The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 130000,
"procLaunch" : "2022-05-12 14:24:09.2305 -0400",
"procRole" : "Foreground",
"version" : 2,
"userID" : 1098008071,
"deployVersion" : 210,
"modelCode" : "iMac17,1",
"procStartAbsTime" : 127461166362742,
"coalitionID" : 581,
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"captureTime" : "2022-05-12 17:14:24.3077 -0400",
"incident" : "A1E683F1-190D-4831-A7AA-7966983BCE7C",
"bug_type" : "309",
"pid" : 28010,
"procExitAbsTime" : 137675847966298,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Users\/USER\/*\/ChimeraX-1.3.app\/Contents\/MacOS\/ChimeraX",
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"parentProc" : "bash",
"parentPid" : 27977,
"coalitionName" : "com.apple.Terminal",
"crashReporterKey" : "1F1F9BC2-9054-010F-018D-82681CED18CA",
"responsiblePid" : 3369,
"responsibleProc" : "Terminal",
"wakeTime" : 28283,
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"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4477829120\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10ae64000-10ae65000 [ 4K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"isCorpse" : 1,
"exception" : {"codes":"0x000000000000000d, 0x0000000000000000","rawCodes":[13,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"UNKNOWN_0xD at 0x0000000000000000"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4477829120\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10ae64000-10ae65000 [ 4K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
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"path" : "\/Users\/USER\/*\/ChimeraX-1.3.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/scipy\/.dylibs\/libopenblas.0.dylib",
"name" : "libopenblas.0.dylib"
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"arch" : "x86_64",
"base" : 140703292370944,
"size" : 290816,
"uuid" : "31d69d55-9895-326c-ad61-621c5ca87314",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703413026816,
"CFBundleShortVersionString" : "1.11",
"CFBundleIdentifier" : "com.apple.QuartzCore",
"size" : 3211264,
"uuid" : "ccb708de-75e3-3a64-81c8-f7c688b43d3b",
"path" : "\/System\/Library\/Frameworks\/QuartzCore.framework\/Versions\/A\/QuartzCore",
"name" : "QuartzCore",
"CFBundleVersion" : "964.19.5"
}
],
"sharedCache" : {
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"size" : 15224815616,
"uuid" : "6cc5ecdc-5119-37f0-9a85-4f48a50f5f78"
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=1.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 640K 5 \nActivity Tracing 256K 1 \nCG backing stores 3840K 4 \nCG image 728K 52 \nCG raster data 60K 1 \nColorSync 240K 28 \nCoreAnimation 11.7M 237 \nCoreGraphics 12K 2 \nCoreServices 624K 2 \nCoreUI image data 5164K 40 \nFoundation 36K 2 \nKernel Alloc Once 12K 2 \nMALLOC 778.0M 1111 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 32K 5 \nOpenGL GLSL 384K 5 \nSTACK GUARD 120K 30 \nStack 158.2M 31 \nStack Guard 56.0M 1 \nVM_ALLOCATE 194.0M 250 \nVM_ALLOCATE (reserved) 128.0M 3 reserved VM address space (unallocated)\n__DATA 57.6M 772 \n__DATA_CONST 31.0M 340 \n__DATA_DIRTY 1642K 213 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 760.0M 216 \n__OBJC_RO 82.6M 1 \n__OBJC_RW 3200K 2 \n__TEXT 885.1M 741 \n__UNICODE 592K 1 \ndyld private memory 1056K 2 \nmapped file 492.8M 69 \nshared memory 3488K 25 \n=========== ======= ======= \nTOTAL 3.8G 4206 \nTOTAL, minus reserved VM space 3.5G 4206 \n",
"legacyInfo" : {
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"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
