Opened 7 months ago

Last modified 7 months ago

#17228 closed defect

ChimeraX bug report submission — at Initial Version

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

Description 

The following bug report has been submitted:
Platform:        macOS-15.3.2-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.
Fatal Python error: Segmentation fault

Thread 0x0000000339ec7000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000000338ebb000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000000337eaf000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000000336ea3000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000000335e97000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000000334e8b000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000000333e7f000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000000332e73000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000000331e67000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000000330e5b000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000000032fe4f000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000000032481f000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000000323813000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00000001ff93c840 (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":"2025-03-28 10:04:35.00 +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 15.3.2 (24D81)","roots_installed":0,"name":"ChimeraX","incident_id":"57C8EE20-39AD-4EDD-9AD3-7C4721295343"}
{
  "uptime" : 250000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 502,
  "deployVersion" : 210,
  "modelCode" : "Mac14,9",
  "coalitionID" : 10461,
  "osVersion" : {
    "train" : "macOS 15.3.2",
    "build" : "24D81",
    "releaseType" : "User"
  },
  "captureTime" : "2025-03-28 10:04:17.3897 +0200",
  "codeSigningMonitor" : 1,
  "incident" : "57C8EE20-39AD-4EDD-9AD3-7C4721295343",
  "pid" : 10021,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-03-22 18:21:53.8563 +0200",
  "procStartAbsTime" : 1866520822782,
  "procExitAbsTime" : 6064418128088,
  "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":"798DEB1B-6975-57D8-A0B5-C478E0AEDC19","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "AFB027DA-CA90-91B1-5FBC-43F4DAD0B01C",
  "lowPowerMode" : 1,
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "bootSessionUUID" : "9D809F34-B7B5-4A21-B11E-CC6770304E22",
  "wakeTime" : 1,
  "sleepWakeUUID" : "DD3101CD-3A4B-4EEB-9668-58D3EE68BD8C",
  "sip" : "enabled",
  "vmRegionInfo" : "0x18 is not in any region.  Bytes before following region: 4377935848\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      104f20000-104f24000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":10021},
  "vmregioninfo" : "0x18 is not in any region.  Bytes before following region: 4377935848\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      104f20000-104f24000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6811549869},{"value":5234785304},{"value":16719952691970174127},{"value":0},{"value":6088908728},{"value":9129172737748017635},{"value":9129172741549025699},{"value":78},{"value":0},{"value":49},{"value":16},{"value":5719982080},{"value":536870912},{"value":328},{"value":8723620544},{"value":0},{"value":11},{"value":259},{"value":8582842656,"symbolLocation":224,"symbol":"_main_thread"},{"value":5182567536},{"value":5182567536},{"value":1},{"value":32769},{"value":32768},{"value":8582848904,"symbolLocation":0,"symbol":"_NSConcreteStackBlock"},{"value":0}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6811336560},"cpsr":{"value":1073745920},"fp":{"value":5234785104},"sp":{"value":5234785072},"esr":{"value":1442840704,"description":" Address size 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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=20.6G written=7051K(0%) resident=7051K(0%) swapped_out=0K(0%) unallocated=20.6G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               512K        4 \nActivity Tracing                   256K        1 \nCG image                          2512K      133 \nColorSync                          720K       37 \nCoreAnimation                     3616K      206 \nCoreGraphics                       256K       16 \nCoreServices                       624K        2 \nCoreUI image data                 5808K       58 \nFoundation                          48K        2 \nKernel Alloc Once                 1472K        6 \nMALLOC                            19.1G      323 \nMALLOC guard page                  288K       18 \nMach message                        64K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        944K       59 \nStack                            390.5M       60 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      458.8M      573 \nVM_ALLOCATE (reserved)           448.0M        4         reserved VM address space (unallocated)\n__AUTH                            5288K      672 \n__AUTH_CONST                      70.9M      921 \n__CTF                               824        1 \n__DATA                            34.8M     1125 \n__DATA_CONST                      34.7M     1137 \n__DATA_DIRTY                      2764K      343 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       643.3M      210 \n__OBJC_RW                         2374K        1 \n__TEXT                             1.3G     1157 \n__TPRO_CONST                       272K        2 \ndyld private memory                256K        1 \nmapped file                      637.6M      110 \nowned unmapped memory            201.0M        1 \npage table in kernel              7051K        1 \nshared memory                     3184K       26 \n===========                     =======  ======= \nTOTAL                             23.4G     7220 \nTOTAL, minus reserved VM space    22.9G     7220 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
  }
},
  "logWritingSignature" : "a337765b6da6d8feb4cf1b30ed96fc92861c360e",
  "trialInfo" : {
  "rollouts" : [
    {
      "rolloutId" : "6246d6a916a70b047e454124",
      "factorPackIds" : {

      },
      "deploymentId" : 240000010
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    {
      "rolloutId" : "64628732bf2f5257dedc8988",
      "factorPackIds" : {

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      "deploymentId" : 240000001
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  "experiments" : [

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}
===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
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  

> open "/Users/Monika/Downloads/DRT4 1.pdb" format pdb

Chain information for DRT4 1.pdb #1  
---  
Chain | Description  
A B C D E F | No description available  
G H I J K L | No description available  
  

