Opened 2 years ago

Closed 2 years ago

#9706 closed defect (can't reproduce)

Crash saving session including maps

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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  "procLaunch" : "2023-09-01 11:56:14.9040 +0100",
  "procRole" : "Foreground",
  "version" : 2,
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  "osVersion" : {
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  "captureTime" : "2023-09-01 11:58:02.4584 +0100",
  "incident" : "F6AFB309-D8A0-449D-B5A2-265264AFAE93",
  "bug_type" : "309",
  "pid" : 31290,
  "procExitAbsTime" : 27063423863086,
  "translated" : true,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Volumes\/VOLUME\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
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  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "15B6FB79-6477-AE8B-B6EC-F37D0AD4E455",
  "wakeTime" : 2113,
  "sleepWakeUUID" : "6EA9A836-DC6F-4D84-875B-4EE310C64C96",
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  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x000000000000000a","rawCodes":[1,10],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000000000000a"},
  "ktriageinfo" : "VM - pmap_enter failed with resource shortage\nVM - pmap_enter failed with resource shortage\nVM - pmap_enter failed with resource shortage\nVM - pmap_enter failed with resource shortage\nVM - pmap_enter failed with resource shortage\n",
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    "size" : 49152,
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    "size" : 561152,
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    "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    "name" : "libsystem_c.dylib"
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    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703596048384,
    "size" : 40960,
    "uuid" : "f6cad74b-ec4d-3ff9-80f3-b066753f9fab",
    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    "name" : "libsystem_platform.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 140703124914176,
    "size" : 196608,
    "uuid" : "0ee8ce32-639c-316a-9551-dab9a2e0c8a5",
    "path" : "\/usr\/libexec\/rosetta\/runtime",
    "name" : "runtime"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4582551552,
    "size" : 63488000,
    "uuid" : "10431d8f-5e3b-3bbc-abd5-81f6a73a5269",
    "path" : "\/Volumes\/VOLUME\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
    "name" : "libopenblas64_.0.dylib"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 5206069248,
    "size" : 165068800,
    "uuid" : "c9795830-14cd-3b40-983d-a3143cd9cbd9",
    "path" : "\/Volumes\/VOLUME\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
    "name" : "QtWebEngineCore"
  },
  {
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    "arch" : "x86_64",
    "base" : 140703596265472,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 5246976,
    "uuid" : "9c8908f2-e5e0-35b7-9f41-fdf8d7476d8b",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "1863"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703639994368,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 15265792,
    "uuid" : "832ad371-d3b8-3061-b4e2-1c4e0cffce0b",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2113.50.132"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4489543680,
    "CFBundleShortVersionString" : "3.9.11, (c) 2001-2021 Python Software Foundation.",
    "CFBundleIdentifier" : "org.python.python",
    "size" : 2527232,
    "uuid" : "ef9cc1f4-5991-3213-9a9e-e68c578b6c1b",
    "path" : "\/Volumes\/VOLUME\/ChimeraX-1.4.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
    "name" : "Python",
    "CFBundleVersion" : "3.9.11"
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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=2.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.7G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               640K        5 \nActivity Tracing                   256K        1 \nCG backing stores                 4288K        8 \nCG image                            52K       13 \nColorSync                          228K       26 \nCoreAnimation                       76K       15 \nCoreGraphics                        16K        3 \nCoreUI image data                 1528K       23 \nFoundation                          16K        1 \nKernel Alloc Once                    8K        1 \nMALLOC                             1.1G       94 \nMALLOC guard page                  192K        8 \nMALLOC_MEDIUM (reserved)         784.0M        8         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           256.0M        1         reserved VM address space (unallocated)\nMach message                        16K        4 \nOpenGL GLSL                        384K        4 \nRosetta Arena                     4096K        2 \nRosetta Generic                   1440K      357 \nRosetta IndirectBranch            2048K        1 \nRosetta JIT                      128.0M        1 \nRosetta Return Stack               740K       74 \nRosetta Thread Context             740K       74 \nSTACK GUARD                         40K       10 \nStack                            169.1M       37 \nStack Guard                       56.1M       27 \nVM_ALLOCATE                      101.1M      194 \nVM_ALLOCATE (reserved)           160.1M       13         reserved VM address space (unallocated)\n__CTF                               756        1 \n__DATA                            44.5M      672 \n__DATA_CONST                      31.0M      341 \n__DATA_DIRTY                      1644K      213 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       737.4M      149 \n__OBJC_RO                         82.7M        1 \n__OBJC_RW                         3200K        2 \n__TEXT                           797.1M      669 \n__UNICODE                          592K        1 \ndyld private memory               1184K        3 \nmapped file                        5.2G     1152 \nshared memory                     3004K       21 \nunshared pmap                     11.6M        8 \n===========                     =======  ======= \nTOTAL                              9.7G     4240 \nTOTAL, minus reserved VM space     8.5G     4240 \n",
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Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure
> 4/Barrel_fitted_cryoET_map_D5.cxs"

