad residue range for struct_conf "100" near line 249
Invalid residue range for struct_conf "101": invalid chain "MB", near line 250
Invalid residue range for struct_conf "102": invalid chain "MB", near line 251
Invalid residue range for struct_conf "103": invalid chain "MB", near line 252
Invalid residue range for struct_conf "104": invalid chain "MB", near line 253
Bad residue range for struct_conf "105" near line 254
Bad residue range for struct_conf "106" near line 255
Bad residue range for struct_conf "107" near line 256
Bad residue range for struct_conf "108" near line 257
Invalid residue range for struct_conf "109": invalid chain "NB", near line 258
Invalid residue range for struct_conf "110": invalid chain "NB", near line 259
Invalid residue range for struct_conf "111": invalid chain "NB", near line 260
Invalid residue range for struct_conf "112": invalid chain "NB", near line 261
Bad residue range for struct_conf "113" near line 262
Bad residue range for struct_conf "114" near line 263
Bad residue range for struct_conf "115" near line 264
Bad residue range for struct_conf "116" near line 265
Invalid residue range for struct_conf "117": invalid chain "OB", near line 266
Invalid residue range for struct_conf "118": invalid chain "OB", near line 267
Invalid residue range for struct_conf "119": invalid chain "OB", near line 268
Invalid residue range for struct_conf "120": invalid chain "OB", near line 269
Invalid residue range for struct_conf "121": invalid chain "a", near line 270
119 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "1 1" near line 2147
Invalid sheet range for struct_sheet_range "2 1" near line 2148
Invalid sheet range for struct_sheet_range "3 1" near line 2149
Invalid sheet range for struct_sheet_range "4 1" near line 2150
Invalid sheet range for struct_sheet_range "5 1" near line 2151
324 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for T209E_SS_correct_real_space_refined_014.cif #1
---
Chain | Description
A AB B BB C CB D DB E EB F FB G GB H HB I IB J JB K KB L LB M MB N NB O OB |
No description available
a ab b bb c cb d db e eb f fb g gb h hb i ib j jb k kb l lb m mb n nb o ob |
No description available
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/phenixStressosome/T209E_LocalRes/RealSpaceRefine_14/T209E_SS_correct_real_space_refined_014.pdb
Chain information for T209E_SS_correct_real_space_refined_014.pdb #2
---
Chain | Description
A AB B BB C CB D DB E EB F FB G GB H HB I IB J JB K KB L LB M MB N NB O OB |
No description available
a ab b bb c cb d db e eb f fb g gb h hb i ib j jb k kb l lb m mb n nb o ob |
No description available
> close #1
> hide atoms
> show cartoons
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/PhosphoPDB_SSCorrection/T209E/T209E_cryosparc_P8_J33_003_volume_map_sharp.mrc
Opened T209E_cryosparc_P8_J33_003_volume_map_sharp.mrc as #1, grid size
600,600,600, pixel 0.835, shown at level 0.137, step 4, values float32
> volume #1 step 1
> volume #1 style mesh
> volume #1 level 0.3131
> set bgColor white
> set bgColor #ffffff00
> volume #1 color #797979
> graphics silhouettes true
> graphics silhouettes false
> hide #!2 models
> show #!2 models
> hide #!1 models
> split #2
Split T209E_SS_correct_real_space_refined_014.pdb (#2) into 60 models
Chain information for T209E_SS_correct_real_space_refined_014.pdb A #2.1
---
Chain | Description
A | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb AB #2.2
---
Chain | Description
AB | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb B #2.3
---
Chain | Description
B | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb BB #2.4
---
Chain | Description
BB | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb C #2.5
---
Chain | Description
C | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb CB #2.6
---
Chain | Description
CB | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb D #2.7
---
Chain | Description
D | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb DB #2.8
---
Chain | Description
DB | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb E #2.9
---
Chain | Description
E | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb EB #2.10
---
Chain | Description
EB | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb F #2.11
---
Chain | Description
F | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb FB #2.12
---
Chain | Description
FB | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb G #2.13
---
Chain | Description
G | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb GB #2.14
---
Chain | Description
GB | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb H #2.15
---
Chain | Description
H | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb HB #2.16
---
Chain | Description
HB | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb I #2.17
---
Chain | Description
I | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb IB #2.18
---
Chain | Description
IB | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb J #2.19
---
Chain | Description
J | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb JB #2.20
---
Chain | Description
JB | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb K #2.21
---
Chain | Description
K | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb KB #2.22
---
Chain | Description
KB | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb L #2.23
---
Chain | Description
L | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb LB #2.24
---
Chain | Description
LB | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb M #2.25
---
Chain | Description
M | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb MB #2.26
---
Chain | Description
MB | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb N #2.27
---
Chain | Description
N | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb NB #2.28
---
Chain | Description
NB | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb O #2.29
---
Chain | Description
O | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb OB #2.30
---
Chain | Description
OB | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb a #2.31
---
Chain | Description
a | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb ab #2.32
---
Chain | Description
ab | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb b #2.33
---
Chain | Description
b | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb bb #2.34
---
Chain | Description
bb | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb c #2.35
---
Chain | Description
c | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb cb #2.36
---
Chain | Description
cb | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb d #2.37
---
Chain | Description
d | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb db #2.38
---
Chain | Description
db | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb e #2.39
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Chain | Description
e | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb eb #2.40
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Chain | Description
eb | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb f #2.41
---
Chain | Description
f | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb fb #2.42
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Chain | Description
fb | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb g #2.43
---
Chain | Description
g | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb gb #2.44
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Chain | Description
gb | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb h #2.45
---
Chain | Description
h | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb hb #2.46
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Chain | Description
hb | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb i #2.47
---
Chain | Description
i | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb ib #2.48
---
Chain | Description
ib | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb j #2.49
---
Chain | Description
j | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb jb #2.50
---
Chain | Description
jb | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb k #2.51
---
Chain | Description
k | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb kb #2.52
---
Chain | Description
kb | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb l #2.53
---
Chain | Description
l | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb lb #2.54
---
Chain | Description
lb | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb m #2.55
---
Chain | Description
m | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb mb #2.56
---
Chain | Description
mb | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb n #2.57
---
Chain | Description
n | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb nb #2.58
---
Chain | Description
nb | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb o #2.59
---
Chain | Description
o | No description available
Chain information for T209E_SS_correct_real_space_refined_014.pdb ob #2.60
---
Chain | Description
ob | No description available
> combine#2
Unknown command: combine#2
> combine #2
> save "/Users/elizabethbond/OneDrive -
> UCSF/PhosphoPDB_SSCorrection/T209E/ChimeraLocalRes/T209E_SS_correct_RSR_split.pdb"
> relModel #3
> hide #!2 models
> save "/Users/elizabethbond/OneDrive -
> UCSF/PhosphoPDB_SSCorrection/T209E/ChimeraLocalRes/T209E_SS_correct_RSR_split.pdb"
> models #3 relModel #3
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/phenixStressosome/T209A_LocalRes/RealSpaceRefine_32/T209A_SS_real_space_refined_032.pdb
Chain information for T209A_SS_real_space_refined_032.pdb #4
---
Chain | Description
A AB B BB C CB D DB E EB F FB G GB H HB I IB J JB K KB L LB M MB N NB O OB P
PB Q QB R RB S SB T TB U UB V VB W WB | No description available
a ab b bb c cb d db e eb f fb g gb | No description available
> hide #!3 models
> hide atoms
> show cartoons
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/phenixStressosome/T175A/RealSpaceRefine_11/T175A_SS_real_space_refined_011.cif
Summary of feedback from opening
/Users/elizabethbond/Library/CloudStorage/OneDrive-
UCSF/phenixStressosome/T175A/RealSpaceRefine_11/T175A_SS_real_space_refined_011.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 2260
Missing entity information. Treating each chain as a separate entity.