> open
> /Users/Monika/Documents/retrons/DRT4/structure/g_DRT4_hexa_rnp_real_space_refined_001.pdb
> format pdb

Chain information for g_DRT4_hexa_rnp_real_space_refined_001.pdb #2  
---  
Chain | Description  
A B C D E F | No description available  
G H I J K L | No description available  
  

> hide #1 models

> set bgColor white

> hide #2 atoms

> show #2 cartoons

> dssp

> color #2 bynucleotide

> undo

Alignment identifier is 1  
Alignment identifier is 2  
Alignment identifier is 3  
Alignment identifier is 4  

> select #2/A-F:209

24 atoms, 18 bonds, 6 residues, 1 model selected  

> select #2/A-F:209-210

66 atoms, 66 bonds, 12 residues, 1 model selected  

> select
> #2/A-F:6-17,41-49,82-94,96-104,128-139,153-156,159-167,169-176,187-198,211-231,249-265,287-294,306-308,312-328,334-342,351-364,366-373,376-378,386-401,404-416,423-432,435-444,448-461,464-479,491-497

13596 atoms, 13770 bonds, 1644 residues, 1 model selected  

> select #2/A-F:205

24 atoms, 18 bonds, 6 residues, 1 model selected  

> select #2/A-F:205

24 atoms, 18 bonds, 6 residues, 1 model selected  

Populating font family aliases took 195 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.  

> rainbow sel

> select #1/A#2/A

12313 atoms, 12511 bonds, 1010 residues, 2 models selected  

> undo

> cartoon style sel modeHelix tube sides 20

> select #1/A#2/A

12313 atoms, 12511 bonds, 1010 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel rebecca purple

> color sel dark slate blue

> color sel slate blue

> color sel indigo

> color sel rebecca purple

> color sel dark magenta

> color sel purple

> color sel rebecca purple

> color sel blue violet

> color sel dark orchid

> color sel rebecca purple

> color sel blue violet

> color sel rebecca purple

> select #1/B#2/B

12313 atoms, 12511 bonds, 1010 residues, 2 models selected  

> select #1/C#2/C

12313 atoms, 12511 bonds, 1010 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel dark violet

> color sel blue violet

> color sel medium orchid

> color sel medium violet red

> color sel dark orchid

> color sel dark magenta

> color sel purple

> color sel medium violet red

> color sel medium orchid

> select #1/D#2/D

12313 atoms, 12511 bonds, 1010 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel pale violet red

> color sel thistle

> color sel pale violet red

> select #1/C#2/C

12313 atoms, 12511 bonds, 1010 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel deep pink

> color sel dark violet

> color sel hot pink

> color sel blue violet

> color sel orchid

> color sel medium orchid

> color sel medium violet red

> color sel medium orchid

> color sel dark orchid

> color sel medium orchid

> select #1/E#2/E

12313 atoms, 12511 bonds, 1010 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel violet

> color sel light pink

> color sel plum

> select #1/F#2/F

12313 atoms, 12511 bonds, 1010 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel medium purple

> select #1/D#2/D

12313 atoms, 12511 bonds, 1010 residues, 2 models selected  

> select #1/B#2/B

12313 atoms, 12511 bonds, 1010 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel rebecca purple

> color sel dark slate blue

> color sel blue violet

> ui tool show "Color Actions"

> color sel plum

> color sel violet

> color sel lavender

> color sel thistle

> color sel orchid

> color sel thistle

> ui tool show "Side View"

> graphics silhouettes true

> lighting soft

> lighting simple

> undo

> lighting soft

> lighting simple

> lighting soft

> lighting full

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting flat

> undo

> lighting full

> lighting soft

> ui tool show "Color Actions"

> color sel orchid

> color sel thistle

> color sel plum

> color sel lavender

> color sel pink

> ui tool show "Color Actions"

> color sel light coral

> color sel light pink

> color sel pale violet red

> set bgColor black

> set bgColor white

> select #1/C#2/C

12313 atoms, 12511 bonds, 1010 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel purple

> color sel dark magenta

> color sel dark orchid

> color sel blue violet

> color sel slate blue

> color sel indigo

> color sel medium purple

> color sel medium slate blue

> select #1/F#2/F

12313 atoms, 12511 bonds, 1010 residues, 2 models selected  

> select #1/E#2/E

12313 atoms, 12511 bonds, 1010 residues, 2 models selected  

> select #1/B#2/B

12313 atoms, 12511 bonds, 1010 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel plum

> color sel lavender

> color sel thistle

> color sel light pink

> select #1/G#2/G

400 atoms, 439 bonds, 15 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel dark slate gray

> color sel gold

> color sel orange

> color sel light salmon

> select #1/H#2/H

400 atoms, 439 bonds, 15 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel light salmon

> select #1/I#2/I

400 atoms, 439 bonds, 15 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel light salmon

> select #1/J#2/J

400 atoms, 439 bonds, 15 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel light salmon

> select #1/K#2/K

400 atoms, 439 bonds, 15 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel dark salmon

> color sel light salmon

> ui tool show "Color Actions"

> color sel light salmon

> select #1/L#2/L

400 atoms, 439 bonds, 15 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel light salmon

> deselect

Unknown command: deselect  

> select clear

> lighting soft

> graphics silhouettes false

> lighting full

> lighting soft

> save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster.cxs

> save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_fig3_1.tif
> width 936 height 768 supersample 3

