The following bug report has been submitted:
Platform: macOS-13.4.1-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
this error happens often if I just put my laptop on standby while I take a break
Fatal Python error: Segmentation fault
Current thread 0x00000001ed255e00 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2023-09-25 12:27:37.00 +0200","app_version":"1.6.1","slice_uuid":"a5992708-d5b4-36ec-ac0a-e525f6105b56","build_version":"1.6.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.4.1 (22F770820d)","roots_installed":0,"name":"ChimeraX","incident_id":"96F4E8B5-0470-4E38-8F3D-F5345038DFC9"}
{
"uptime" : 170000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookAir10,1",
"coalitionID" : 1764,
"osVersion" : {
"train" : "macOS 13.4.1",
"build" : "22F770820d",
"releaseType" : "User"
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"captureTime" : "2023-09-25 12:27:24.8101 +0200",
"incident" : "96F4E8B5-0470-4E38-8F3D-F5345038DFC9",
"pid" : 39315,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-09-25 09:28:30.6428 +0200",
"procStartAbsTime" : 3922686433562,
"procExitAbsTime" : 4160989376269,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"1B20862E-6908-5E11-9F81-BDEDD50F43C6","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "92D3BFCB-074E-98D7-0094-F2BDA68A1B13",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 1381,
"sleepWakeUUID" : "7EE3A33A-7677-447E-8E26-B81334106764",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 105555666403304\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600098000000-6000a0000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 105555666403304\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600098000000-6000a0000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)",
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===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> cd /Users/klarab/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/BPS/RP2/Cryo
Current working directory is: /Users/klarab/Library/CloudStorage/OneDrive-
UniversiteitLeiden/BPS/RP2/Cryo
> open /Users/klarab/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/117_open_map_A.mrc
Opened 117_open_map_A.mrc as #1, grid size 512,512,512, pixel 0.976, shown at
level 0.0329, step 2, values float32
> open /Users/klarab/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/117_open_map_B.mrc
Opened 117_open_map_B.mrc as #2, grid size 512,512,512, pixel 0.976, shown at
level 0.0329, step 2, values float32
> open /Users/klarab/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/Version_control/22.09_7sxt_spike_without_Fab_rotameres_1.pdb
Chain information for 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open /Users/klarab/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/117_open_map_sharp.mrc
Opened 117_open_map_sharp.mrc as #4, grid size 512,512,512, pixel 0.976, shown
at level 0.118, step 2, values float32
> open /Users/klarab/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/117_open_local_sharp.mrc
Opened 117_open_local_sharp.mrc as #5, grid size 512,512,512, pixel 0.976,
shown at level 0.0325, step 2, values float32
> open /Users/klarab/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/117_RBD_fitted.pdb
Chain information for 117_RBD_fitted.pdb #6
---
Chain | Description
D | No description available
H | No description available
L | No description available
> mousemode rightMode zoom
> mousemode middleMode translate
> mousemode shift middleMode clip
> volume #1 level 0.139
> volume #1 step 1
> transparency #1 50
> volume #2 level 0.1
> volume #2 step 1
> volume #2 style mesh
> transparency #2 50
> volume #4 level 0.223
> volume #4 step 1
> volume #4 style mesh
> transparency #4 50
> volume #5 level 0.211
> volume #5 step 1
> transparency #5 50
> show #3 cartoons
> set bgColor white
> isolde start
> set selectionWidth 4
> clipper associate #1 toModel #3
Opened 117_open_map_A.mrc as #1.1.1.1, grid size 512,512,512, pixel 0.976,
shown at level 0.282, step 1, values float32
Chain information for 22.09_7sxt_spike_without_Fab_rotameres_1.pdb
---
Chain | Description
1.2/A | No description available
1.2/B | No description available
1.2/C | No description available
> addh
Summary of feedback from adding hydrogens to multiple structures
---
notes | No usable SEQRES records for 117_RBD_fitted.pdb (#6) chain D; guessing
termini instead
No usable SEQRES records for 117_RBD_fitted.pdb (#6) chain H; guessing termini