Bad residue range for struct_conf "1" near line 190
Bad residue range for struct_conf "2" near line 191
Bad residue range for struct_conf "3" near line 192
Invalid residue range for struct_conf "4": invalid chain "a", near line 193
Invalid residue range for struct_conf "5": invalid chain "a", near line 194
Invalid residue range for struct_conf "6": invalid chain "a", near line 195
Invalid residue range for struct_conf "7": invalid chain "b", near line 196
Invalid residue range for struct_conf "8": invalid chain "b", near line 197
25 messages similar to the above omitted
Bad residue range for struct_conf "34" near line 223
Bad residue range for struct_conf "35" near line 224
Bad residue range for struct_conf "36" near line 225
Bad residue range for struct_conf "37" near line 226
Bad residue range for struct_conf "38" near line 227
15 messages similar to the above omitted
Invalid residue range for struct_conf "54": invalid chain "CB", near line 243
Invalid residue range for struct_conf "55": invalid chain "CB", near line 244
Invalid residue range for struct_conf "56": invalid chain "CB", near line 245
Invalid residue range for struct_conf "57": invalid chain "CB", near line 246
Bad residue range for struct_conf "58" near line 247
Bad residue range for struct_conf "59" near line 248
Bad residue range for struct_conf "60" near line 249
Bad residue range for struct_conf "61" near line 250
Invalid residue range for struct_conf "62": invalid chain "DB", near line 251
Invalid residue range for struct_conf "63": invalid chain "DB", near line 252
Invalid residue range for struct_conf "64": invalid chain "DB", near line 253
Invalid residue range for struct_conf "65": invalid chain "DB", near line 254
Bad residue range for struct_conf "66" near line 255
Bad residue range for struct_conf "67" near line 256
Bad residue range for struct_conf "68" near line 257
Bad residue range for struct_conf "69" near line 258
Invalid residue range for struct_conf "70": invalid chain "EB", near line 259
Invalid residue range for struct_conf "71": invalid chain "EB", near line 260
Invalid residue range for struct_conf "72": invalid chain "EB", near line 261
Invalid residue range for struct_conf "73": invalid chain "EB", near line 262
Bad residue range for struct_conf "74" near line 263
Bad residue range for struct_conf "75" near line 264
Bad residue range for struct_conf "76" near line 265
Bad residue range for struct_conf "77" near line 266
Invalid residue range for struct_conf "78": invalid chain "FB", near line 267
Invalid residue range for struct_conf "79": invalid chain "FB", near line 268
Invalid residue range for struct_conf "80": invalid chain "FB", near line 269
Invalid residue range for struct_conf "81": invalid chain "FB", near line 270
Bad residue range for struct_conf "82" near line 271
Bad residue range for struct_conf "83" near line 272
Bad residue range for struct_conf "84" near line 273
Bad residue range for struct_conf "85" near line 274
Invalid residue range for struct_conf "86": invalid chain "GB", near line 275
Invalid residue range for struct_conf "87": invalid chain "GB", near line 276
Invalid residue range for struct_conf "88": invalid chain "GB", near line 277
Invalid residue range for struct_conf "89": invalid chain "GB", near line 278
Bad residue range for struct_conf "90" near line 279
Bad residue range for struct_conf "91" near line 280
Bad residue range for struct_conf "92" near line 281
Bad residue range for struct_conf "93" near line 282
Invalid residue range for struct_conf "94": invalid chain "HB", near line 283
Invalid residue range for struct_conf "95": invalid chain "HB", near line 284
Invalid residue range for struct_conf "96": invalid chain "HB", near line 285
Invalid residue range for struct_conf "97": invalid chain "HB", near line 286
Bad residue range for struct_conf "98" near line 287
Bad residue range for struct_conf "99" near line 288
Bad residue range for struct_conf "100" near line 289
Invalid residue range for struct_conf "101": invalid chain "IB", near line 290
Invalid residue range for struct_conf "102": invalid chain "IB", near line 291
Invalid residue range for struct_conf "103": invalid chain "IB", near line 292
Invalid residue range for struct_conf "104": invalid chain "IB", near line 293
Bad residue range for struct_conf "105" near line 294
Bad residue range for struct_conf "106" near line 295
Bad residue range for struct_conf "107" near line 296
Bad residue range for struct_conf "108" near line 297
Invalid residue range for struct_conf "109": invalid chain "JB", near line 298
Invalid residue range for struct_conf "110": invalid chain "JB", near line 299
Invalid residue range for struct_conf "111": invalid chain "JB", near line 300
Invalid residue range for struct_conf "112": invalid chain "JB", near line 301
Bad residue range for struct_conf "113" near line 302
Bad residue range for struct_conf "114" near line 303
Bad residue range for struct_conf "115" near line 304
Bad residue range for struct_conf "116" near line 305
Invalid residue range for struct_conf "117": invalid chain "KB", near line 306
Invalid residue range for struct_conf "118": invalid chain "KB", near line 307
Invalid residue range for struct_conf "119": invalid chain "KB", near line 308
Invalid residue range for struct_conf "120": invalid chain "KB", near line 309
Bad residue range for struct_conf "121" near line 310
Bad residue range for struct_conf "122" near line 311
Bad residue range for struct_conf "123" near line 312
Bad residue range for struct_conf "124" near line 313
Invalid residue range for struct_conf "125": invalid chain "LB", near line 314
Invalid residue range for struct_conf "126": invalid chain "LB", near line 315
Invalid residue range for struct_conf "127": invalid chain "LB", near line 316
Invalid residue range for struct_conf "128": invalid chain "LB", near line 317
Bad residue range for struct_conf "129" near line 318
Bad residue range for struct_conf "130" near line 319
Bad residue range for struct_conf "131" near line 320
Bad residue range for struct_conf "132" near line 321
Invalid residue range for struct_conf "133": invalid chain "MB", near line 322
Invalid residue range for struct_conf "134": invalid chain "MB", near line 323
Invalid residue range for struct_conf "135": invalid chain "MB", near line 324
Invalid residue range for struct_conf "136": invalid chain "MB", near line 325
Bad residue range for struct_conf "137" near line 326
Bad residue range for struct_conf "138" near line 327
Bad residue range for struct_conf "139" near line 328
Bad residue range for struct_conf "140" near line 329
Invalid residue range for struct_conf "141": invalid chain "NB", near line 330
Invalid residue range for struct_conf "142": invalid chain "NB", near line 331
Invalid residue range for struct_conf "143": invalid chain "NB", near line 332
Invalid residue range for struct_conf "144": invalid chain "NB", near line 333
Bad residue range for struct_conf "145" near line 334
Bad residue range for struct_conf "146" near line 335
Bad residue range for struct_conf "147" near line 336
Bad residue range for struct_conf "148" near line 337
Invalid residue range for struct_conf "149": invalid chain "OB", near line 338
Invalid residue range for struct_conf "150": invalid chain "OB", near line 339
Invalid residue range for struct_conf "151": invalid chain "OB", near line 340
Invalid residue range for struct_conf "152": invalid chain "OB", near line 341
Bad residue range for struct_conf "153" near line 342
Bad residue range for struct_conf "154" near line 343
Bad residue range for struct_conf "155" near line 344
Invalid residue range for struct_conf "156": invalid chain "PB", near line 345
Invalid residue range for struct_conf "157": invalid chain "PB", near line 346
Invalid residue range for struct_conf "158": invalid chain "PB", near line 347