> save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_fig3_2.tif
> width 704 height 543 supersample 3

> save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_fig3_3.tif
> width 920 height 723 supersample 3

> select #1/G#2/G

400 atoms, 439 bonds, 15 residues, 2 models selected  

> style sel & #2 stick

Changed 141 atom styles  

> show sel & #2 atoms

> hide sel & #2 cartoons

> show sel & #2 atoms

> style sel & #2 stick

Changed 141 atom styles  

> select #2/A-F:125

72 atoms, 72 bonds, 6 residues, 1 model selected  

> select #1/G#2/G

400 atoms, 439 bonds, 15 residues, 2 models selected  

> color sel & #2 byhetero

> interfaces select & #2 & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select #2/A-F:240

48 atoms, 42 bonds, 6 residues, 1 model selected  

> select #2/A-F:240-241

96 atoms, 90 bonds, 12 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 96 atom styles  

> color sel byhetero

> select #2/A-F:125

72 atoms, 72 bonds, 6 residues, 1 model selected  

> select #2/A-F:125

72 atoms, 72 bonds, 6 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 72 atom styles  

> color sel byhetero

> select #1/G-L:1

162 atoms, 174 bonds, 6 residues, 1 model selected  

> select #1/G-L:1

162 atoms, 174 bonds, 6 residues, 1 model selected  

> open "/Users/Monika/Downloads/DRT4 1.pdb" format pdb

Chain information for DRT4 1.pdb #3  
---  
Chain | Description  
A B C D E F | No description available  
G H I J K L | No description available  
  

> hide #2 models

> close #1

> hide #3 atoms

> show #3 cartoons

> select #2/G#3/G

400 atoms, 439 bonds, 15 residues, 2 models selected  

> show sel & #3 atoms

> hide sel & #3 atoms

> style sel & #3 stick

Changed 259 atom styles  

> style sel & #3 stick

Changed 259 atom styles  

> style sel & #3 stick

Changed 259 atom styles  

> color sel & #3 byhetero

> hide sel & #3 cartoons

> style sel & #3 stick

Changed 259 atom styles  

> show sel & #3 cartoons

> style sel & #3 stick

Changed 259 atom styles  

> show sel & #3 atoms

> style sel & #3 stick

Changed 259 atom styles  

> style sel & #3 stick

Changed 259 atom styles  

> style sel & #3 stick

Changed 259 atom styles  

> style sel & #3 stick

Changed 259 atom styles  

> nucleotides sel & #3 atoms

> style nucleic & sel & #3 stick

Changed 259 atom styles  

> nucleotides sel & #3 atoms

> style nucleic & sel & #3 stick

Changed 259 atom styles  

> style sel & #3 ball

Changed 259 atom styles  

> open
> /Users/Monika/Downloads/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_summary_confidences_0.json

Failed opening file
/Users/Monika/Downloads/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_summary_confidences_0.json:  
fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_summary_confidences_0.json
does not look like Mole Online json file, does not contain Channels.  

> select #2/A-F:125

72 atoms, 72 bonds, 6 residues, 1 model selected  

> select #2/A-F:125-126

126 atoms, 126 bonds, 12 residues, 1 model selected  

> select #2/A-F:125

72 atoms, 72 bonds, 6 residues, 1 model selected  

> select #2/A-F:128-129

84 atoms, 78 bonds, 12 residues, 1 model selected  

> select #2/A-F:124-129

306 atoms, 306 bonds, 36 residues, 1 model selected  

> select add #3

50892 atoms, 51630 bonds, 3114 residues, 2 models selected  

> select #2/A-F:125-126

126 atoms, 126 bonds, 12 residues, 1 model selected  

> select #2/A-F:125

72 atoms, 72 bonds, 6 residues, 1 model selected  

> select
> #2/A-F:6-17,41-49,82-94,96-104,128-139,153-156,159-167,169-176,187-198,211-231,249-265,287-294,306-308,312-328,334-342,351-364,366-373,376-378,386-401,404-416,423-432,435-444,448-461,464-479,491-497

13596 atoms, 13770 bonds, 1644 residues, 1 model selected  

> select #2/A-F:125-126

126 atoms, 126 bonds, 12 residues, 1 model selected  

> select #2/A-F:125-126

126 atoms, 126 bonds, 12 residues, 1 model selected  

> select #2/A-F:125

72 atoms, 72 bonds, 6 residues, 1 model selected  

> select
> #2/A-F:6-17,41-49,82-94,96-104,128-139,153-156,159-167,169-176,187-198,211-231,249-265,287-294,306-308,312-328,334-342,351-364,366-373,376-378,386-401,404-416,423-432,435-444,448-461,464-479,491-497