Opened postprocess_D5.mrc as #3, grid size 80,80,80, pixel 3.26, shown at
level 4.63, step 1, values float32  
Log from Fri Sep 1 13:16:38 2023UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure
> 4/Barrel_fitted_cryoET_map_C1.cxs"

Opened postprocess.mrc as #2, grid size 80,80,80, pixel 3.26, shown at level
6.48, step 1, values float32  
Log from Fri Aug 4 16:39:05 2023UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Users/houghtf/Documents/Documents/barrel
> paper/Data/Tomography/Barrel_fitted_final_map_job178.cxs"

Opened postprocess.mrc as #2, grid size 80,80,80, pixel 3.26, shown at level
6.79, step 1, values float32  
Log from Tue Aug 1 11:09:11 2023UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Users/houghtf/Documents/Documents/barrel paper/Data/Figure 1/Colour
> barrel.cxs"

Log from Mon Jul 31 17:27:57 2023UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/houghtf/Documents/Documents/barrel paper/Data/Figure
> 1/barrel.pdb"

Chain information for barrel.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C M | No description available  
D F J | No description available  
E | No description available  
G | No description available  
H L | No description available  
I | No description available  
K | No description available  
N P R T | No description available  
O | No description available  
Q | No description available  
S | No description available  
  

> set bgColor white

> select add #1

46489 atoms, 47072 bonds, 3 pseudobonds, 3049 residues, 2 models selected  

> cartoon (#!1 & sel)

> hide (#!1 & sel) target a

> select clear

> select /A

3128 atoms, 3168 bonds, 207 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel green

> select /B

1508 atoms, 1526 bonds, 98 residues, 1 model selected  

> color sel sandy brown

> select /C

3111 atoms, 3153 bonds, 206 residues, 1 model selected  

> color sel green

> select /D

1607 atoms, 1627 bonds, 101 residues, 1 model selected  

> color sel sandy brown

> select /E

3101 atoms, 3142 bonds, 206 residues, 1 model selected  

> color sel green

> select /F

1594 atoms, 1614 bonds, 101 residues, 1 model selected  

> color sel sandy brown

> select /G

3100 atoms, 3141 bonds, 205 residues, 1 model selected  

> color sel green

> select /H

1572 atoms, 1592 bonds, 99 residues, 1 model selected  

> color sel sandy brown

> select /I

3069 atoms, 3109 bonds, 1 pseudobond, 202 residues, 2 models selected  

> color sel green

> select /J

1571 atoms, 1590 bonds, 100 residues, 1 model selected  

> color sel khaki

> select /L

1520 atoms, 1538 bonds, 97 residues, 1 model selected  

> color sel khaki

> select /N

1555 atoms, 1574 bonds, 97 residues, 1 model selected  

> color sel khaki

> select /P

1540 atoms, 1559 bonds, 97 residues, 1 model selected  

> color sel khaki

> select /R

1529 atoms, 1547 bonds, 96 residues, 1 model selected  

> color sel khaki

> select /T

1516 atoms, 1534 bonds, 96 residues, 1 model selected  

> color sel khaki

> select /S

3087 atoms, 3128 bonds, 204 residues, 1 model selected  

> color sel green

> select /Q

3061 atoms, 3101 bonds, 1 pseudobond, 203 residues, 2 models selected  

> color sel green

> select /O

3131 atoms, 3173 bonds, 207 residues, 1 model selected  

> color sel green

> select /M

3100 atoms, 3141 bonds, 205 residues, 1 model selected  

> color sel green

> select ::name="FUC"::name="HOH"::name="NAG"