Invalid residue range for struct_conf "159": invalid chain "PB", near line 348
Bad residue range for struct_conf "160" near line 349
Bad residue range for struct_conf "161" near line 350
Bad residue range for struct_conf "162" near line 351
Bad residue range for struct_conf "163" near line 352
Invalid residue range for struct_conf "164": invalid chain "QB", near line 353
Invalid residue range for struct_conf "165": invalid chain "QB", near line 354
Invalid residue range for struct_conf "166": invalid chain "QB", near line 355
Invalid residue range for struct_conf "167": invalid chain "QB", near line 356
Bad residue range for struct_conf "168" near line 357
Bad residue range for struct_conf "169" near line 358
Bad residue range for struct_conf "170" near line 359
Bad residue range for struct_conf "171" near line 360
Invalid residue range for struct_conf "172": invalid chain "RB", near line 361
Invalid residue range for struct_conf "173": invalid chain "RB", near line 362
Invalid residue range for struct_conf "174": invalid chain "RB", near line 363
Invalid residue range for struct_conf "175": invalid chain "RB", near line 364
Bad residue range for struct_conf "176" near line 365
Bad residue range for struct_conf "177" near line 366
Bad residue range for struct_conf "178" near line 367
Bad residue range for struct_conf "179" near line 368
Invalid residue range for struct_conf "180": invalid chain "SB", near line 369
Invalid residue range for struct_conf "181": invalid chain "SB", near line 370
Invalid residue range for struct_conf "182": invalid chain "SB", near line 371
Invalid residue range for struct_conf "183": invalid chain "SB", near line 372
Invalid residue range for struct_conf "184": invalid chain "TB", near line 373
33 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "1 1" near line 1883
Invalid sheet range for struct_sheet_range "2 1" near line 1884
Invalid sheet range for struct_sheet_range "3 1" near line 1885
Invalid sheet range for struct_sheet_range "4 1" near line 1886
Invalid sheet range for struct_sheet_range "5 1" near line 1887
371 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for T175A_SS_real_space_refined_011.cif #5
---
Chain | Description
A AB B BB D DB F FB G GB I IB J JB K KB L LB M MB N NB O OB P PB Q QB R RB |
No description available
C CB E EB H HB S SB | No description available
T TB | No description available
a ab b bb c cb d db e eb f fb g gb h hb i ib j jb | No description available
> hide #!4 models
> hide atoms
> show cartoons
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/PhosphoPDB_SSCorrection/T209E/ChimeraLocalRes/T209E_SS_correct_RSR_split.pdb
Chain information for T209E_SS_correct_RSR_split.pdb #6
---
Chain | Description
A AB B BB C CB D DB E EB F FB G GB H HB I IB J JB K KB L LB M MB N NB O OB |
No description available
a ab b bb c cb d db e eb f fb g gb h hb i ib j jb k kb l lb m mb n nb o ob |
No description available
> ui mousemode right translate
> ui mousemode right zoom
> hide #!5 models
> hide atoms
> show cartoons
> sel#6/A
Unknown command: sel#6/A
> select #6/A
877 atoms, 883 bonds, 1 pseudobond, 115 residues, 2 models selected
> view sel
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/phenixStressosome/T175A/RealSpaceRefine_9/T175A_mod72_coot_0_real_space_refined_006_real_space_refined_009.cif
Summary of feedback from opening
/Users/elizabethbond/Library/CloudStorage/OneDrive-
UCSF/phenixStressosome/T175A/RealSpaceRefine_9/T175A_mod72_coot_0_real_space_refined_006_real_space_refined_009.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 1884
Missing entity information. Treating each chain as a separate entity.
Bad residue range for struct_conf "1" near line 190
Bad residue range for struct_conf "2" near line 191
Bad residue range for struct_conf "3" near line 192
Bad residue range for struct_conf "4" near line 193
Bad residue range for struct_conf "5" near line 194
15 messages similar to the above omitted
Invalid residue range for struct_conf "21": invalid chain "CB", near line 210
Invalid residue range for struct_conf "22": invalid chain "CB", near line 211
Invalid residue range for struct_conf "23": invalid chain "CB", near line 212
Invalid residue range for struct_conf "24": invalid chain "CB", near line 213
Bad residue range for struct_conf "25" near line 214
Bad residue range for struct_conf "26" near line 215
Bad residue range for struct_conf "27" near line 216
Bad residue range for struct_conf "28" near line 217
Invalid residue range for struct_conf "29": invalid chain "DB", near line 218
Invalid residue range for struct_conf "30": invalid chain "DB", near line 219
Invalid residue range for struct_conf "31": invalid chain "DB", near line 220
Invalid residue range for struct_conf "32": invalid chain "DB", near line 221
Bad residue range for struct_conf "33" near line 222
Bad residue range for struct_conf "34" near line 223
Bad residue range for struct_conf "35" near line 224
Bad residue range for struct_conf "36" near line 225
Invalid residue range for struct_conf "37": invalid chain "EB", near line 226
Invalid residue range for struct_conf "38": invalid chain "EB", near line 227
Invalid residue range for struct_conf "39": invalid chain "EB", near line 228
Invalid residue range for struct_conf "40": invalid chain "EB", near line 229
Bad residue range for struct_conf "41" near line 230
Bad residue range for struct_conf "42" near line 231
Bad residue range for struct_conf "43" near line 232
Bad residue range for struct_conf "44" near line 233
Invalid residue range for struct_conf "45": invalid chain "FB", near line 234
Invalid residue range for struct_conf "46": invalid chain "FB", near line 235
Invalid residue range for struct_conf "47": invalid chain "FB", near line 236
Invalid residue range for struct_conf "48": invalid chain "FB", near line 237
Bad residue range for struct_conf "49" near line 238
Bad residue range for struct_conf "50" near line 239
Bad residue range for struct_conf "51" near line 240
Bad residue range for struct_conf "52" near line 241
Invalid residue range for struct_conf "53": invalid chain "GB", near line 242
Invalid residue range for struct_conf "54": invalid chain "GB", near line 243
Invalid residue range for struct_conf "55": invalid chain "GB", near line 244
Invalid residue range for struct_conf "56": invalid chain "GB", near line 245
Bad residue range for struct_conf "57" near line 246
Bad residue range for struct_conf "58" near line 247
Bad residue range for struct_conf "59" near line 248
Bad residue range for struct_conf "60" near line 249
Invalid residue range for struct_conf "61": invalid chain "HB", near line 250
Invalid residue range for struct_conf "62": invalid chain "HB", near line 251
Invalid residue range for struct_conf "63": invalid chain "HB", near line 252
Invalid residue range for struct_conf "64": invalid chain "HB", near line 253
Bad residue range for struct_conf "66" near line 254
Bad residue range for struct_conf "67" near line 255
Bad residue range for struct_conf "68" near line 256
Invalid residue range for struct_conf "69": invalid chain "IB", near line 257
Invalid residue range for struct_conf "70": invalid chain "IB", near line 258
Invalid residue range for struct_conf "71": invalid chain "IB", near line 259
Invalid residue range for struct_conf "72": invalid chain "IB", near line 260
Bad residue range for struct_conf "73" near line 261
Bad residue range for struct_conf "74" near line 262
Bad residue range for struct_conf "75" near line 263
Bad residue range for struct_conf "76" near line 264
Invalid residue range for struct_conf "77": invalid chain "JB", near line 265
Invalid residue range for struct_conf "78": invalid chain "JB", near line 266
Invalid residue range for struct_conf "79": invalid chain "JB", near line 267