13596 atoms, 13770 bonds, 1644 residues, 1 model selected  

> select #2/A-F:125

72 atoms, 72 bonds, 6 residues, 1 model selected  

> select #2/A-F:125

72 atoms, 72 bonds, 6 residues, 1 model selected  

> select add #2

25692 atoms, 26382 bonds, 3072 residues, 1 model selected  

> select subtract #2

Nothing selected  

> select add #3

50586 atoms, 51324 bonds, 3078 residues, 1 model selected  

> select #2/A-F:125

72 atoms, 72 bonds, 6 residues, 1 model selected  

> select #2/A-F:125

72 atoms, 72 bonds, 6 residues, 1 model selected  

> select add #2

25692 atoms, 26382 bonds, 3072 residues, 1 model selected  

> select subtract #2

Nothing selected  

> select
> #2/A-F:6-17,41-49,82-94,96-104,128-139,153-156,159-167,169-176,187-198,211-231,249-265,287-294,306-308,312-328,334-342,351-364,366-373,376-378,386-401,404-416,423-432,435-444,448-461,464-479,491-497

13596 atoms, 13770 bonds, 1644 residues, 1 model selected  

> show #2 models

> hide #2 models

Alignment identifier is 1  

> select #2/A-F:125

72 atoms, 72 bonds, 6 residues, 1 model selected  

> select #2/A-F:125

72 atoms, 72 bonds, 6 residues, 1 model selected  

> select #2/A-F:204

60 atoms, 60 bonds, 6 residues, 1 model selected  

> select #2/A-F:204-206

126 atoms, 126 bonds, 18 residues, 1 model selected  

> select add #2

25692 atoms, 26382 bonds, 3072 residues, 1 model selected  

> select subtract #2

Nothing selected  

> select add #3

50586 atoms, 51324 bonds, 3078 residues, 1 model selected  

> select subtract #3

Nothing selected  

> select add #3

50586 atoms, 51324 bonds, 3078 residues, 1 model selected  

> select subtract #3

Nothing selected  

> select add #3

50586 atoms, 51324 bonds, 3078 residues, 1 model selected  

> select subtract #3

Nothing selected  

> select add #3

50586 atoms, 51324 bonds, 3078 residues, 1 model selected  

> select :125

210 atoms, 210 bonds, 12 residues, 2 models selected  

> style sel & #3 stick

Changed 138 atom styles  

> nucleotides sel & #3 atoms

> style nucleic & sel & #3 stick

Changed 0 atom styles  

> show sel & #3 atoms

Alignment identifier is 1  
Alignment identifier is 2  
Alignment identifier is 1  
Alignment identifier is 3  

> select #3/G

259 atoms, 282 bonds, 8 residues, 1 model selected  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 259 atom styles  

> style sel stick

Changed 259 atom styles  

> style sel ball

Changed 259 atom styles  

> style sel sphere

Changed 259 atom styles  

> style sel ball

Changed 259 atom styles  

> style sel stick

Changed 259 atom styles  

> show sel atoms

> style sel stick

Changed 259 atom styles  

> show sel atoms

> hide sel cartoons

> select #3/C

8172 atoms, 8271 bonds, 505 residues, 1 model selected  

> open
> /Users/Monika/Documents/retrons/DRT4/structure/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_summary_confidences_1.json

Failed opening file
/Users/Monika/Documents/retrons/DRT4/structure/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_summary_confidences_1.json:  
fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_summary_confidences_1.json
does not look like Mole Online json file, does not contain Channels.  

> open
> /Users/Monika/Documents/retrons/DRT4/structure/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_model_0.cif

Chain information for
fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_model_0.cif #1  
---  
Chain | Description  
A B C D E F | .  
G H I J K L | .  
M N O P Q R | .  
  

> open
> /Users/Monika/Documents/retrons/DRT4/structure/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_model_0.cif

Chain information for
fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_model_0.cif #4  
---  
Chain | Description  
A B C D E F | .  
G H I J K L | .  
M N O P Q R | .  
  

> open
> /Users/Monika/Documents/retrons/DRT4/structure/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_model_0.cif

Chain information for
fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_model_0.cif #5  
---  
Chain | Description  
A B C D E F | .  
G H I J K L | .  
M N O P Q R | .  
  

> hide #3 models

> hide #1 models

> hide #4 models

> hide #5 models

> show #4 models

> open
> /Users/Monika/Documents/retrons/DRT4/structure/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_summary_confidences_4.json

Failed opening file
/Users/Monika/Documents/retrons/DRT4/structure/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_summary_confidences_4.json:  
fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_summary_confidences_4.json
does not look like Mole Online json file, does not contain Channels.  

> show #1 models

> hide #4 models

> hide #1 models

> show #3 models

> select :G-L

42984 atoms, 39690 bonds, 4842 residues, 5 models selected  

> select :.G-L

Expected an objects specifier or a keyword  

> select :.G-L

Expected an objects specifier or a keyword  

> select #3/G

259 atoms, 282 bonds, 8 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light salmon

> select #3/H

259 atoms, 282 bonds, 8 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light salmon

> select #3/I

259 atoms, 282 bonds, 8 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light salmon

> select #3/J

259 atoms, 282 bonds, 8 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light salmon

> ui tool show "Color Actions"

> color sel light salmon

> select #3/L

259 atoms, 282 bonds, 8 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light salmon

> select #3/L

259 atoms, 282 bonds, 8 residues, 1 model selected  

> select #3/K

259 atoms, 282 bonds, 8 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light salmon

> select #3/A

8172 atoms, 8271 bonds, 505 residues, 1 model selected  

> close #1

> close #4

> close #5

> show #2 models

> hide #3 models

> select #2/A

4141 atoms, 4240 bonds, 505 residues, 1 model selected  

> ui tool show "Color Actions"