698 atoms, 690 bonds, 48 residues, 1 model selected  

> show sel target ab

> color sel byhetero

> select H

22664 atoms, 3013 residues, 1 model selected  

> hide sel target a

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select /A:149-150

36 atoms, 35 bonds, 2 residues, 1 model selected  

> select /A:149-225

1174 atoms, 1189 bonds, 77 residues, 1 model selected  

> select /A:149-150

36 atoms, 35 bonds, 2 residues, 1 model selected  

> select /A:149-224

1163 atoms, 1178 bonds, 76 residues, 1 model selected  

> color sel lime target a

> ui tool show "Show Sequence Viewer"

> sequence chain /C

Alignment identifier is 1/C  

> sequence chain /E

Alignment identifier is 1/E  

> sequence chain /G

Alignment identifier is 1/G  

> sequence chain /I

Alignment identifier is 1/I  

> sequence chain /K

Alignment identifier is 1/K  

> sequence chain /M

Alignment identifier is 1/M  

> sequence chain /O

Alignment identifier is 1/O  

> sequence chain /Q

Alignment identifier is 1/Q  

> sequence chain /S

Alignment identifier is 1/S  

> select /S:151

13 atoms, 12 bonds, 1 residue, 1 model selected  

> select /S:151-224

1126 atoms, 1141 bonds, 74 residues, 1 model selected  

> color sel lime target a

> select /Q:151

13 atoms, 12 bonds, 1 residue, 1 model selected  

> select /Q:151-224

1118 atoms, 1133 bonds, 1 pseudobond, 73 residues, 2 models selected  

> color sel lime target a

> select /O:150-151

20 atoms, 19 bonds, 2 residues, 1 model selected  

> select /O:150-224

1129 atoms, 1144 bonds, 75 residues, 1 model selected  

> color sel lime target a

> select /M:151-152

27 atoms, 26 bonds, 2 residues, 1 model selected  

> select /M:151-225

1137 atoms, 1152 bonds, 75 residues, 1 model selected  

> color sel lime target a

> select /K:150

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select /K:150-224

1141 atoms, 1156 bonds, 75 residues, 1 model selected  

> color sel lime target a

> select /I:151-152

27 atoms, 26 bonds, 2 residues, 1 model selected  

> select /I:151-224

1106 atoms, 1120 bonds, 1 pseudobond, 72 residues, 2 models selected  

> color sel lime target a

> select /G:150-151

28 atoms, 27 bonds, 2 residues, 1 model selected  

> select /G:150-224

1141 atoms, 1156 bonds, 75 residues, 1 model selected  

> color sel lime target a

> select /E:150-151

28 atoms, 27 bonds, 2 residues, 1 model selected  

> select /E:150-224

1141 atoms, 1156 bonds, 75 residues, 1 model selected  

> color sel lime target a

> select /C:151-152

27 atoms, 26 bonds, 2 residues, 1 model selected  

> select /C:151-224

1126 atoms, 1141 bonds, 74 residues, 1 model selected  

> color sel lime target a

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> sequence chain /C

Alignment identifier is 1/C  

> sequence chain /E

Alignment identifier is 1/E  

> sequence chain /G

Alignment identifier is 1/G  

> sequence chain /I

Alignment identifier is 1/I  

> sequence chain /K

Alignment identifier is 1/K  

> sequence chain /M

Alignment identifier is 1/M  

> sequence chain /O

Alignment identifier is 1/O  

> sequence chain /Q

Alignment identifier is 1/Q  

> sequence chain /S

Alignment identifier is 1/S  

> select /S:151

13 atoms, 12 bonds, 1 residue, 1 model selected  

> select /S:151-224

1126 atoms, 1141 bonds, 74 residues, 1 model selected  

> color sel lime target c

> select clear

> select /Q:151-152

27 atoms, 26 bonds, 2 residues, 1 model selected  

> select /Q:151-224

1118 atoms, 1133 bonds, 1 pseudobond, 73 residues, 2 models selected  

> color sel lime target c

> select /O:150

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /O:150-224

1129 atoms, 1144 bonds, 75 residues, 1 model selected  

> color sel lime target c

[Repeated 1 time(s)]