Invalid residue range for struct_conf "80": invalid chain "JB", near line 268
Bad residue range for struct_conf "81" near line 269
Bad residue range for struct_conf "82" near line 270
Bad residue range for struct_conf "83" near line 271
Bad residue range for struct_conf "84" near line 272
Invalid residue range for struct_conf "85": invalid chain "KB", near line 273
Invalid residue range for struct_conf "86": invalid chain "KB", near line 274
Invalid residue range for struct_conf "87": invalid chain "KB", near line 275
Invalid residue range for struct_conf "88": invalid chain "KB", near line 276
Bad residue range for struct_conf "89" near line 277
Bad residue range for struct_conf "90" near line 278
Bad residue range for struct_conf "91" near line 279
Bad residue range for struct_conf "92" near line 280
Invalid residue range for struct_conf "93": invalid chain "LB", near line 281
Invalid residue range for struct_conf "94": invalid chain "LB", near line 282
Invalid residue range for struct_conf "95": invalid chain "LB", near line 283
Invalid residue range for struct_conf "96": invalid chain "LB", near line 284
Bad residue range for struct_conf "97" near line 285
Bad residue range for struct_conf "98" near line 286
Bad residue range for struct_conf "99" near line 287
Bad residue range for struct_conf "100" near line 288
Invalid residue range for struct_conf "101": invalid chain "MB", near line 289
Invalid residue range for struct_conf "102": invalid chain "MB", near line 290
Invalid residue range for struct_conf "103": invalid chain "MB", near line 291
Invalid residue range for struct_conf "104": invalid chain "MB", near line 292
Bad residue range for struct_conf "105" near line 293
Bad residue range for struct_conf "106" near line 294
Bad residue range for struct_conf "107" near line 295
Bad residue range for struct_conf "108" near line 296
Invalid residue range for struct_conf "109": invalid chain "NB", near line 297
Invalid residue range for struct_conf "110": invalid chain "NB", near line 298
Invalid residue range for struct_conf "111": invalid chain "NB", near line 299
Invalid residue range for struct_conf "112": invalid chain "NB", near line 300
Bad residue range for struct_conf "113" near line 301
Bad residue range for struct_conf "114" near line 302
Bad residue range for struct_conf "115" near line 303
Bad residue range for struct_conf "116" near line 304
Invalid residue range for struct_conf "117": invalid chain "OB", near line 305
Invalid residue range for struct_conf "118": invalid chain "OB", near line 306
Invalid residue range for struct_conf "119": invalid chain "OB", near line 307
Invalid residue range for struct_conf "120": invalid chain "OB", near line 308
Bad residue range for struct_conf "121" near line 309
Bad residue range for struct_conf "122" near line 310
Bad residue range for struct_conf "123" near line 311
Invalid residue range for struct_conf "125": invalid chain "PB", near line 312
Invalid residue range for struct_conf "126": invalid chain "PB", near line 313
Invalid residue range for struct_conf "127": invalid chain "PB", near line 314
Invalid residue range for struct_conf "128": invalid chain "PB", near line 315
Bad residue range for struct_conf "129" near line 316
Bad residue range for struct_conf "130" near line 317
Bad residue range for struct_conf "131" near line 318
Bad residue range for struct_conf "132" near line 319
Invalid residue range for struct_conf "133": invalid chain "QB", near line 320
Invalid residue range for struct_conf "134": invalid chain "QB", near line 321
Invalid residue range for struct_conf "135": invalid chain "QB", near line 322
Invalid residue range for struct_conf "136": invalid chain "QB", near line 323
Bad residue range for struct_conf "137" near line 324
Bad residue range for struct_conf "138" near line 325
Bad residue range for struct_conf "139" near line 326
Bad residue range for struct_conf "140" near line 327
Invalid residue range for struct_conf "141": invalid chain "RB", near line 328
Invalid residue range for struct_conf "142": invalid chain "RB", near line 329
Invalid residue range for struct_conf "143": invalid chain "RB", near line 330
Invalid residue range for struct_conf "144": invalid chain "RB", near line 331
Bad residue range for struct_conf "145" near line 332
Bad residue range for struct_conf "146" near line 333
Bad residue range for struct_conf "147" near line 334
Bad residue range for struct_conf "148" near line 335
Invalid residue range for struct_conf "149": invalid chain "SB", near line 336
Invalid residue range for struct_conf "150": invalid chain "SB", near line 337
Invalid residue range for struct_conf "151": invalid chain "SB", near line 338
Invalid residue range for struct_conf "152": invalid chain "SB", near line 339
Bad residue range for struct_conf "153" near line 340
Bad residue range for struct_conf "154" near line 341
Bad residue range for struct_conf "155" near line 342
Invalid residue range for struct_conf "157": invalid chain "TB", near line 343
Invalid residue range for struct_conf "158": invalid chain "TB", near line 344
Invalid residue range for struct_conf "159": invalid chain "TB", near line 345
Invalid residue range for struct_conf "160": invalid chain "TB", near line 346
Invalid residue range for struct_conf "161": invalid chain "h", near line 347
77 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "1 1": invalid chain "a", near line
1672
Invalid sheet range for struct_sheet_range "3 1": invalid chain "a", near line
1673
Invalid sheet range for struct_sheet_range "4 1": invalid chain "a", near line
1674
Invalid sheet range for struct_sheet_range "5 1": invalid chain "ab", near
line 1675
Invalid sheet range for struct_sheet_range "7 1": invalid chain "ab", near
line 1676
206 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for
T175A_mod72_coot_0_real_space_refined_006_real_space_refined_009.cif #7
---
Chain | Description
A AB B BB D DB F FB G GB I IB J JB K KB L LB M MB N NB O OB P PB Q QB R RB |
No description available
C CB E EB H HB S SB | No description available
T TB | No description available
a ab b bb c cb d db e eb f fb g gb h hb i ib j jb | No description available
> hide sel atoms
> hide #!6 models
> select add #6
52740 atoms, 53130 bonds, 32 pseudobonds, 6990 residues, 2 models selected
> select subtract #6
Nothing selected
> view #7
> hide #!7 atoms
> show #!7 cartoons
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/phenixStressosome/T175E/RealSpaceRefine_19/T175A_SS_real_space_refined_019.pdb
Chain information for T175A_SS_real_space_refined_019.pdb #8
---
Chain | Description
A AB B BB D DB F FB G GB I IB J JB K KB L LB M MB N NB O OB P PB Q QB R RB |
No description available
C CB E EB H HB S SB | No description available
T TB | No description available
a ab b bb c cb d db e eb f fb g gb h hb i ib j jb | No description available
> hide #!7 models
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/phenixStressosome/T175E/RealSpaceRefine_19/T175A_SS_real_space_refined_019.pdb
Chain information for T175A_SS_real_space_refined_019.pdb #9
---
Chain | Description
A AB B BB D DB F FB G GB I IB J JB K KB L LB M MB N NB O OB P PB Q QB R RB |
No description available
C CB E EB H HB S SB | No description available
T TB | No description available
a ab b bb c cb d db e eb f fb g gb h hb i ib j jb | No description available
> hide #!8 models
> hide atoms
> show cartoons
> close
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/phenixStressosome/T175A/RealSpaceRefine_13/T175A_SS_real_space_refined_013.cif
Summary of feedback from opening
/Users/elizabethbond/Library/CloudStorage/OneDrive-
UCSF/phenixStressosome/T175A/RealSpaceRefine_13/T175A_SS_real_space_refined_013.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 2260
Missing entity information. Treating each chain as a separate entity.