> hide #2 models

> show #3 models

> select #3/A

8172 atoms, 8271 bonds, 505 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel dark violet

> color sel purple

> color sel rebecca purple

> color sel dark slate blue

> color sel dark violet

> color sel blue violet

> color sel dark magenta

> color sel purple

> color sel dark violet

> select #3/B

8172 atoms, 8271 bonds, 505 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel medium purple

> color sel midnight blue

> color sel medium blue

> color sel blue

> color sel royal blue

> color sel slate blue

> color sel dark slate blue

> color sel slate blue

> color sel medium slate blue

> select #3/C

8172 atoms, 8271 bonds, 505 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel pale violet red

> select add #3

50586 atoms, 51324 bonds, 3078 residues, 1 model selected  

> select subtract #3

Nothing selected  

> cartoon style #3 modeHelix tube sides 20

> lighting soft

> select add #3

50586 atoms, 51324 bonds, 3078 residues, 1 model selected  

> lighting soft

> graphics silhouettes true

> graphics silhouettes false

> lighting soft

> lighting full

> lighting soft

> show #2 models

> hide #3 models

> show #3 models

> hide #2 models

> select #3/A

8172 atoms, 8271 bonds, 505 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel medium purple

> color sel purple

> color sel rebecca purple

> select #3/D

8172 atoms, 8271 bonds, 505 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel thistle

> color sel plum

> select #3/F

8172 atoms, 8271 bonds, 505 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel lavender

> color sel plum

> color sel thistle

> color sel light pink

> ui tool show "Color Actions"

> color sel plum

> color sel lavender

> color sel thistle

> color sel medium purple

> color sel medium slate blue

> color sel medium purple

> select #3/E

8172 atoms, 8271 bonds, 505 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel thistle

> select add #3

50586 atoms, 51324 bonds, 3078 residues, 1 model selected  

> select subtract #3

Nothing selected  

> select #3/G

259 atoms, 282 bonds, 8 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select add #3

50586 atoms, 51324 bonds, 3078 residues, 1 model selected  

> select subtract #3

Nothing selected  

> save /Users/Monika/Desktop/image1.png supersample 3

> save /Users/Monika/Desktop/image2.png supersample 3

> save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_fig3_1.tif
> width 776 height 507 supersample 3

> save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_fig3_2.tif
> width 776 height 507 supersample 3

> save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_fig3_3.tif
> width 776 height 507 supersample 3

> select #3/G

259 atoms, 282 bonds, 8 residues, 1 model selected  

> show sel atoms

> hide sel cartoons

> style sel stick

Changed 259 atom styles  

> style sel ball

Changed 259 atom styles  

> style sel ball

Changed 259 atom styles  

> style sel stick

Changed 259 atom styles  

> color sel byhetero

> select
> #3/A-F:6-16,41-49,82-94,96-102,128-138,153-156,159-167,169-176,187-198,211-230,249-265,287-294,305-307,312-328,334-342,351-364,366-374,376-378,386-401,404-417,423-432,435-444,448-461,464-479,491-497

26826 atoms, 26994 bonds, 1626 residues, 1 model selected  

> select add #3

50586 atoms, 51324 bonds, 3078 residues, 1 model selected  

> select subtract #3

Nothing selected  

> ui mousemode right select

> select add #3/A:125@O2P

1 atom, 2 bonds, 1 residue, 1 model selected  

> select add #3/A:357

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

> select add #3/A:125@HB2

23 atoms, 31 bonds, 2 residues, 1 model selected  

> select #3/A:357

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

> select add #3/A:125@HD1

1 atom, 1 bond, 1 residue, 1 model selected  

> select add #3/A:125@HE1

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

> select add #3/A:125@HB3

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

> select add #3/A:125@HD2

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

> select add #3/A:125@HE2

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

> select add #3/A:125@HB2

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

> select add #3/A:125@O2P

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

> select add #3/A:125@O3P

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

> color sel byhetero

> select #3/A-F:240

72 atoms, 66 bonds, 6 residues, 1 model selected  

> select #3/A-F:240-241

144 atoms, 138 bonds, 12 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 144 atom styles  

> color sel byhetero

> ui tool show "Side View"

> select add #3

50586 atoms, 51324 bonds, 3078 residues, 1 model selected  

> select subtract #3

Nothing selected  

> select #3/G

259 atoms, 282 bonds, 8 residues, 1 model selected  

> show sel cartoons

> show sel atoms

> hide sel atoms

> select clear

> select #3/G:1

27 atoms, 29 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel cartoons

> view sel

> view

> ui tool show "Side View"

> select #3/G

259 atoms, 282 bonds, 8 residues, 1 model selected  

> show sel atoms

> hide sel cartoons

> graphics silhouettes true

> select add #3

50586 atoms, 51324 bonds, 3078 residues, 1 model selected  

> select subtract #3

Nothing selected  

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> select #3/G

259 atoms, 282 bonds, 8 residues, 1 model selected  

> graphics silhouettes true

> graphics silhouettes false

> style sel stick

Changed 259 atom styles  

> style sel stick

Changed 259 atom styles  

> style sel stick

Changed 259 atom styles  

> show sel atoms

> style sel stick

Changed 259 atom styles  

> color sel byhetero

> style sel ball

Changed 259 atom styles  

> style sel stick

Changed 259 atom styles  

> select add #3

50586 atoms, 51324 bonds, 3078 residues, 1 model selected  

> select subtract #3

Nothing selected  

> select #3/G

259 atoms, 282 bonds, 8 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> show sel atoms