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"trialInfo" : {
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Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open GATA4_ZnF2_mutated_from_4hc7_fit_in_relion_J106_map.cxs
Opened relion_j106_run_class001.mrc as #1, grid size 256,256,256, pixel 1.32,
shown at level 0.0151, step 1, values float32
Opened relion_j107_postprocessed_of_j106.mrc as #3, grid size 256,256,256,
pixel 1.32, shown at level 0.0328, step 1, values float32
Log from Thu May 12 16:52:27 2022
> alias nucrib cartoon style nucleic xsect oval width 1.6 thick 1.6
> alias cylinders cartoon style protein modeh tube rad 2 sides 24
> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open cryosparc_P43_J205_008_volume_map_sharp.mrc
Opened cryosparc_P43_J205_008_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.31, shown at level 0.103, step 1, values float32
> volume #1 level 0.1982
> volume #1 level 0.1409
> volume #1 level 0.3829
> volume #1 level 0.2428
> open
> /largedata/zhou/cryosparc_projects/FoxA1_ALBN1_Nuc186/P43/J205/cryosparc_P43_J205_008_volume_map.mrc
No such file/path:
/largedata/zhou/cryosparc_projects/FoxA1_ALBN1_Nuc186/P43/J205/cryosparc_P43_J205_008_volume_map.mrc
> open
> /Users/zhoub2/Volumes/helix_zhoub2/RELION_proj/GATA4_ALBN1_Nuc186_FoxA1_20220421/Refine3D/job106/run_class001.mrc
Opened run_class001.mrc as #2, grid size 256,256,256, pixel 1.32, shown at
level 0.00557, step 1, values float32
> close #1
> volume #2 level 0.01588
> volume #2 level 0.01397
> open /Users/zhoub2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/projects/GATA4/GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb
Chain information for GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb #1
---
Chain | Description
A | No description available
> fitmap #1 inMap #2
Fit molecule GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) to map
run_class001.mrc (#2) using 351 atoms
average map value = 0.01742, steps = 80
shifted from previous position = 3.62
rotated from previous position = 13.4 degrees
atoms outside contour = 207, contour level = 0.013971
Position of GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) relative to
run_class001.mrc (#2) coordinates:
Matrix rotation and translation
0.98601583 0.02057341 0.16537691 -29.66066787
0.00646053 0.98688576 -0.16129091 23.87844932
-0.16652642 0.16010382 0.97295206 2.30958235
Axis 0.69531834 0.71805305 -0.03053238
Axis point -13.30669656 0.00000000 163.30880604
Rotation angle (degrees) 13.36262942
Shift along axis -3.54812989
> select #2
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-0.16273,0,1,0,-0.0043412,0,0,1,0.33885
> ~select #2
Nothing selected
> undo
[Repeated 2 time(s)]
> select #1
351 atoms, 355 bonds, 4 pseudobonds, 53 residues, 2 models selected
> view matrix models
> #1,0.98602,0.020573,0.16538,-26.308,0.0064605,0.98689,-0.16129,22.705,-0.16653,0.1601,0.97295,-2.6993
> view matrix models
> #1,0.98602,0.020573,0.16538,-25.584,0.0064605,0.98689,-0.16129,23.451,-0.16653,0.1601,0.97295,-1.3066
> fitmap #1 inMap #2
Fit molecule GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) to map
run_class001.mrc (#2) using 351 atoms
average map value = 0.01741, steps = 124
shifted from previous position = 5.43
rotated from previous position = 0.524 degrees
atoms outside contour = 203, contour level = 0.013971
Position of GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) relative to
run_class001.mrc (#2) coordinates:
Matrix rotation and translation
0.98518791 0.02887895 0.16902898 -31.80172581
-0.00116414 0.98682040 -0.16181513 25.40778115