> select /M:151-152

27 atoms, 26 bonds, 2 residues, 1 model selected  

> select /M:151-224

1126 atoms, 1141 bonds, 74 residues, 1 model selected  

> color sel lime target c

> select /K:150-151

28 atoms, 27 bonds, 2 residues, 1 model selected  

> select /K:150-224

1141 atoms, 1156 bonds, 75 residues, 1 model selected  

> color sel lime target c

> select /I:151

13 atoms, 12 bonds, 1 residue, 1 model selected  

> select /I:151-224

1106 atoms, 1120 bonds, 1 pseudobond, 72 residues, 2 models selected  

> color sel lime target c

> select /G:150-151

28 atoms, 27 bonds, 2 residues, 1 model selected  

> select /G:150-224

1141 atoms, 1156 bonds, 75 residues, 1 model selected  

> color sel lime target c

> select /E:150-151

28 atoms, 27 bonds, 2 residues, 1 model selected  

> select /E:150-225

1152 atoms, 1167 bonds, 76 residues, 1 model selected  

> color sel lime target c

> select /C:151-152

27 atoms, 26 bonds, 2 residues, 1 model selected  

> select /C:151-224

1126 atoms, 1141 bonds, 74 residues, 1 model selected  

> color sel lime target c

> select /A:149

21 atoms, 20 bonds, 1 residue, 1 model selected  

> select /A:149-236

1361 atoms, 1378 bonds, 88 residues, 1 model selected  

> color sel lime target c

> lighting shadows false

> select /A:225-227

50 atoms, 49 bonds, 3 residues, 1 model selected  

> select /A:225-237

209 atoms, 209 bonds, 13 residues, 1 model selected  

> color sel crimson target c

> color sel lime target c

[Repeated 1 time(s)]

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> sequence chain /C

Alignment identifier is 1/C  

> sequence chain /E

Alignment identifier is 1/E  

> sequence chain /G

Alignment identifier is 1/G  

> sequence chain /I

Alignment identifier is 1/I  

> sequence chain /K

Alignment identifier is 1/K  

> sequence chain /M

Alignment identifier is 1/M  

> sequence chain /O

Alignment identifier is 1/O  

> sequence chain /Q

Alignment identifier is 1/Q  

> sequence chain /S

Alignment identifier is 1/S  

> select /A:149

21 atoms, 20 bonds, 1 residue, 1 model selected  

> select /A:149-236

1361 atoms, 1378 bonds, 88 residues, 1 model selected  

> color sel lime target c

> select /S:151-152

27 atoms, 26 bonds, 2 residues, 1 model selected  

> select /S:151-236

1324 atoms, 1341 bonds, 86 residues, 1 model selected  

> color sel lime target c

> select /Q:151

13 atoms, 12 bonds, 1 residue, 1 model selected  

> select /Q:151-236

1316 atoms, 1333 bonds, 1 pseudobond, 85 residues, 2 models selected  

> color sel lime target c

> select /O:150-151

20 atoms, 19 bonds, 2 residues, 1 model selected  

> select /O:150-236

1327 atoms, 1344 bonds, 87 residues, 1 model selected  

> color sel lime target c

> select /M:151

13 atoms, 12 bonds, 1 residue, 1 model selected  

> select /M:151-236

1324 atoms, 1341 bonds, 86 residues, 1 model selected  

> color sel lime target c

> select /K:150

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select /K:150-236

1339 atoms, 1356 bonds, 87 residues, 1 model selected  

> color sel lime target c

> select /I:151

13 atoms, 12 bonds, 1 residue, 1 model selected  

> select /I:151-236

1304 atoms, 1320 bonds, 1 pseudobond, 84 residues, 2 models selected  

> color sel lime target c

> select /G:150-151

28 atoms, 27 bonds, 2 residues, 1 model selected  

> select /G:150-236

1339 atoms, 1356 bonds, 87 residues, 1 model selected  

> color sel lime target c

> select /E:150

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select /E:150-236

1339 atoms, 1356 bonds, 87 residues, 1 model selected  

> color sel lime target c

> select /C:151-152

27 atoms, 26 bonds, 2 residues, 1 model selected  

> select /C:151-236

1324 atoms, 1341 bonds, 86 residues, 1 model selected  

> color sel lime target c

> save "/Users/houghtf/Documents/Documents/barrel paper/Data/Figure 1/Colour
> barrel.cxs"