Bad residue range for struct_conf "1" near line 190
Bad residue range for struct_conf "2" near line 191
Bad residue range for struct_conf "3" near line 192
Invalid residue range for struct_conf "4": invalid chain "a", near line 193
Invalid residue range for struct_conf "5": invalid chain "a", near line 194
Invalid residue range for struct_conf "6": invalid chain "a", near line 195
Invalid residue range for struct_conf "7": invalid chain "b", near line 196
Invalid residue range for struct_conf "8": invalid chain "b", near line 197
25 messages similar to the above omitted
Bad residue range for struct_conf "34" near line 223
Bad residue range for struct_conf "35" near line 224
Bad residue range for struct_conf "36" near line 225
Bad residue range for struct_conf "37" near line 226
Bad residue range for struct_conf "38" near line 227
15 messages similar to the above omitted
Invalid residue range for struct_conf "54": invalid chain "CB", near line 243
Invalid residue range for struct_conf "55": invalid chain "CB", near line 244
Invalid residue range for struct_conf "56": invalid chain "CB", near line 245
Invalid residue range for struct_conf "57": invalid chain "CB", near line 246
Bad residue range for struct_conf "58" near line 247
Bad residue range for struct_conf "59" near line 248
Bad residue range for struct_conf "60" near line 249
Bad residue range for struct_conf "61" near line 250
Invalid residue range for struct_conf "62": invalid chain "DB", near line 251
Invalid residue range for struct_conf "63": invalid chain "DB", near line 252
Invalid residue range for struct_conf "64": invalid chain "DB", near line 253
Invalid residue range for struct_conf "65": invalid chain "DB", near line 254
Bad residue range for struct_conf "66" near line 255
Bad residue range for struct_conf "67" near line 256
Bad residue range for struct_conf "68" near line 257
Bad residue range for struct_conf "69" near line 258
Invalid residue range for struct_conf "70": invalid chain "EB", near line 259
Invalid residue range for struct_conf "71": invalid chain "EB", near line 260
Invalid residue range for struct_conf "72": invalid chain "EB", near line 261
Invalid residue range for struct_conf "73": invalid chain "EB", near line 262
Bad residue range for struct_conf "74" near line 263
Bad residue range for struct_conf "75" near line 264
Bad residue range for struct_conf "76" near line 265
Bad residue range for struct_conf "77" near line 266
Invalid residue range for struct_conf "78": invalid chain "FB", near line 267
Invalid residue range for struct_conf "79": invalid chain "FB", near line 268
Invalid residue range for struct_conf "80": invalid chain "FB", near line 269
Invalid residue range for struct_conf "81": invalid chain "FB", near line 270
Bad residue range for struct_conf "82" near line 271
Bad residue range for struct_conf "83" near line 272
Bad residue range for struct_conf "84" near line 273
Bad residue range for struct_conf "85" near line 274
Invalid residue range for struct_conf "86": invalid chain "GB", near line 275
Invalid residue range for struct_conf "87": invalid chain "GB", near line 276
Invalid residue range for struct_conf "88": invalid chain "GB", near line 277
Invalid residue range for struct_conf "89": invalid chain "GB", near line 278
Bad residue range for struct_conf "90" near line 279
Bad residue range for struct_conf "91" near line 280
Bad residue range for struct_conf "92" near line 281
Bad residue range for struct_conf "93" near line 282
Invalid residue range for struct_conf "94": invalid chain "HB", near line 283
Invalid residue range for struct_conf "95": invalid chain "HB", near line 284
Invalid residue range for struct_conf "96": invalid chain "HB", near line 285
Invalid residue range for struct_conf "97": invalid chain "HB", near line 286
Bad residue range for struct_conf "98" near line 287
Bad residue range for struct_conf "99" near line 288
Bad residue range for struct_conf "100" near line 289
Invalid residue range for struct_conf "101": invalid chain "IB", near line 290
Invalid residue range for struct_conf "102": invalid chain "IB", near line 291
Invalid residue range for struct_conf "103": invalid chain "IB", near line 292
Invalid residue range for struct_conf "104": invalid chain "IB", near line 293
Bad residue range for struct_conf "105" near line 294
Bad residue range for struct_conf "106" near line 295
Bad residue range for struct_conf "107" near line 296
Bad residue range for struct_conf "108" near line 297
Invalid residue range for struct_conf "109": invalid chain "JB", near line 298
Invalid residue range for struct_conf "110": invalid chain "JB", near line 299
Invalid residue range for struct_conf "111": invalid chain "JB", near line 300
Invalid residue range for struct_conf "112": invalid chain "JB", near line 301
Bad residue range for struct_conf "113" near line 302
Bad residue range for struct_conf "114" near line 303
Bad residue range for struct_conf "115" near line 304
Bad residue range for struct_conf "116" near line 305
Invalid residue range for struct_conf "117": invalid chain "KB", near line 306
Invalid residue range for struct_conf "118": invalid chain "KB", near line 307
Invalid residue range for struct_conf "119": invalid chain "KB", near line 308
Invalid residue range for struct_conf "120": invalid chain "KB", near line 309
Bad residue range for struct_conf "121" near line 310
Bad residue range for struct_conf "122" near line 311
Bad residue range for struct_conf "123" near line 312
Bad residue range for struct_conf "124" near line 313
Invalid residue range for struct_conf "125": invalid chain "LB", near line 314
Invalid residue range for struct_conf "126": invalid chain "LB", near line 315
Invalid residue range for struct_conf "127": invalid chain "LB", near line 316
Invalid residue range for struct_conf "128": invalid chain "LB", near line 317
Bad residue range for struct_conf "129" near line 318
Bad residue range for struct_conf "130" near line 319
Bad residue range for struct_conf "131" near line 320
Bad residue range for struct_conf "132" near line 321
Invalid residue range for struct_conf "133": invalid chain "MB", near line 322
Invalid residue range for struct_conf "134": invalid chain "MB", near line 323
Invalid residue range for struct_conf "135": invalid chain "MB", near line 324
Invalid residue range for struct_conf "136": invalid chain "MB", near line 325
Bad residue range for struct_conf "137" near line 326
Bad residue range for struct_conf "138" near line 327
Bad residue range for struct_conf "139" near line 328
Bad residue range for struct_conf "140" near line 329
Invalid residue range for struct_conf "141": invalid chain "NB", near line 330
Invalid residue range for struct_conf "142": invalid chain "NB", near line 331
Invalid residue range for struct_conf "143": invalid chain "NB", near line 332
Invalid residue range for struct_conf "144": invalid chain "NB", near line 333
Bad residue range for struct_conf "145" near line 334
Bad residue range for struct_conf "146" near line 335
Bad residue range for struct_conf "147" near line 336
Bad residue range for struct_conf "148" near line 337
Invalid residue range for struct_conf "149": invalid chain "OB", near line 338
Invalid residue range for struct_conf "150": invalid chain "OB", near line 339
Invalid residue range for struct_conf "151": invalid chain "OB", near line 340
Invalid residue range for struct_conf "152": invalid chain "OB", near line 341
Bad residue range for struct_conf "153" near line 342
Bad residue range for struct_conf "154" near line 343
Bad residue range for struct_conf "155" near line 344
Invalid residue range for struct_conf "156": invalid chain "PB", near line 345
Invalid residue range for struct_conf "157": invalid chain "PB", near line 346
Invalid residue range for struct_conf "158": invalid chain "PB", near line 347
Invalid residue range for struct_conf "159": invalid chain "PB", near line 348
Bad residue range for struct_conf "160" near line 349
Bad residue range for struct_conf "161" near line 350
Bad residue range for struct_conf "162" near line 351
Bad residue range for struct_conf "163" near line 352
Invalid residue range for struct_conf "164": invalid chain "QB", near line 353
Invalid residue range for struct_conf "165": invalid chain "QB", near line 354
Invalid residue range for struct_conf "166": invalid chain "QB", near line 355
Invalid residue range for struct_conf "167": invalid chain "QB", near line 356
Bad residue range for struct_conf "168" near line 357
Bad residue range for struct_conf "169" near line 358
Bad residue range for struct_conf "170" near line 359
Bad residue range for struct_conf "171" near line 360
Invalid residue range for struct_conf "172": invalid chain "RB", near line 361
Invalid residue range for struct_conf "173": invalid chain "RB", near line 362
Invalid residue range for struct_conf "174": invalid chain "RB", near line 363
Invalid residue range for struct_conf "175": invalid chain "RB", near line 364
Bad residue range for struct_conf "176" near line 365
Bad residue range for struct_conf "177" near line 366
Bad residue range for struct_conf "178" near line 367
Bad residue range for struct_conf "179" near line 368
Invalid residue range for struct_conf "180": invalid chain "SB", near line 369
Invalid residue range for struct_conf "181": invalid chain "SB", near line 370
Invalid residue range for struct_conf "182": invalid chain "SB", near line 371
Invalid residue range for struct_conf "183": invalid chain "SB", near line 372
Invalid residue range for struct_conf "184": invalid chain "TB", near line 373
33 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "1 1" near line 1883
Invalid sheet range for struct_sheet_range "2 1" near line 1884
Invalid sheet range for struct_sheet_range "3 1" near line 1885
Invalid sheet range for struct_sheet_range "4 1" near line 1886
Invalid sheet range for struct_sheet_range "5 1" near line 1887
371 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for T175A_SS_real_space_refined_013.cif #1
---
Chain | Description
A AB B BB D DB F FB G GB I IB J JB K KB L LB M MB N NB O OB P PB Q QB R RB |
No description available
C CB E EB H HB S SB | No description available
T TB | No description available
a ab b bb c cb d db e eb f fb g gb h hb i ib j jb | No description available
> hide atoms
> show cartoons
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/phenixStressosome/T175E/RealSpaceRefine_20/T175A_SS_real_space_refined_020.cif
Summary of feedback from opening
/Users/elizabethbond/Library/CloudStorage/OneDrive-
UCSF/phenixStressosome/T175E/RealSpaceRefine_20/T175A_SS_real_space_refined_020.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 2260
Missing entity information. Treating each chain as a separate entity.