-0.17147430 0.15922154 0.97223715 3.53922793
Axis 0.68459313 0.72610460 -0.06406525
Axis point -8.69698109 0.00000000 173.00639626
Rotation angle (degrees) 13.56053659
Shift along axis -3.54927763
> view matrix models
> #1,0.98519,0.028879,0.16903,-28.625,-0.0011641,0.98682,-0.16182,23.284,-0.17147,0.15922,0.97224,0.052983
> fitmap #1 inMap #2
Fit molecule GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) to map
run_class001.mrc (#2) using 351 atoms
average map value = 0.01742, steps = 92
shifted from previous position = 5.19
rotated from previous position = 0.232 degrees
atoms outside contour = 204, contour level = 0.013971
Position of GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) relative to
run_class001.mrc (#2) coordinates:
Matrix rotation and translation
0.98562027 0.02537279 0.16705961 -30.83922830
0.00191167 0.98692460 -0.16117128 24.70795920
-0.16896460 0.15917304 0.97268438 3.01484266
Axis 0.68913856 0.72286981 -0.05047056
Axis point -10.54866682 0.00000000 169.07269384
Rotation angle (degrees) 13.43980924
Shift along axis -3.54402426
> view matrix models
> #1,0.98562,0.025373,0.16706,-25.954,0.0019117,0.98692,-0.16117,24.347,-0.16896,0.15917,0.97268,-2.69
> view matrix models
> #1,0.85016,0.14263,0.50684,-73.882,-0.024161,0.97217,-0.23305,42.09,-0.52597,0.18588,0.82994,81.492
> view matrix models
> #1,0.82994,0.55679,0.034416,-87.76,-0.51734,0.79129,-0.3259,189.48,-0.20869,0.25267,0.94478,-11.271
> view matrix models
> #1,0.94617,0.27969,0.16287,-69.789,-0.31275,0.91962,0.23768,41.636,-0.083299,-0.27583,0.95759,74.587
> view matrix models
> #1,0.94617,0.27969,0.16287,-69.028,-0.31275,0.91962,0.23768,41.5,-0.083299,-0.27583,0.95759,75.848
> fitmap #1 inMap #2
Fit molecule GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) to map
run_class001.mrc (#2) using 351 atoms
average map value = 0.0165, steps = 180
shifted from previous position = 12.9
rotated from previous position = 26.9 degrees
atoms outside contour = 218, contour level = 0.013971
Position of GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) relative to
run_class001.mrc (#2) coordinates:
Matrix rotation and translation
0.95850114 0.28234253 0.03947496 -61.40358064
-0.26845940 0.94049602 -0.20831897 91.49853928
-0.09594334 0.18907654 0.97726401 -16.71162069
Axis 0.57380380 0.19553198 -0.79530903
Axis point 288.01724337 251.57748700 0.00000000
Rotation angle (degrees) 20.26005521
Shift along axis -4.05181396
> undo
> view matrix models
> #1,0.94617,0.27969,0.16287,-72.011,-0.31275,0.91962,0.23768,40.896,-0.083299,-0.27583,0.95759,79.144
> fitmap #1 inMap #2
Fit molecule GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) to map
run_class001.mrc (#2) using 351 atoms
average map value = 0.0165, steps = 176
shifted from previous position = 9.25
rotated from previous position = 27 degrees
atoms outside contour = 218, contour level = 0.013971
Position of GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) relative to
run_class001.mrc (#2) coordinates:
Matrix rotation and translation
0.95865158 0.28192375 0.03880920 -61.24041715
-0.26812819 0.94048416 -0.20879853 91.51130099
-0.09536471 0.18975920 0.97718832 -16.95148052
Axis 0.57562358 0.19378289 -0.79442161
Axis point 288.45388091 251.25730687 0.00000000
Rotation angle (degrees) 20.25485103
Shift along axis -4.05148146
> undo
> show sel atoms
> hide sel atoms
> show sel cartoons
> show sel atoms
> hide sel cartoons
> view matrix models
> #1,0.94617,0.27969,0.16287,-74.686,-0.31275,0.91962,0.23768,40.817,-0.083299,-0.27583,0.95759,78.205
> view matrix models