> hide sel atoms

> show sel atoms

> hide sel cartoons

> select down

259 atoms, 282 bonds, 8 residues, 1 model selected  

> view sel

> select add #3

50586 atoms, 51324 bonds, 3078 residues, 1 model selected  

> select subtract #3

Nothing selected  

> save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_fig3_4.tif
> width 987 height 643 supersample 3

> save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_fig3_4_1.tif
> width 987 height 643 supersample 3

> select #3/G

259 atoms, 282 bonds, 8 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select #3/A-F:125

138 atoms, 138 bonds, 6 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select add #3

50586 atoms, 51324 bonds, 3078 residues, 1 model selected  

> select subtract #3

Nothing selected  

> save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_fig3_5.tif
> width 987 height 643 supersample 3

> save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_fig3_6.png
> width 987 height 602 supersample 3

> open
> /Users/Monika/Documents/retrons/DRT4/structure/cryosparc_P12_J29_006_volume_map.mrc

Opened cryosparc_P12_J29_006_volume_map.mrc as #1, grid size 400,400,400,
pixel 1.1, shown at level 0.0462, step 2, values float32  

> volume #1 level 0.7081

> close #1

> open
> /Users/Monika/Documents/retrons/DRT4/structure/DRT4emready_P12_J29_006_volume.mrc

Opened DRT4emready_P12_J29_006_volume.mrc as #1, grid size 439,439,439, pixel
1, shown at level 0.000799, step 2, values float32  

> volume #1 level 1.402

> volume #1 level 4.629

> hide #3 models

> volume #1 level 1.954

> hide #!1 models

> show #3 models

Drag select of 52 residues  
Drag select of 39 residues  

> open
> /Users/Monika/Documents/retrons/DRT4/structure/cryosparc_P12_J31_005_volume_map_sharp.mrc

Opened cryosparc_P12_J31_005_volume_map_sharp.mrc as #4, grid size
400,400,400, pixel 1.1, shown at level 1.05, step 2, values float32  

> volume #1 level 3.568

> hide #3 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!4 models

> show #!1 models

> volume #4 level 1.496

> hide #!4 models

> volume #1 level 3.016

> select #1

3 models selected  

> volume #1 level 2.846

> lighting soft

> show #3 models

> hide #3 models

> close #4

> volume #1 level 3.738

> show #2 models

> volume #1 color #b2b2b268

> volume #1 color #b2b2b269

> volume #1 level 6.158

> volume #1 level 2.761

> hide #!1 models

> hide #2 models

> show #3 models

> show #!1 models

> hide #!1 models

> save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_V2.cxs

> show #!1 models

> hide #3 models

> volume #1 level 3.355

> volume #1 color #b2b2b2

> volume #1 level 2.124

> volume #1 level 1.147

> volume #1 level 1.19

> select add #1

4 models selected  

> select subtract #1

Nothing selected  

> volume #1 level 1.232

> show #3 models

> volume #1 level 1.02

> volume #1 color #b2b2b275

> color zone #1 near #3 distance 2.5

> color zone #1 near #3 distance 3

> color zone #1 near #3 distance 3.5

> select #2/G#3/G

400 atoms, 439 bonds, 15 residues, 2 models selected  

> nucleotides sel & #3 atoms

> style nucleic & sel & #3 stick

Changed 259 atom styles  

> show sel & #3 atoms

> hide sel & #3 atoms

> show sel & #3 cartoons

> color sel & #3 byhetero

> color sel & #3 bychain

> hide #!1 models

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> show #!1 models

> color zone #1 near sel & #3 distance 6

> undo

> hide #!1 models

> ui tool show "Color Actions"

> color sel light salmon

> show #!1 models

> hide #!1 models

> show #!1 models

> volume #1 level 1.657

> color sel & #3 bychain

> hide #!1 models

> select add #3

50727 atoms, 51481 bonds, 3085 residues, 2 models selected  

> select subtract #3

141 atoms, 157 bonds, 7 residues, 1 model selected  

> select #3/G

259 atoms, 282 bonds, 8 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light salmon

> select add #3

50586 atoms, 51324 bonds, 3078 residues, 1 model selected  

> select subtract #3

Nothing selected  

> show #!1 models

> volume #1 step 1

> hide #3 models

> hide #!1 models

> show #3 models

> show #2 models

> hide #2 models

> color #3 /g light salmon

> show #!1 models

> color zone #1 near #3 distance 4

> color #1 light grey

> color zone #1 near #3 distance 4

> hide #3 models

> show #3 models

> hide #!1 models

> show #3 atoms

> show #!1 models

> hide #3 models

> volume #1 level 1.84

> volume #1 level 1.52

> show #3 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> style #3 ball

Changed 50586 atom styles  

> hide #3 models

> show #3 models

> hide #!1 models

> select #3/A:125@CG

1 atom, 1 residue, 1 model selected  

> select add #3

50586 atoms, 51324 bonds, 3078 residues, 1 model selected  

> hide sel atoms

> show sel atoms

> select #3/A:125@CZ

1 atom, 1 residue, 1 model selected  

> select add #3/A:125@CA

2 atoms, 1 residue, 1 model selected  

> select add #3/A:125@CB

3 atoms, 1 bond, 1 residue, 1 model selected  

> select add #3/A:125@HB2

4 atoms, 1 bond, 1 residue, 1 model selected  

> select add #3/A:125@CD1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select add #3/A:125@HD1