instead
No usable SEQRES records for 117_RBD_fitted.pdb (#6) chain L; guessing termini
instead
Chain-initial residues that are actual N termini: 117_RBD_fitted.pdb #6/D ASN
331, 117_RBD_fitted.pdb #6/H LEU 4, 117_RBD_fitted.pdb #6/L ILE 2
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 117_RBD_fitted.pdb #6/D
LYS 529, 117_RBD_fitted.pdb #6/H ALA 119, 117_RBD_fitted.pdb #6/L ARG 108
251 hydrogen bonds
117_RBD_fitted.pdb #6/D LYS 529 is not terminus, removing H atom from 'C'
117_RBD_fitted.pdb #6/H ALA 119 is not terminus, removing H atom from 'C'
117_RBD_fitted.pdb #6/L ARG 108 is not terminus, removing H atom from 'C'
No usable SEQRES records for 22.09_7sxt_spike_without_Fab_rotameres_1.pdb
(#1.2) chain A; guessing termini instead
No usable SEQRES records for 22.09_7sxt_spike_without_Fab_rotameres_1.pdb
(#1.2) chain B; guessing termini instead
No usable SEQRES records for 22.09_7sxt_spike_without_Fab_rotameres_1.pdb
(#1.2) chain C; guessing termini instead
Chain-initial residues that are actual N termini:
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A GLN 14,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B GLN 14,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C GLN 14
Chain-initial residues that are not actual N termini:
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A LYS 77,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A MET 153,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A ASN 185,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A GLY 257,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A SER 530,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A ASN 641,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A SER 691,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A ASN 856,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B LYS 77,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B MET 153,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B ASN 185,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B GLY 257,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B ASN 641,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B SER 691,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B ALA 855,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C LYS 77,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C MET 153,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C ASN 185,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C GLY 257,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C ASN 641,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C SER 691,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C ASN 856
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A SER 1147,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A HIS 69,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A TYR 145,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A LEU 176,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A SER 247,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A ILE 332,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A VAL 620,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A GLN 675,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A THR 827,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B SER 1147,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B HIS 69,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B TYR 145,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B LEU 176,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B SER 247,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B VAL 620,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B GLN 675,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B THR 827,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C SER 1147,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C HIS 69,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C TYR 145,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C LEU 176,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C SER 247,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C VAL 620,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C GLN 675,
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C THR 827
2224 hydrogen bonds
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/A SER 1147 is not terminus,
removing H atom from 'C'
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/B SER 1147 is not terminus,
removing H atom from 'C'