——— End of log from Mon Jul 31 17:27:57 2023 ———

opened ChimeraX session  

> select /W:5@O

1 atom, 1 residue, 1 model selected  

> select /W:10@O

1 atom, 1 residue, 1 model selected  

> select /W:10@O

1 atom, 1 residue, 1 model selected  

> select /W:5@O

1 atom, 1 residue, 1 model selected  

> hide sel target a

> select /W:10@O

1 atom, 1 residue, 1 model selected  

> hide sel target a

> select /W:23@O

1 atom, 1 residue, 1 model selected  

> hide sel target a

> select /W:12@O

1 atom, 1 residue, 1 model selected  

> hide sel target a

> select /W:22@O

1 atom, 1 residue, 1 model selected  

> hide sel target a

> select /W:11@O

1 atom, 1 residue, 1 model selected  

> hide sel target a

> select /W:14@O

1 atom, 1 residue, 1 model selected  

> hide sel target a

> select /W:3@O

1 atom, 1 residue, 1 model selected  

> hide sel target a

> select /W:25@O

1 atom, 1 residue, 1 model selected  

> hide sel target a

> select /W:7@O

1 atom, 1 residue, 1 model selected  

> hide sel target a

> select /W:17@O

1 atom, 1 residue, 1 model selected  

> hide sel target a

> select /W:4@O

1 atom, 1 residue, 1 model selected  

> hide sel target a

> select /W:16@O

1 atom, 1 residue, 1 model selected  

> hide sel target a

> select /W:6@O

1 atom, 1 residue, 1 model selected  

> hide sel target a

> select /W:1@O

1 atom, 1 residue, 1 model selected  

> hide sel target a

> select /W:2@O

1 atom, 1 residue, 1 model selected  

> hide sel target a

> select /W:15@O

1 atom, 1 residue, 1 model selected  

> hide sel target a

> select /W:9@O

1 atom, 1 residue, 1 model selected  

> hide sel target a

> select /W:8@O

1 atom, 1 residue, 1 model selected  

> hide sel target a

> ui tool show "Show Sequence Viewer"

> sequence chain /K

Alignment identifier is 1/K  

> select /K:237

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /K:237-354

1704 atoms, 1725 bonds, 1 pseudobond, 115 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel green

> select clear

> save "/Users/houghtf/Documents/Documents/barrel paper/Data/Figure 1/Colour
> barrel.cxs"

> open "/Users/houghtf/Documents/Documents/barrel
> paper/Data/Tomography/Relion4
> jobs/Job178_Tomo_reconstruct/PostProcess/postprocess.mrc"

Opened postprocess.mrc as #2, grid size 80,80,80, pixel 3.26, shown at level
14.5, step 1, values float32  

> volume #2 level 3.236

> tile

2 models tiled  

> ui tool show "Model Panel"

> hide #!1 models

> show #!1 models

> select add #2

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.78642,0.61676,-0.033974,-178.25,-0.6172,0.78242,-0.082895,-187.42,-0.024544,0.086159,0.99598,-91.525

> view matrix models
> #2,0.46935,0.81933,-0.32927,-121.09,-0.49735,0.55341,0.66812,-275.69,0.72963,-0.14982,0.66723,-120

> volume #2 level 6.304

> transparency #2.1 70

> select add #1

46489 atoms, 47072 bonds, 3 pseudobonds, 3049 residues, 4 models selected  

> select subtract #2

46489 atoms, 47072 bonds, 3 pseudobonds, 3049 residues, 2 models selected  

> ui mousemode right "move picked models"

[Repeated 1 time(s)]

> view matrix models #1,1,0,0,-27.091,0,1,0,-200.08,0,0,1,-2.1825

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.99521,-0.00043184,0.09773,-31.977,0.00083095,0.99999,-0.0040431,-199.89,-0.097727,0.0041049,0.9952,0.41268

> view matrix models
> #1,0.97583,-0.19657,0.095468,-26.269,0.19334,0.98023,0.042091,-206.58,-0.10185,-0.022616,0.99454,1.2458

> ui tool show "Fit in Map"

> fitmap #1 inMap #2

Fit molecule barrel.pdb (#1) to map postprocess.mrc (#2) using 46489 atoms  
average map value = 12.17, steps = 60  
shifted from previous position = 10.2  
rotated from previous position = 8.31 degrees  
atoms outside contour = 5212, contour level = 6.3038  
  