> #1,0.94617,0.27969,0.16287,-73.72,-0.31275,0.91962,0.23768,40.108,-0.083299,-0.27583,0.95759,79.66
> volume #2 color #ffffb2c9
> lighting soft
> lighting simple
> lighting full
> lighting simple
> view matrix models
> #1,0.94417,0.26332,0.19798,-74.93,-0.31042,0.91236,0.26689,36.978,-0.11035,-0.31345,0.94317,94.945
> view matrix models
> #1,0.94417,0.26332,0.19798,-74.57,-0.31042,0.91236,0.26689,37.629,-0.11035,-0.31345,0.94317,92.35
> view matrix models
> #1,0.94417,0.26332,0.19798,-71.788,-0.31042,0.91236,0.26689,34.971,-0.11035,-0.31345,0.94317,91.545
> view matrix models
> #1,0.96671,0.24262,-0.081259,-31.483,-0.23494,0.96748,0.093744,33.671,0.10136,-0.071532,0.99227,-7.7423
> view matrix models
> #1,0.96671,0.24262,-0.081259,-30.666,-0.23494,0.96748,0.093744,34.458,0.10136,-0.071532,0.99227,-6.1126
> view matrix models
> #1,0.99376,0.073426,-0.083904,0.32666,-0.061704,0.98897,0.13464,-9.5036,0.092865,-0.12862,0.98734,8.3383
> view matrix models
> #1,0.98562,0.10378,-0.13336,2.6066,-0.07581,0.97688,0.1999,-13.626,0.15102,-0.18691,0.9707,11.836
> view matrix models
> #1,0.98562,0.10378,-0.13336,3.488,-0.07581,0.97688,0.1999,-12.865,0.15102,-0.18691,0.9707,11.635
> view matrix models
> #1,0.97908,0.16947,-0.11258,-12.163,-0.14985,0.97494,0.16444,6.9814,0.13763,-0.14413,0.97994,3.8305
> fitmap #1 inMap #2
Fit molecule GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) to map
run_class001.mrc (#2) using 351 atoms
average map value = 0.01523, steps = 76
shifted from previous position = 0.719
rotated from previous position = 12.6 degrees
atoms outside contour = 151, contour level = 0.013971
Position of GATA3_Znf2_4hc7_fit_relion_j98_run_class001.pdb (#1) relative to
run_class001.mrc (#2) coordinates:
Matrix rotation and translation
0.99833250 0.00426001 -0.05756792 10.99393893
-0.00313856 0.99980382 0.01955690 -3.68263610
0.05763994 -0.01934361 0.99815002 -10.11234833
Axis -0.31932000 -0.94569887 -0.06073213
Axis point 180.88787044 0.00000000 188.98551510
Rotation angle (degrees) 3.49213291
Shift along axis 0.58622456
> color #2 #33ffff models transparency 0
> color #2 cyan models transparency 0
> color #2 #006666 models transparency 0
> color #2 #33ffff models transparency 0
> lighting soft
> select clear
> select /A:402@ZN
1 atom, 1 residue, 1 model selected
> delete sel
> open
> /Users/zhoub2/Volumes/helix_zhoub2/RELION_proj/GATA4_ALBN1_Nuc186_FoxA1_20220421/MaskCreate/job103/mask.mrc
Opened mask.mrc as #3, grid size 256,256,256, pixel 1.32, shown at level 1,
step 1, values float32
> volume #3 level 1
[Repeated 1 time(s)]
> open
> /Users/zhoub2/Volumes/helix_zhoub2/RELION_proj/GATA4_ALBN1_Nuc186_FoxA1_20220421/PostProcess/job107/postprocess.mrc
Opened postprocess.mrc as #4, grid size 256,256,256, pixel 1.32, shown at
level 0.00868, step 1, values float32
> close #3
> volume #4 level 0.0179
> volume #4 level 0.01585
> volume #4 level 0.02046
> volume #4 level 0.07269
> volume #4 level 0.02046
> volume #4 level 0.01431
> volume #4 level 0.02199
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!4 models
> show #!2 models
> color #2 #33ffff8f models
> color #2 #33ffffcb models
> lighting simple
> volume #2 level 0.01168
> volume #4 level 0.02609
> volume #2 level 0.01168
> volume #2 level 0.01473
> pwd
Current working directory is: /Users/zhoub2/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/projects/FoxA1/FoxA1_ALBN1_Nuc186/model_building
> cd ../../GATA4
Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword
> cd ../../
Current working directory is: /Users/zhoub2/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/projects/FoxA1
> cd ..