22.09_7sxt_spike_without_Fab_rotameres_1.pdb #1.2/C SER 1147 is not terminus,
removing H atom from 'C'
3153 hydrogens added
> isolde restrain ligands #1
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
> hide #!2 models
> hide #!4 models
> hide #!5 models
> hide #6 models
> show #!5 models
> select clear
> hide #!5 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select clear
Window position QRect(1985,901 575x202) outside any known screen, using
primary screen
> open /Users/klarab/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/Version_control/22.09_7sxt_spike_without_Fab_rotameres_1.pdb
Chain information for 22.09_7sxt_spike_without_Fab_rotameres_1.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!1 models
> color #3 bychain
> select clear
> open "/Users/klarab/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/Version_control/22.09_7sxt_spike_without_Fab_rotameres_1
> copy.pdb"
Chain information for 22.09_7sxt_spike_without_Fab_rotameres_1 copy.pdb #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
> close #7
> hide #!3 models
> open /Users/klarab/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/Version_control/25.09_7sxt_A_done_copying_B&C.pdb
Summary of feedback from opening /Users/klarab/Library/CloudStorage/OneDrive-
UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/Version_control/25.09_7sxt_A_done_copying_B&C.pdb
---
warnings | Duplicate atom serial number found: 7303
Duplicate atom serial number found: 7304
Duplicate atom serial number found: 7305
Duplicate atom serial number found: 7306
Duplicate atom serial number found: 7307
11397 messages similar to the above omitted
CONECT record to nonexistent atom: (23239, 23557)
CONECT record for nonexistent atom: 23557
note | Combining 2 symmetry atoms into SER /B:750 H
Chain information for 25.09_7sxt_A_done_copying_B&C.pdb #7
---
Chain | Description
A | No description available
B C | No description available
> color #7 bychain
> select clear
> hide #7 chain A
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select clear
> ui mousemode right select
> select #7/C:192
20 atoms, 20 bonds, 1 residue, 1 model selected
> ui mousemode right zoom
> select up
183 atoms, 184 bonds, 10 residues, 1 model selected
> select up
1056 atoms, 1069 bonds, 63 residues, 1 model selected
> select up
1403 atoms, 1421 bonds, 87 residues, 1 model selected
> select up
9536 atoms, 9669 bonds, 611 residues, 1 model selected
> select up
9566 atoms, 9698 bonds, 613 residues, 1 model selected
> select up
10389 atoms, 10528 bonds, 670 residues, 1 model selected
> cofr sel
> ui mousemode right select
> select #7/B:723
14 atoms, 13 bonds, 1 residue, 1 model selected
> select up
189 atoms, 190 bonds, 12 residues, 1 model selected
> select up
853 atoms, 859 bonds, 59 residues, 1 model selected
> select up
1011 atoms, 1016 bonds, 68 residues, 1 model selected
> select up
8189 atoms, 8289 bonds, 536 residues, 1 model selected
> select up
8330 atoms, 8429 bonds, 545 residues, 1 model selected
> select up
13701 atoms, 13863 bonds, 891 residues, 1 model selected
> select up
14290 atoms, 14462 bonds, 928 residues, 1 model selected
> select up
16090 atoms, 16290 bonds, 1040 residues, 1 model selected
> select up
45182 atoms, 45736 bonds, 2923 residues, 1 model selected
> select down
16090 atoms, 16290 bonds, 1040 residues, 1 model selected
> select #7/C:643
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
53 atoms, 53 bonds, 3 residues, 1 model selected
> select up
6091 atoms, 6173 bonds, 399 residues, 1 model selected
> select up
6203 atoms, 6284 bonds, 406 residues, 1 model selected
> select up
8000 atoms, 8101 bonds, 521 residues, 1 model selected
> select up
8393 atoms, 8498 bonds, 546 residues, 1 model selected
> select up
11633 atoms, 11785 bonds, 748 residues, 1 model selected
> select up
11654 atoms, 11805 bonds, 750 residues, 1 model selected
> select up
16089 atoms, 16290 bonds, 1040 residues, 1 model selected
> select up
45182 atoms, 45736 bonds, 2923 residues, 1 model selected
> select down
16089 atoms, 16290 bonds, 1040 residues, 1 model selected
> select #7 /B:750-1147
5701 atoms, 5762 bonds, 1 pseudobond, 370 residues, 2 models selected
Drag select of 14 residues
> select #7 /B:750-1147
5701 atoms, 5762 bonds, 1 pseudobond, 370 residues, 2 models selected
> ui mousemode right zoom
> turn x -1
> turn x 1
> turn z 1 sel
Expected 'forever' or an integer >= 1 or a keyword
> turn sel z 1
Expected an axis vector or a keyword