6 atoms, 4 bonds, 1 residue, 1 model selected  

> select add #3/A:125@CG

7 atoms, 4 bonds, 1 residue, 1 model selected  

> select add #3/A:125@CD2

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

> select add #3/A:125@CE2

9 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #3/A:125@HE2

10 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #3/A:125@CE1

11 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #3/A:125@HE1

12 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #3/A:125@OH

13 atoms, 9 bonds, 1 residue, 1 model selected  

> select add #3/A:125@P

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

> select add #3/A:125@O3P

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

> select add #3/A:125@O2P

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

> select add #3/A:125@O1P

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

> color sel byhetero

> color sel bychain

> select add #3/A:125@HB3

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

> select add #3/A:125@HD2

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

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> show sel atoms

> hide sel atoms

> show sel atoms

> show sel cartoons

> show sel atoms

> ui tool show "Color Actions"

> color sel rebecca purple

> show #!1 models

> style sel ball

Changed 19 atom styles  

> style sel stick

Changed 19 atom styles  

> color sel bychain

> hide #3 models

> show #3 models

> hide #!1 models

> ui tool show "Color Actions"

> color sel rebecca purple

> style sel ball

Changed 19 atom styles  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> show #!1 models

> hide #!1 models

> color zone #1 near #3/A PTR 125 distance 4

Expected a keyword  

> color zone #1 near #3/A :125 distance 4

> show #!1 models

> color zone #1 near #3 distance 4

> hide #3 models

Drag select of 1 DRT4emready_P12_J29_006_volume.mrc  

> select clear

> color zone #1 near #3 distance 4.5

> color zone #1 near #3 distance 5

> color zone #1 near #3 distance 5.5

> volume #1 level 1.84

> volume #1 level 1.794

> save /Users/Monika/Documents/retrons/DRT4/structure/cryoemmap_1.tif models
> #1 format imagejtiff

> save /Users/Monika/Documents/retrons/DRT4/structure/cryoemmap_2.tif models
> #1 format imagejtiff

> show #3 models

> select add #3

50586 atoms, 51324 bonds, 3078 residues, 1 model selected  

> style sel stick

Changed 50586 atom styles  

> volume #1 color #d3d3d3c3

> volume #1 color #d3d3d39a

> volume #1 color #d3d3d399

> volume #1 color #d3d3d396

> volume #1 color #d3d3d395

> volume #1 color #d3d3d394

> select subtract #3

Nothing selected  

> volume #1 level 0.652

> volume #1 color #d3d3d35c

> select add #1

4 models selected  

> graphics silhouettes true

> graphics silhouettes false

> select subtract #1

Nothing selected  

> select add #3

50586 atoms, 51324 bonds, 3078 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> select subtract #3

Nothing selected  

> select #3/G

259 atoms, 282 bonds, 8 residues, 1 model selected  

> hide #!1 models

> show sel atoms

> color sel byhetero

> hide sel cartoons

> show #!1 models

> volume #1 color #ffffff5c

> volume #1 color #c3c3c35c

> volume #1 color #c3c3c31b

> volume #1 color #c3c3c31c

> color zone #1 near #3 distance 5.5

> undo

> show sel cartoons

> hide sel atoms

> color zone #1 near #3 distance 5.5

Drag select of 37 residues, 1 DRT4emready_P12_J29_006_volume.mrc  

> select add #1

570 atoms, 34 residues, 5 models selected  

> select add #3

50586 atoms, 51324 bonds, 3078 residues, 5 models selected  

> select subtract #3

4 models selected  

> select subtract #1

Nothing selected  

> color zone #1 near #3 distance 6

> color zone #1 near #3 distance 3

> color zone #1 near #3 distance 5

> color zone #1 near #3 distance 6

> volume #1 level 2.707

> volume #1 level 2.388

> volume #1 level 2.159

> volume #1 level 1.291

> hide #3 models

> volume #1 level 0.9718

Drag select of 1 DRT4emready_P12_J29_006_volume.mrc  

> select add #1

4 models selected  

> select subtract #1

Nothing selected  

> volume #1 level 1.246

> volume #1 step 2

> volume #1 step 1

Drag select of 1 DRT4emready_P12_J29_006_volume.mrc  

> ui tool show "Side View"

> select add #1

4 models selected  

> select subtract #1

Nothing selected  

> save /Users/Monika/Documents/retrons/DRT4/structure/cryoemmap_1.tif models
> #1 format imagejtiff

> save /Users/Monika/Documents/retrons/DRT4/structure/cryomemap.png width 987
> height 602 supersample 3

> show #3 models

> hide #!1 models

> show #!1 models

> hide #3 models

> save /Users/Monika/Documents/retrons/DRT4/structure/cryomemap2.png width 987
> height 602 supersample 3

> open
> /Users/Monika/Documents/retrons/DRT4/structure/fold_2025_03_27_17_32_no_atp/fold_2025_03_27_17_32_no_atp_model_0.cif

Summary of feedback from opening
/Users/Monika/Documents/retrons/DRT4/structure/fold_2025_03_27_17_32_no_atp/fold_2025_03_27_17_32_no_atp_model_0.cif  
---  
note | Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif  
  
Chain information for fold_2025_03_27_17_32_no_atp_model_0.cif #4  
---  
Chain | Description  
A B C D E F | .  
G H I J K L | .  
S T U V W X | .  
  