Bad residue range for struct_conf "1" near line 190
Bad residue range for struct_conf "2" near line 191
Bad residue range for struct_conf "3" near line 192
Invalid residue range for struct_conf "4": invalid chain "a", near line 193
Invalid residue range for struct_conf "5": invalid chain "a", near line 194
Invalid residue range for struct_conf "6": invalid chain "a", near line 195
Invalid residue range for struct_conf "7": invalid chain "b", near line 196
Invalid residue range for struct_conf "8": invalid chain "b", near line 197
25 messages similar to the above omitted
Bad residue range for struct_conf "34" near line 223
Bad residue range for struct_conf "35" near line 224
Bad residue range for struct_conf "36" near line 225
Bad residue range for struct_conf "37" near line 226
Bad residue range for struct_conf "38" near line 227
15 messages similar to the above omitted
Invalid residue range for struct_conf "54": invalid chain "CB", near line 243
Invalid residue range for struct_conf "55": invalid chain "CB", near line 244
Invalid residue range for struct_conf "56": invalid chain "CB", near line 245
Invalid residue range for struct_conf "57": invalid chain "CB", near line 246
Bad residue range for struct_conf "58" near line 247
Bad residue range for struct_conf "59" near line 248
Bad residue range for struct_conf "60" near line 249
Bad residue range for struct_conf "61" near line 250
Invalid residue range for struct_conf "62": invalid chain "DB", near line 251
Invalid residue range for struct_conf "63": invalid chain "DB", near line 252
Invalid residue range for struct_conf "64": invalid chain "DB", near line 253
Invalid residue range for struct_conf "65": invalid chain "DB", near line 254
Bad residue range for struct_conf "66" near line 255
Bad residue range for struct_conf "67" near line 256
Bad residue range for struct_conf "68" near line 257
Bad residue range for struct_conf "69" near line 258
Invalid residue range for struct_conf "70": invalid chain "EB", near line 259
Invalid residue range for struct_conf "71": invalid chain "EB", near line 260
Invalid residue range for struct_conf "72": invalid chain "EB", near line 261
Invalid residue range for struct_conf "73": invalid chain "EB", near line 262
Bad residue range for struct_conf "74" near line 263
Bad residue range for struct_conf "75" near line 264
Bad residue range for struct_conf "76" near line 265
Bad residue range for struct_conf "77" near line 266
Invalid residue range for struct_conf "78": invalid chain "FB", near line 267
Invalid residue range for struct_conf "79": invalid chain "FB", near line 268
Invalid residue range for struct_conf "80": invalid chain "FB", near line 269
Invalid residue range for struct_conf "81": invalid chain "FB", near line 270
Bad residue range for struct_conf "82" near line 271
Bad residue range for struct_conf "83" near line 272
Bad residue range for struct_conf "84" near line 273
Bad residue range for struct_conf "85" near line 274
Invalid residue range for struct_conf "86": invalid chain "GB", near line 275
Invalid residue range for struct_conf "87": invalid chain "GB", near line 276
Invalid residue range for struct_conf "88": invalid chain "GB", near line 277
Invalid residue range for struct_conf "89": invalid chain "GB", near line 278
Bad residue range for struct_conf "90" near line 279
Bad residue range for struct_conf "91" near line 280
Bad residue range for struct_conf "92" near line 281
Bad residue range for struct_conf "93" near line 282
Invalid residue range for struct_conf "94": invalid chain "HB", near line 283
Invalid residue range for struct_conf "95": invalid chain "HB", near line 284
Invalid residue range for struct_conf "96": invalid chain "HB", near line 285
Invalid residue range for struct_conf "97": invalid chain "HB", near line 286
Bad residue range for struct_conf "98" near line 287
Bad residue range for struct_conf "99" near line 288
Bad residue range for struct_conf "100" near line 289
Invalid residue range for struct_conf "101": invalid chain "IB", near line 290
Invalid residue range for struct_conf "102": invalid chain "IB", near line 291
Invalid residue range for struct_conf "103": invalid chain "IB", near line 292
Invalid residue range for struct_conf "104": invalid chain "IB", near line 293
Bad residue range for struct_conf "105" near line 294
Bad residue range for struct_conf "106" near line 295
Bad residue range for struct_conf "107" near line 296
Bad residue range for struct_conf "108" near line 297
Invalid residue range for struct_conf "109": invalid chain "JB", near line 298
Invalid residue range for struct_conf "110": invalid chain "JB", near line 299
Invalid residue range for struct_conf "111": invalid chain "JB", near line 300
Invalid residue range for struct_conf "112": invalid chain "JB", near line 301
Bad residue range for struct_conf "113" near line 302
Bad residue range for struct_conf "114" near line 303
Bad residue range for struct_conf "115" near line 304
Bad residue range for struct_conf "116" near line 305
Invalid residue range for struct_conf "117": invalid chain "KB", near line 306
Invalid residue range for struct_conf "118": invalid chain "KB", near line 307
Invalid residue range for struct_conf "119": invalid chain "KB", near line 308
Invalid residue range for struct_conf "120": invalid chain "KB", near line 309
Bad residue range for struct_conf "121" near line 310
Bad residue range for struct_conf "122" near line 311
Bad residue range for struct_conf "123" near line 312
Bad residue range for struct_conf "124" near line 313
Invalid residue range for struct_conf "125": invalid chain "LB", near line 314
Invalid residue range for struct_conf "126": invalid chain "LB", near line 315
Invalid residue range for struct_conf "127": invalid chain "LB", near line 316
Invalid residue range for struct_conf "128": invalid chain "LB", near line 317
Bad residue range for struct_conf "129" near line 318
Bad residue range for struct_conf "130" near line 319
Bad residue range for struct_conf "131" near line 320
Bad residue range for struct_conf "132" near line 321
Invalid residue range for struct_conf "133": invalid chain "MB", near line 322
Invalid residue range for struct_conf "134": invalid chain "MB", near line 323
Invalid residue range for struct_conf "135": invalid chain "MB", near line 324
Invalid residue range for struct_conf "136": invalid chain "MB", near line 325
Bad residue range for struct_conf "137" near line 326
Bad residue range for struct_conf "138" near line 327
Bad residue range for struct_conf "139" near line 328
Bad residue range for struct_conf "140" near line 329
Invalid residue range for struct_conf "141": invalid chain "NB", near line 330
Invalid residue range for struct_conf "142": invalid chain "NB", near line 331
Invalid residue range for struct_conf "143": invalid chain "NB", near line 332
Invalid residue range for struct_conf "144": invalid chain "NB", near line 333
Bad residue range for struct_conf "145" near line 334
Bad residue range for struct_conf "146" near line 335
Bad residue range for struct_conf "147" near line 336
Bad residue range for struct_conf "148" near line 337
Invalid residue range for struct_conf "149": invalid chain "OB", near line 338
Invalid residue range for struct_conf "150": invalid chain "OB", near line 339
Invalid residue range for struct_conf "151": invalid chain "OB", near line 340
Invalid residue range for struct_conf "152": invalid chain "OB", near line 341
Bad residue range for struct_conf "153" near line 342
Bad residue range for struct_conf "154" near line 343
Bad residue range for struct_conf "155" near line 344
Invalid residue range for struct_conf "156": invalid chain "PB", near line 345
Invalid residue range for struct_conf "157": invalid chain "PB", near line 346
Invalid residue range for struct_conf "158": invalid chain "PB", near line 347
Invalid residue range for struct_conf "159": invalid chain "PB", near line 348
Bad residue range for struct_conf "160" near line 349
Bad residue range for struct_conf "161" near line 350