Position of barrel.pdb (#1) relative to postprocess.mrc (#2) coordinates:  
Matrix rotation and translation  
0.40034478 -0.62961202 0.66581736 96.61861426  
0.89139750 0.43602363 -0.12366848 104.13230329  
-0.21244895 0.64301796 0.73579436 84.17677080  
Axis 0.40006376 0.45828712 0.79367620  
Axis point -1.59484684 57.64046084 0.00000000  
Rotation angle (degrees) 73.37650062  
Shift along axis 153.18519836  
  

> select clear

> volume #2 level 6.795

> fitmap #1 inMap #2

Fit molecule barrel.pdb (#1) to map postprocess.mrc (#2) using 46489 atoms  
average map value = 12.17, steps = 44  
shifted from previous position = 0.0518  
rotated from previous position = 0.0326 degrees  
atoms outside contour = 6052, contour level = 6.7948  
  
Position of barrel.pdb (#1) relative to postprocess.mrc (#2) coordinates:  
Matrix rotation and translation  
0.40003055 -0.62940740 0.66619958 96.61067856  
0.89145208 0.43599686 -0.12336906 104.06639494  
-0.21281153 0.64323640 0.73549860 84.18577427  
Axis 0.39998184 0.45863029 0.79351924  
Axis point -1.50101650 57.58528401 0.00000000  
Rotation angle (degrees) 73.39553772  
Shift along axis 153.17354966  
  

> select add #2

2 models selected  

> select subtract #2

Nothing selected  

> lighting full

> lighting soft

> transparency 70

> transparency 60

> transparency 70

> save "/Users/houghtf/Documents/Documents/barrel
> paper/Data/Tomography/Barrel_fitted_final_map_job178.cxs"

——— End of log from Tue Aug 1 11:09:11 2023 ———

opened ChimeraX session  

> lighting shadows true intensity 0.5

> lighting shadows false

> graphics silhouettes true

> lighting full

> lighting soft

> transparency 60

> lighting full

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> lighting full

> transparency 50

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting soft

> lighting full

> lighting soft

> lighting full

> lighting soft

> lighting full

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> volume #2 level 7.419

> lighting shadows false

> volume #2 level 7.169

> save "/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure
> 4/Barrel_fitted_cryoET_map_side.tif" width 2500 height 2094 supersample 3
> transparentBackground true

> save "/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure
> 4/Barrel_fitted_cryoET_map_top.tif" width 2500 height 2094 supersample 3
> transparentBackground true

> save "/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure
> 4/Barrel_fitted_cryoET_map.cxs" includeMaps true

> select add #2

2 models selected  

> ui tool show "Color Actions"

> color sel gold

> color sel indian red

> color sel coral

> color sel chocolate

> color sel olive

> color sel lawn green

> color sel light gray

> color sel light steel blue

> color sel light blue

> color sel sky blue

> color sel light cyan

> color sel seashell

> color sel blanched almond

> color sel bisque

> color sel navajo white

> color sel aquamarine

> color sel purple

> color sel dark slate gray

> color sel dark olive green

> color sel sandy brown

> color sel goldenrod

> color sel green yellow

> color sel dark orange

> color sel gold

> color sel indian red

> color sel fire brick

> color sel maroon

> color sel dark red

> color sel crimson

> color sel orange red

[Repeated 1 time(s)]

> color sel peru

> color sel light salmon

> color sel dark goldenrod

> color sel dark turquoise

> color sel cornflower blue

> color sel teal

> color sel steel blue

> color sel cadet blue

> color sel light slate gray

> color sel slate gray

> color sel light slate gray

> select clear

> lighting full

> lighting soft

> lighting full

> lighting shadows false

> lighting shadows true

> lighting shadows false

> save "/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure
> 4/Barrel_fitted_cryoET_map_top2.tif" width 2500 height 2094 supersample 3
> transparentBackground true

> select add #1

46489 atoms, 47072 bonds, 3 pseudobonds, 3049 residues, 2 models selected  

> transparency (#!1 & sel) 60

> select clear

> save "/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure
> 4/Barrel_fitted_cryoET_map_top2.tif" width 2500 height 2094 supersample 3
> transparentBackground true

> select add #1

46489 atoms, 47072 bonds, 3 pseudobonds, 3049 residues, 2 models selected  

> transparency (#!1 & sel) 70

> select clear

> select add #2

2 models selected  

> transparency #2.1 60

> select clear

> save "/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure
> 4/Barrel_fitted_cryoET_map_top2.tif" width 2500 height 2094 supersample 3
> transparentBackground true