> hide #!1 models

> color byattribute

Missing or invalid "attrName" argument: Expected a text string  

> color bfactor

117018 atoms, 11040 residues, atom bfactor range 12.6 to 224  

> show #4 cartoons

> hide #4 atoms

> color bfactor #4

40740 atoms, 4890 residues, atom bfactor range 12.6 to 96.3  

> undo

> alphafold

Unknown command: palette alphafold  

> color byattributee

Missing or invalid "attrName" argument: Expected a text string  

> color byattribute bfactor /A range 0,100

16735 atoms, 1550 residues, atom bfactor range 29.2 to 224  

> color byattribute bfactor

117018 atoms, 11040 residues, atom bfactor range 12.6 to 224  

> show #!1 models

> hide #4 models

> save
> /Users/Monika/Documents/retrons/DRT4/structure/fold_2025_03_27_17_32_no_atp/DRT4_J29_cryoEM_map_coloured.cxs

> hide #!1 models

> show #4 models

> ui tool show "Color Actions"

Alignment identifier is 1  
Alignment identifier is 3  
Alignment identifier is 4  
Alignment identifier is 5  
Alignment identifier is 6  
Alignment identifier is 7  
Alignment identifier is 8  

> close #4

> open
> /Users/Monika/Documents/retrons/DRT4/structure/AF/fold_2025_03_27_17_53_6_atps_12MG/fold_2025_03_27_17_53_6_atps_model_0.cif

Summary of feedback from opening
/Users/Monika/Documents/retrons/DRT4/structure/AF/fold_2025_03_27_17_53_6_atps_12MG/fold_2025_03_27_17_53_6_atps_model_0.cif  
---  
note | Fetching CCD ATP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ATP/ATP.cif  
  
Chain information for fold_2025_03_27_17_53_6_atps_model_0.cif #4  
---  
Chain | Description  
A B C D E F | .  
EA FA GA HA IA JA | .  
G H I J K L | .  
  

> show #4 surfaces

> show #!4 cartoons

> hide #!4 surfaces

> hide #!4 atoms

> close #4

> open
> /Users/Monika/Documents/retrons/DRT4/structure/AF/fold_2025_03_27_17_53_6_atps_12MG/fold_2025_03_27_17_53_6_atps_model_1.cif

Chain information for fold_2025_03_27_17_53_6_atps_model_1.cif #4  
---  
Chain | Description  
A B C D E F | .  
EA FA GA HA IA JA | .  
G H I J K L | .  
  

> show #4 cartoons

> hide #4 atoms

> color bfactor #4

40932 atoms, 4902 residues, atom bfactor range 16 to 97.5  

> color bfactor #4

40932 atoms, 4902 residues, atom bfactor range 16 to 97.5  

> undo

> color bfactor #4

40932 atoms, 4902 residues, atom bfactor range 16 to 97.5  

> rangecolor bfactor key 100 blue 50 white 0 red

Unknown command: rangecolor bfactor key 100 blue 50 white 0 red  

> bfactor key 100 blue 50 white 0 red

Unknown command: bfactor key 100 blue 50 white 0 red  

> ui tool show "Color Actions"

> undo

> open
> /Users/Monika/Documents/retrons/DRT4/structure/AF/fold_2025_03_27_17_53_6_atps_12MG/fold_2025_03_27_17_53_6_atps_model_2.cif

Chain information for fold_2025_03_27_17_53_6_atps_model_2.cif #5  
---  
Chain | Description  
A B C D E F | .  
EA FA GA HA IA JA | .  
G H I J K L | .  
  

> hide #4 models

> show #5 cartoons

> hide #5 atoms

> hide #5 models

> close #4

> close #5

> open
> /Users/Monika/Documents/retrons/DRT4/structure/AF/fold_2025_03_27_17_53_6_atps_12MG/fold_2025_03_27_17_53_6_atps_model_0.cif

Chain information for fold_2025_03_27_17_53_6_atps_model_0.cif #4  
---  
Chain | Description  
A B C D E F | .  
EA FA GA HA IA JA | .  
G H I J K L | .  
  

Unsupported scale factor (0.000000) detected on Display0  

QPainter::begin: Paint device returned engine == 0, type: 3  


===== Log before crash end =====

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
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 - 89.3
OpenGL renderer: Apple M2 Pro
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 Pro
      Model Identifier: Mac14,9
      Model Number: MPHE3ZE/A
      Chip: Apple M2 Pro
      Total Number of Cores: 10 (6 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.81.4
      OS Loader Version: 11881.81.4

Software:

    System Software Overview:

      System Version: macOS 15.3.2 (24D81)
      Kernel Version: Darwin 24.3.0
      Time since boot: 8 days, 22 hours, 9 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


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-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-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

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