Bad residue range for struct_conf "162" near line 351
Bad residue range for struct_conf "163" near line 352
Invalid residue range for struct_conf "164": invalid chain "QB", near line 353
Invalid residue range for struct_conf "165": invalid chain "QB", near line 354
Invalid residue range for struct_conf "166": invalid chain "QB", near line 355
Invalid residue range for struct_conf "167": invalid chain "QB", near line 356
Bad residue range for struct_conf "168" near line 357
Bad residue range for struct_conf "169" near line 358
Bad residue range for struct_conf "170" near line 359
Bad residue range for struct_conf "171" near line 360
Invalid residue range for struct_conf "172": invalid chain "RB", near line 361
Invalid residue range for struct_conf "173": invalid chain "RB", near line 362
Invalid residue range for struct_conf "174": invalid chain "RB", near line 363
Invalid residue range for struct_conf "175": invalid chain "RB", near line 364
Bad residue range for struct_conf "176" near line 365
Bad residue range for struct_conf "177" near line 366
Bad residue range for struct_conf "178" near line 367
Bad residue range for struct_conf "179" near line 368
Invalid residue range for struct_conf "180": invalid chain "SB", near line 369
Invalid residue range for struct_conf "181": invalid chain "SB", near line 370
Invalid residue range for struct_conf "182": invalid chain "SB", near line 371
Invalid residue range for struct_conf "183": invalid chain "SB", near line 372
Invalid residue range for struct_conf "184": invalid chain "TB", near line 373
33 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "1 1" near line 1883
Invalid sheet range for struct_sheet_range "2 1" near line 1884
Invalid sheet range for struct_sheet_range "3 1" near line 1885
Invalid sheet range for struct_sheet_range "4 1" near line 1886
Invalid sheet range for struct_sheet_range "5 1" near line 1887
371 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for T175A_SS_real_space_refined_020.cif #2
---
Chain | Description
A AB B BB D DB F FB G GB I IB J JB K KB L LB M MB N NB O OB P PB Q QB R RB |
No description available
C CB E EB H HB S SB | No description available
T TB | No description available
a ab b bb c cb d db e eb f fb g gb h hb i ib j jb | No description available
> hide #!1 models
> show cartoons
> hide atoms
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/phenixStressosome/T175E/RealSpaceRefine_19/T175A_SS_real_space_refined_019.cif
Summary of feedback from opening
/Users/elizabethbond/Library/CloudStorage/OneDrive-
UCSF/phenixStressosome/T175E/RealSpaceRefine_19/T175A_SS_real_space_refined_019.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 2260
Missing entity information. Treating each chain as a separate entity.
Bad residue range for struct_conf "1" near line 190
Bad residue range for struct_conf "2" near line 191
Bad residue range for struct_conf "3" near line 192
Invalid residue range for struct_conf "4": invalid chain "a", near line 193
Invalid residue range for struct_conf "5": invalid chain "a", near line 194
Invalid residue range for struct_conf "6": invalid chain "a", near line 195
Invalid residue range for struct_conf "7": invalid chain "b", near line 196
Invalid residue range for struct_conf "8": invalid chain "b", near line 197
25 messages similar to the above omitted
Bad residue range for struct_conf "34" near line 223
Bad residue range for struct_conf "35" near line 224
Bad residue range for struct_conf "36" near line 225
Bad residue range for struct_conf "37" near line 226
Bad residue range for struct_conf "38" near line 227
15 messages similar to the above omitted
Invalid residue range for struct_conf "54": invalid chain "CB", near line 243
Invalid residue range for struct_conf "55": invalid chain "CB", near line 244
Invalid residue range for struct_conf "56": invalid chain "CB", near line 245
Invalid residue range for struct_conf "57": invalid chain "CB", near line 246
Bad residue range for struct_conf "58" near line 247
Bad residue range for struct_conf "59" near line 248
Bad residue range for struct_conf "60" near line 249
Bad residue range for struct_conf "61" near line 250
Invalid residue range for struct_conf "62": invalid chain "DB", near line 251
Invalid residue range for struct_conf "63": invalid chain "DB", near line 252
Invalid residue range for struct_conf "64": invalid chain "DB", near line 253
Invalid residue range for struct_conf "65": invalid chain "DB", near line 254
Bad residue range for struct_conf "66" near line 255
Bad residue range for struct_conf "67" near line 256
Bad residue range for struct_conf "68" near line 257
Bad residue range for struct_conf "69" near line 258
Invalid residue range for struct_conf "70": invalid chain "EB", near line 259
Invalid residue range for struct_conf "71": invalid chain "EB", near line 260
Invalid residue range for struct_conf "72": invalid chain "EB", near line 261
Invalid residue range for struct_conf "73": invalid chain "EB", near line 262
Bad residue range for struct_conf "74" near line 263
Bad residue range for struct_conf "75" near line 264
Bad residue range for struct_conf "76" near line 265
Bad residue range for struct_conf "77" near line 266
Invalid residue range for struct_conf "78": invalid chain "FB", near line 267
Invalid residue range for struct_conf "79": invalid chain "FB", near line 268
Invalid residue range for struct_conf "80": invalid chain "FB", near line 269
Invalid residue range for struct_conf "81": invalid chain "FB", near line 270
Bad residue range for struct_conf "82" near line 271
Bad residue range for struct_conf "83" near line 272
Bad residue range for struct_conf "84" near line 273
Bad residue range for struct_conf "85" near line 274
Invalid residue range for struct_conf "86": invalid chain "GB", near line 275
Invalid residue range for struct_conf "87": invalid chain "GB", near line 276
Invalid residue range for struct_conf "88": invalid chain "GB", near line 277
Invalid residue range for struct_conf "89": invalid chain "GB", near line 278
Bad residue range for struct_conf "90" near line 279
Bad residue range for struct_conf "91" near line 280
Bad residue range for struct_conf "92" near line 281
Bad residue range for struct_conf "93" near line 282
Invalid residue range for struct_conf "94": invalid chain "HB", near line 283
Invalid residue range for struct_conf "95": invalid chain "HB", near line 284
Invalid residue range for struct_conf "96": invalid chain "HB", near line 285
Invalid residue range for struct_conf "97": invalid chain "HB", near line 286
Bad residue range for struct_conf "98" near line 287
Bad residue range for struct_conf "99" near line 288
Bad residue range for struct_conf "100" near line 289
Invalid residue range for struct_conf "101": invalid chain "IB", near line 290
Invalid residue range for struct_conf "102": invalid chain "IB", near line 291
Invalid residue range for struct_conf "103": invalid chain "IB", near line 292
Invalid residue range for struct_conf "104": invalid chain "IB", near line 293
Bad residue range for struct_conf "105" near line 294
Bad residue range for struct_conf "106" near line 295
Bad residue range for struct_conf "107" near line 296
Bad residue range for struct_conf "108" near line 297
Invalid residue range for struct_conf "109": invalid chain "JB", near line 298
Invalid residue range for struct_conf "110": invalid chain "JB", near line 299
Invalid residue range for struct_conf "111": invalid chain "JB", near line 300
Invalid residue range for struct_conf "112": invalid chain "JB", near line 301
Bad residue range for struct_conf "113" near line 302
Bad residue range for struct_conf "114" near line 303
Bad residue range for struct_conf "115" near line 304
Bad residue range for struct_conf "116" near line 305
Invalid residue range for struct_conf "117": invalid chain "KB", near line 306
Invalid residue range for struct_conf "118": invalid chain "KB", near line 307
Invalid residue range for struct_conf "119": invalid chain "KB", near line 308