> volume #2 level 6.483

> save "/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure
> 4/Barrel_fitted_cryoET_map_side2.tif" width 2500 height 2094 supersample 3
> transparentBackground true

> save "/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure
> 4/Barrel_fitted_cryoET_map_top2.tif" width 2500 height 2094 supersample 3
> transparentBackground true

> save "/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure
> 4/Barrel_fitted_cryoET_map.cxs"

——— End of log from Fri Aug 4 16:39:05 2023 ———

opened ChimeraX session  

> graphics silhouettes true width 1

> graphics silhouettes false

> open "/Users/houghtf/Documents/Documents/barrel paper/Data/Figure
> 3/Tomography/postprocess_D5.mrc"

Opened postprocess_D5.mrc as #3, grid size 80,80,80, pixel 3.26, shown at
level 15.6, step 1, values float32  

> volume #3 level 5.6

> hide #!2 models

> hide #!1 models

> volume #3 color #919191

> volume #3 color #797979

> volume #3 color #919191

> lighting soft

> lighting full

> lighting shadows false

> lighting shadows true

> lighting shadows false

> save "/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure
> 4/Figure 4 supplementary/D5_map_top_view.png" width 2000 height 1474
> supersample 3 transparentBackground true

[Repeated 1 time(s)]

> volume #3 level 4.011

> save "/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure
> 4/Figure 4 supplementary/D5_map_top_view.png" width 2000 height 1474
> supersample 3 transparentBackground true

> volume #3 level 6.318

> save "/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure
> 4/Figure 4 supplementary/D5_map_side_view.png" width 2000 height 1474
> supersample 3 transparentBackground true

> volume #3 level 4.729

> save "/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure
> 4/Figure 4 supplementary/D5_map_top_view.png" width 2000 height 1474
> supersample 3 transparentBackground true

> transparency #3 40

> transparency #3 60

> hide #!3 models

> show #!3 models

> show #!1 models

> ui mousemode right "translate selected models"

> hide #!3 models

> show #!3 models

> select add #1

46489 atoms, 47072 bonds, 3 pseudobonds, 3049 residues, 2 models selected  

> view matrix models
> #1,0.99963,-0.0030275,-0.027213,110.16,0.0040774,0.99925,0.038609,101.69,0.027075,-0.038706,0.99888,-29.384

> view matrix models
> #1,0.99963,-0.0030275,-0.027213,108.61,0.0040774,0.99925,0.038609,109.69,0.027075,-0.038706,0.99888,80.045

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.99823,-0.0045389,0.059253,104.25,0.0025678,0.99944,0.0333,109.99,-0.059371,-0.033089,0.99769,82.132

> view matrix models
> #1,0.98492,0.0033303,0.173,98.539,0.022103,0.9892,-0.14488,118.92,-0.17161,0.14652,0.97421,81.487

> view matrix models
> #1,0.99277,-0.017764,0.11868,101.68,0.012706,0.99898,0.043241,109.24,-0.11933,-0.041421,0.99199,84.143

> view matrix models
> #1,0.75562,-0.6496,0.084038,125.79,0.63782,0.7589,0.13136,95.233,-0.14911,-0.045661,0.98777,85.218

> ui tool show "Fit in Map"

> fitmap #1 inMap #2

Fit molecule barrel.pdb (#1) to map postprocess.mrc (#2) using 46489 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 46489, contour level = 6.4828  
  
Position of barrel.pdb (#1) relative to postprocess.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.19827520 -0.73775716 0.64529165 40.29012050  
0.96933156 -0.24512634 0.01759003 355.31075172  
0.14520081 0.62898923 0.76373377 317.87111077  
Axis 0.32504447 0.26586846 0.90755719  
Axis point -133.46374530 96.89250027 0.00000000  
Rotation angle (degrees) 109.86675385  
Shift along axis 396.04821469  
  

> fitmap #1 inMap #2

Fit molecule barrel.pdb (#1) to map postprocess.mrc (#2) using 46489 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 46489, contour level = 6.4828  
  
Position of barrel.pdb (#1) relative to postprocess.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.19827520 -0.73775716 0.64529165 40.29012050  
0.96933156 -0.24512634 0.01759003 355.31075172  
0.14520081 0.62898923 0.76373377 317.87111077  
Axis 0.32504447 0.26586846 0.90755719  
Axis point -133.46374530 96.89250027 0.00000000  
Rotation angle (degrees) 109.86675385  
Shift along axis 396.04821469  
  