> turn z sel 1
Expected a number or a keyword
> cofr sel
> turn z 1
> turn z -1
> rotate z -1
Unknown command: rotate z -1
> rotate z -1 coordinateSystem #7 sel
Unknown command: rotate z -1 coordinateSystem #7 sel
> turn z -1 coordinateSystem #7 sel
Expected a keyword
> turn z -1 coordinateSystem #7 /B:750-1147
> turn z -10 coordinateSystem #7 /B:750-1147
> turn z -10 coordinateSystem #7/B:750-1147
> turn z -10 coordinateSystem #7/C:750-1147
> rotate z -10 coordinateSystem #7/C:750-1147
Unknown command: rotate z -10 coordinateSystem #7/C:750-1147
> turn z -10 coordinateSystem #7 /C
> turn z -10 coordinateSystem #7 sel
Expected a keyword
> turn z -10 coordinateSystem #7 sel
Expected a keyword
> turn z -10 coordinateSystem #7 sel
Expected a keyword
> turn z -10 coordinateSystem #7 sel
Expected a keyword
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #2 style surface
> hide #!2 models
> ui mousemode right "rotate selected models"
> view matrix models
> #7,1,-0.0010422,-0.0026379,0.92232,0.0010368,1,-0.002071,0.27634,0.00264,0.0020682,0.99999,-1.1348
> view matrix models
> #7,0.9998,0.019087,-0.0057994,-2.9834,-0.019133,0.99978,-0.0080887,6.8087,0.0056437,0.0081981,0.99995,-3.3098
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.75212,0.63779,-0.16595,-47.698,-0.65287,0.75543,-0.055607,232.07,0.0899,0.15017,0.98456,-53.609
> view matrix models
> #7,0.42951,0.86503,-0.2593,1.4733,-0.89321,0.44923,0.019098,344.3,0.13301,0.22341,0.96561,-76.651
> select #7 /B
16090 atoms, 16290 bonds, 9 pseudobonds, 1040 residues, 2 models selected
> view matrix models
> #7,-0.41577,-0.85066,-0.32174,630.48,0.86217,-0.48126,0.15829,98.681,-0.2895,-0.21158,0.9335,138.01
> close #7
> open /Users/klarab/Library/CloudStorage/OneDrive-
> UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/Version_control/25.09_7sxt_A_done_copying_B&C.pdb
Summary of feedback from opening /Users/klarab/Library/CloudStorage/OneDrive-
UniversiteitLeiden/BPS/RP2/Cryo/spike_ab117_versions/Version_control/25.09_7sxt_A_done_copying_B&C.pdb
---
warnings | Duplicate atom serial number found: 7303
Duplicate atom serial number found: 7304
Duplicate atom serial number found: 7305
Duplicate atom serial number found: 7306
Duplicate atom serial number found: 7307
11397 messages similar to the above omitted
CONECT record to nonexistent atom: (23239, 23557)
CONECT record for nonexistent atom: 23557
note | Combining 2 symmetry atoms into SER /B:750 H
Chain information for 25.09_7sxt_A_done_copying_B&C.pdb #7
---
Chain | Description
A | No description available
B C | No description available
> color #7 bychain
> view all
> select #7 /B
16090 atoms, 16290 bonds, 9 pseudobonds, 1040 residues, 2 models selected
> turn z 1 coordinateSystem system #7 /B:750-1147
Invalid "coordinateSystem" argument: invalid coordinate-system
> turn z 1 coordinateSystem #7 /B:750-1147
> view matrix models
> #7,0.99407,0.02141,0.1066,-30.882,-0.038572,0.9861,0.16164,-28.605,-0.10166,-0.16479,0.98108,68.74
> turn z 1 coordinateSystem #7 /B:750-1147
> turn z 1 coordinateSystem #7 sel
Expected a keyword
> turn z 1 coordinateSystem #7 select
Expected a keyword
> turn z 1 coordinateSystem #7 selected
Expected a keyword
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Model Number: MGN63D/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 8422.121.1
OS Loader Version: 8422.121.1
Software:
System Software Overview:
System Version: macOS 13.4.1 (c) (22F770820d)
Kernel Version: Darwin 22.5.0
Time since boot: 10 days, 23 hours, 39 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 7
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
EV2780:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
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: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
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: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.21.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
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: 1.1.1
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: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
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: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
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: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
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: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Hi Klara,
--Eric