Invalid residue range for struct_conf "120": invalid chain "KB", near line 309
Bad residue range for struct_conf "121" near line 310
Bad residue range for struct_conf "122" near line 311
Bad residue range for struct_conf "123" near line 312
Bad residue range for struct_conf "124" near line 313
Invalid residue range for struct_conf "125": invalid chain "LB", near line 314
Invalid residue range for struct_conf "126": invalid chain "LB", near line 315
Invalid residue range for struct_conf "127": invalid chain "LB", near line 316
Invalid residue range for struct_conf "128": invalid chain "LB", near line 317
Bad residue range for struct_conf "129" near line 318
Bad residue range for struct_conf "130" near line 319
Bad residue range for struct_conf "131" near line 320
Bad residue range for struct_conf "132" near line 321
Invalid residue range for struct_conf "133": invalid chain "MB", near line 322
Invalid residue range for struct_conf "134": invalid chain "MB", near line 323
Invalid residue range for struct_conf "135": invalid chain "MB", near line 324
Invalid residue range for struct_conf "136": invalid chain "MB", near line 325
Bad residue range for struct_conf "137" near line 326
Bad residue range for struct_conf "138" near line 327
Bad residue range for struct_conf "139" near line 328
Bad residue range for struct_conf "140" near line 329
Invalid residue range for struct_conf "141": invalid chain "NB", near line 330
Invalid residue range for struct_conf "142": invalid chain "NB", near line 331
Invalid residue range for struct_conf "143": invalid chain "NB", near line 332
Invalid residue range for struct_conf "144": invalid chain "NB", near line 333
Bad residue range for struct_conf "145" near line 334
Bad residue range for struct_conf "146" near line 335
Bad residue range for struct_conf "147" near line 336
Bad residue range for struct_conf "148" near line 337
Invalid residue range for struct_conf "149": invalid chain "OB", near line 338
Invalid residue range for struct_conf "150": invalid chain "OB", near line 339
Invalid residue range for struct_conf "151": invalid chain "OB", near line 340
Invalid residue range for struct_conf "152": invalid chain "OB", near line 341
Bad residue range for struct_conf "153" near line 342
Bad residue range for struct_conf "154" near line 343
Bad residue range for struct_conf "155" near line 344
Invalid residue range for struct_conf "156": invalid chain "PB", near line 345
Invalid residue range for struct_conf "157": invalid chain "PB", near line 346
Invalid residue range for struct_conf "158": invalid chain "PB", near line 347
Invalid residue range for struct_conf "159": invalid chain "PB", near line 348
Bad residue range for struct_conf "160" near line 349
Bad residue range for struct_conf "161" near line 350
Bad residue range for struct_conf "162" near line 351
Bad residue range for struct_conf "163" near line 352
Invalid residue range for struct_conf "164": invalid chain "QB", near line 353
Invalid residue range for struct_conf "165": invalid chain "QB", near line 354
Invalid residue range for struct_conf "166": invalid chain "QB", near line 355
Invalid residue range for struct_conf "167": invalid chain "QB", near line 356
Bad residue range for struct_conf "168" near line 357
Bad residue range for struct_conf "169" near line 358
Bad residue range for struct_conf "170" near line 359
Bad residue range for struct_conf "171" near line 360
Invalid residue range for struct_conf "172": invalid chain "RB", near line 361
Invalid residue range for struct_conf "173": invalid chain "RB", near line 362
Invalid residue range for struct_conf "174": invalid chain "RB", near line 363
Invalid residue range for struct_conf "175": invalid chain "RB", near line 364
Bad residue range for struct_conf "176" near line 365
Bad residue range for struct_conf "177" near line 366
Bad residue range for struct_conf "178" near line 367
Bad residue range for struct_conf "179" near line 368
Invalid residue range for struct_conf "180": invalid chain "SB", near line 369
Invalid residue range for struct_conf "181": invalid chain "SB", near line 370
Invalid residue range for struct_conf "182": invalid chain "SB", near line 371
Invalid residue range for struct_conf "183": invalid chain "SB", near line 372
Invalid residue range for struct_conf "184": invalid chain "TB", near line 373
33 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "1 1" near line 1883
Invalid sheet range for struct_sheet_range "2 1" near line 1884
Invalid sheet range for struct_sheet_range "3 1" near line 1885
Invalid sheet range for struct_sheet_range "4 1" near line 1886
Invalid sheet range for struct_sheet_range "5 1" near line 1887
371 messages similar to the above omitted
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for T175A_SS_real_space_refined_019.cif #3
---
Chain | Description
A AB B BB D DB F FB G GB I IB J JB K KB L LB M MB N NB O OB P PB Q QB R RB |
No description available
C CB E EB H HB S SB | No description available
T TB | No description available
a ab b bb c cb d db e eb f fb g gb h hb i ib j jb | No description available
> hide #!2 models
> hide atoms
> show cartoons
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/phenixStressosome/T175E/RealSpaceRefine_19/T175A_SS_real_space_refined_019.pdb
Chain information for T175A_SS_real_space_refined_019.pdb #4
---
Chain | Description
A AB B BB D DB F FB G GB I IB J JB K KB L LB M MB N NB O OB P PB Q QB R RB |
No description available
C CB E EB H HB S SB | No description available
T TB | No description available
a ab b bb c cb d db e eb f fb g gb h hb i ib j jb | No description available
> hide #!3 models
> hide atoms
> show cartoons
> save "/Users/elizabethbond/OneDrive -
> UCSF/PhosphoPDB_SSCorrection/T175A/ChimeraX/T175A_RSR_019_chimeraCiF.cif"
> models #4 relModel #4
Not saving entity_poly_seq for non-authoritative sequences
> open /Users/elizabethbond/Library/CloudStorage/OneDrive-
> UCSF/PhosphoPDB_SSCorrection/T175A/ChimeraX/T175A_RSR_019_chimeraCiF.cif
Summary of feedback from opening
/Users/elizabethbond/Library/CloudStorage/OneDrive-
UCSF/PhosphoPDB_SSCorrection/T175A/ChimeraX/T175A_RSR_019_chimeraCiF.cif
---
warnings | Unknown polymer entity '1' near line 237
Unknown polymer entity '2' near line 3725
Unknown polymer entity '3' near line 33431
Unknown polymer entity '4' near line 35261
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for T175A_RSR_019_chimeraCiF.cif #5
---
Chain | Description
A AB B BB D DB F FB G GB I IB J JB K KB L LB M MB N NB O OB P PB Q QB R RB |
No description available
C CB E EB H HB S SB | No description available
T TB | No description available
a ab b bb c cb d db e eb f fb g gb h hb i ib j jb | No description available
> hide #!4 models
> show cartoons
> hide atoms
> show #!4 models
> hide #!4 models
> close #4
> close #3
> close #2
> close #1
> select sel/i,ib,O,OB,QB,Q
Expected an objects specifier or a keyword
> select /i,ib,O,OB,QB,Q
5226 atoms, 5262 bonds, 4 pseudobonds, 696 residues, 2 models selected
> select #5/i,ib,O,OB,QB,Q
5226 atoms, 5262 bonds, 4 pseudobonds, 696 residues, 2 models selected
> hide #5
> hide #5 cartoons
> show sel cartoons
> show sel
> save "/Users/elizabethbond/OneDrive -
> UCSF/PhosphoPDB_SSCorrection/T175A/ChimeraX/T175A_hexamer_CIF.cif"
> displayedOnly true relModel #5
Not saving entity_poly_seq for non-authoritative sequences
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,4
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 10151.121.1
OS Loader Version: 7459.141.1.701.1
Software:
System Software Overview:
System Version: macOS 12.7.5 (21H1222)
Kernel Version: Darwin 21.6.0
Time since boot: 6 days 11:50
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
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
PA278CV:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 75.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 12 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 12 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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