Current working directory is: /Users/zhoub2/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/projects
> cd GATA4
Current working directory is: /Users/zhoub2/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/projects/GATA4
> save relion_j106_run_class001.mrc #2
> save GATA3_ZnF2_4hc7_fit_relion_j106_run_class001.pdb #1
> volume #4 level 0.02456
> open /Users/zhoub2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/projects/GATA4/GATA4_ZnF2_mutated_from_4hc7_fit_relion_j106_run_class001-coot-0.pdb
Summary of feedback from opening /Users/zhoub2/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/projects/GATA4/GATA4_ZnF2_mutated_from_4hc7_fit_relion_j106_run_class001-coot-0.pdb
---
warnings | End residue of secondary structure not found: HELIX 1 1 CYS A 339
ASN A 350 1 12
End residue of secondary structure not found: HELIX 2 2 PRO A 354 LYS A 358 1
5
Chain information for
GATA4_ZnF2_mutated_from_4hc7_fit_relion_j106_run_class001-coot-0.pdb #3
---
Chain | Description
A | No description available
> close #1
> show atoms
> ui tool show AlphaFold
> alphafold predict #3
Running AlphaFold prediction
[Repeated 2 time(s)]
> volume #4 level 0.02772
> volume #2 level 0.01395
> show cartoons
> hide atoms
> open
> /Users/zhoub2/Volumes/helix_zhoub2/RELION_proj/GATA4_ALBN1_Nuc186_FoxA1_20220421/MaskCreate/job103/mask.mrc
Opened mask.mrc as #1, grid size 256,256,256, pixel 1.32, shown at level 1,
step 1, values float32
> volume #1 level 1
> volume #4 level 0.003466
> volume #4 level 0.007684
> close #1
> volume #4 level 0.03278
> show cartoons
> color #3 #330033 transparency 0
> color #3 #663366 transparency 0
> color zone #2 near #3 distance 3
> lighting soft
> set bgColor white
> color zone #2 near #3 distance 2
> color zone #2 near #3 distance 3
> volume #2 color #6666cc
> color zone #2 near #3 distance 3
> volume #2 color #00ccff
> color zone #2 near #3 distance 3
> color #3 #006600 transparency 0
> color zone #2 near #3 distance 3
> color #3 #cc3300 transparency 0
> color zone #2 near #3 distance 3
> color #3 #993300 transparency 0
> color zone #2 near #3 distance 3
> color #3 #cc9966 transparency 0
> color zone #2 near #3 distance 3
> hide #!3 models
> volume #2 level 0.01509
> rename #2 id #2
> rename #2 id #1
> rename #3 id #2
> rename #4 id #3
> rename #1 relion_j106_run_class001.mrc
> rename #3 relion_j107_postprocessed_of_j106.mrc
> save /Users/zhoub2/NIH-
> OneDrive/projects/GATA4/GATA4_ZnF2_mutated_from_4hc7_fit_in_relion_J106_map.cxs
> pwd
Current working directory is: /Users/zhoub2/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/projects/GATA4
> save relion_j107_postprocessed_of_j106.mrc #3
> save relion_j106_run_class001.mrc #1
> save /Users/zhoub2/NIH-
> OneDrive/projects/GATA4/GATA4_ZnF2_mutated_from_4hc7_fit_in_relion_J106_map.cxs
[Repeated 1 time(s)]
——— End of log from Thu May 12 16:52:27 2022 ———
opened ChimeraX session
OpenGL version: 4.1 ATI-4.8.15
OpenGL renderer: AMD Radeon R9 M395X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac17,1
Processor Name: Quad-Core Intel Core i7
Processor Speed: 4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 170.0.0.0.0
OS Loader Version: 540.100.7~23
SMC Version (system): 2.34f3
Software:
System Software Overview:
System Version: macOS 12.3.1 (21E258)
Kernel Version: Darwin 21.4.0
Time since boot: 3 days 7:04
Graphics/Displays:
AMD Radeon R9 M395X:
Chipset Model: AMD Radeon R9 M395X
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x6920
Revision ID: 0x0000
ROM Revision: 113-C905AA-799
VBIOS Version: 113-C905A0-007
EFI Driver Version: 01.00.799
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-Clipper: 0.17.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.3
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Was only using 3.5GB