> fitmap #1 inMap #3

Fit molecule barrel.pdb (#1) to map postprocess_D5.mrc (#3) using 46489 atoms  
average map value = 12.98, steps = 52  
shifted from previous position = 6.1  
rotated from previous position = 3.64 degrees  
atoms outside contour = 2262, contour level = 4.7286  
  
Position of barrel.pdb (#1) relative to postprocess_D5.mrc (#3) coordinates:  
Matrix rotation and translation  
0.76128068 -0.64307053 0.08313854 127.23977321  
0.63943948 0.76580601 0.06825179 92.55169719  
-0.10755871 0.00120330 0.99419801 81.39406835  
Axis -0.05164161 0.14687748 0.98780572  
Axis point -43.68057914 221.09846877 0.00000000  
Rotation angle (degrees) 40.47914099  
Shift along axis 87.42442058  
  

> select subtract #1

Nothing selected  

> fitmap #1 inMap #3

Fit molecule barrel.pdb (#1) to map postprocess_D5.mrc (#3) using 46489 atoms  
average map value = 12.98, steps = 28  
shifted from previous position = 0.0663  
rotated from previous position = 0.0344 degrees  
atoms outside contour = 2265, contour level = 4.7286  
  
Position of barrel.pdb (#1) relative to postprocess_D5.mrc (#3) coordinates:  
Matrix rotation and translation  
0.76119496 -0.64324100 0.08260293 127.25214416  
0.63962916 0.76566310 0.06807753 92.62301550  
-0.10703627 0.00101497 0.99425460 81.38018517  
Axis -0.05164442 0.14603989 0.98792976  
Axis point -43.85158218 221.12303548 0.00000000  
Rotation angle (degrees) 40.48673266  
Shift along axis 87.35269780  
  

> volume #3 color #6c6091

> volume #3 color #6c6091c3

> volume #3 color #6d7691c3

> volume #3 color #6d76919d

> volume #3 color #7683919d

> volume #2 level 5.776

> volume #2 level 4.877

> volume #3 level 3.293

> volume #3 level 4.575

> hide #!2 models

> close #2

> volume #3 level 5.446

> volume #3 level 4.216

> save "/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure
> 4/Barrel_fitted_cryoET_map_top_D5.tif" width 2000 height 1474 supersample 3

> volume #3 color #95a2b29d

> volume #3 color #95a2b280

> volume #3 color #8995a380

> volume #3 color #8995a371

> volume #3 color #828d9b71

> volume #3 color #828d9b6a

> volume #3 color #828d9b6b

> save "/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure
> 4/Barrel_fitted_cryoET_map_top_D5.tif" width 936 height 690 supersample 3
> transparentBackground true

> save "/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure
> 4/Barrel_fitted_cryoET_map_top_D5.tif" width 2000 height 1474 supersample 3
> transparentBackground true

> select /R

1529 atoms, 1547 bonds, 96 residues, 1 model selected  

> select /L

1520 atoms, 1538 bonds, 97 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel sandy brown

> select clear

> volume #3 level 4.216

> save "/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure
> 4/Barrel_fitted_cryoET_map_side_D5_1.tif" width 2000 height 1474 supersample
> 3 transparentBackground true

> save "/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure
> 4/Barrel_fitted_cryoET_map_side_D5_2.tif" width 2000 height 1474 supersample
> 3 transparentBackground true

> hide #!1 models

> volume #3 level 4.626

> show #!1 models

> save "/Users/houghtf/Documents/Documents/barrel paper/Figures/Figure
> 4/Barrel_fitted_cryoET_map_D5.cxs" includeMaps true

——— End of log from Fri Sep 1 13:16:38 2023 ———

opened ChimeraX session  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache: 16 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 12.4 (21F79)
      Kernel Version: Darwin 21.5.0
      Time since boot: 90 days 4:56

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      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
        DELL U2415:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60.00Hz
          Mirror: Off
          Online: Yes


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    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: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    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-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Sessions
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash saving session including maps

comment:2 by Eric Pettersen, 2 years ago

Resolution: → can't reproduce
Status: assigned → closed
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