Crash in garbage collection

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-12.6.1-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x0000000316462000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x0000000202be2600 (most recent call first):
  Garbage-collecting
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in 
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in __iter__
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py", line 77 in assign_charges
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/cmd.py", line 99 in cmd_coulombic
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 525 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 582 in run_expanded_command
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 72 in func_plus_tip
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 339 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 420 in run_shortcut
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 402 in try_shortcut
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 1376 in run_provider
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py", line 66 in run_provider
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 205 in callback
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 60)


{"app_name":"ChimeraX","timestamp":"2024-03-29 14:09:05.00 -0700","app_version":"1.7.1","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.7.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.6.1 (21G217)","incident_id":"F35518E3-B2B5-4B1D-B3A4-0F9D47E530B6","name":"ChimeraX"}
{
  "uptime" : 140000,
  "procLaunch" : "2024-03-29 13:55:02.6519 -0700",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,2",
  "procStartAbsTime" : 3561855061761,
  "coalitionID" : 19635,
  "osVersion" : {
    "train" : "macOS 12.6.1",
    "build" : "21G217",
    "releaseType" : "User"
  },
  "captureTime" : "2024-03-29 14:09:03.8705 -0700",
  "incident" : "F35518E3-B2B5-4B1D-B3A4-0F9D47E530B6",
  "bug_type" : "309",
  "pid" : 95174,
  "procExitAbsTime" : 3582043487754,
  "translated" : true,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"3963FDE2-4226-5C97-BDB6-0409F41D3D50","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "1B4A0CC3-B743-B7C2-04B9-60B5BB2A8FBE",
  "wakeTime" : 2962,
  "sleepWakeUUID" : "B32CD086-E0D2-4F0E-B88A-CF04D69DEE6B",
  "sip" : "enabled",
  "vmRegionInfo" : "0xa9 is not in any region.  Bytes before following region: 140722896994135\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffc9a498000-7ffc9aad4000 [ 6384K] r-x\/r-x SM=COW  ...ct_id=a919cc7",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
  "vmregioninfo" : "0xa9 is not in any region.  Bytes before following region: 140722896994135\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffc9a498000-7ffc9aad4000 [ 6384K] r-x\/r-x SM=COW  ...ct_id=a919cc7",
  "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" : 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    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 5246976,
    "uuid" : "bddb824d-15df-3210-88e8-6aac5c154403",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "1866"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703611842560,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 15269888,
    "uuid" : "d2726161-3c3f-3b59-bd8d-4a088d4545ef",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2113.60.148"
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],
  "sharedCache" : {
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  "size" : 19331678208,
  "uuid" : "47e1dd7d-5e37-3ec3-a85c-901263ec66b5"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=3.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.3G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               640K        5 \nActivity Tracing                   256K        1 \nCG backing stores                 4032K        4 \nCG image                           828K       72 \nColorSync                          232K       28 \nCoreAnimation                     2580K      188 \nCoreGraphics                        12K        2 \nCoreServices                       256K        1 \nCoreUI image data                 5004K       37 \nFoundation                          36K        2 \nKernel Alloc Once                    8K        1 \nMALLOC                             1.4G      324 \nMALLOC guard page                  192K        9 \nMALLOC_MEDIUM (reserved)         952.0M       10         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           128.0M        1         reserved VM address space (unallocated)\nMach message                        16K        4 \nOpenGL GLSL                        384K        4 \nRosetta Arena                     4096K        2 \nRosetta Generic                   1620K      402 \nRosetta IndirectBranch            2048K        1 \nRosetta JIT                      128.0M        1 \nRosetta Return Stack               800K       80 \nRosetta Thread Context             800K       80 \nSTACK GUARD                         44K       11 \nStack                            170.7M       40 \nStack Guard                       56.1M       29 \nVM_ALLOCATE                      224.1M      360 \nVM_ALLOCATE (reserved)           224.1M       11         reserved VM address space (unallocated)\n__CTF                               756        1 \n__DATA                            46.6M      690 \n__DATA_CONST                      31.4M      347 \n__DATA_DIRTY                      1662K      219 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       736.7M      164 \n__OBJC_RO                         82.8M        1 \n__OBJC_RW                         3200K        2 \n__TEXT                           810.2M      692 \n__UNICODE                          592K        1 \ndyld private memory               1184K        3 \nmapped file                        5.4G     1201 \nshared memory                     3008K       23 \nunshared pmap                     12.2M        9 \n===========                     =======  ======= \nTOTAL                             10.3G     5065 \nTOTAL, minus reserved VM space     9.1G     5065 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
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},
  "trialInfo" : {
  "rollouts" : [
    {
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      "factorPackIds" : {

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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  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1kqg format mmcif fromDatabase pdb

1kqg title:  
Formate dehydrogenase N from E. Coli [more info...]  
  
Chain information for 1kqg #1  
---  
Chain | Description | UniProt  
A | FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, MAJOR SUBUNIT | FDNG_ECOLI
1-1015  
B | FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, IRON-SULFUR SUBUNIT | FDNH_ECOLI
1-294  
C | FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, CYTOCHROME B556(FDN) SUBUNIT |
FDNI_ECOLI 1-217  
  
Non-standard residues in 1kqg #1  
---  
6MO — molybdenum(VI) ion  
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)  
HEM — protoporphyrin IX containing Fe (HEME)  
HQO — 2-heptyl-4-hydroxy quinoline N-oxide (2-heptyl-1-oxy-quinolin-4-ol)  
MGD —
2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-
anthracen-4-one guanosine dinucleotide (molybdopterin guanosine dinucleotide)  
SEC — selenocysteine  
SF4 — iron/sulfur cluster  
  
1kqg mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> open /Users/jill/Documents/Borg_multi_copy_gene_AP2/Ruby_pdb/FINAL-
> manually_curated_Ruby-bin53_Illumina_curated_805_Ruby_Borg_SR-
> VP_9_9_2021_75_5A_0_95m_2_SR-VP_9_9_2021_87_5B_1_2m_curated_SR-
> VP_9_9_2021_87_5B_1_2m_2___656632___656853___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/Ruby_pdb/FINAL-
> manually_curated_Ruby-bin53_Illumina_curated_806_Ruby_Borg_SR-
> VP_9_9_2021_75_5A_0_95m_2_SR-VP_9_9_2021_87_5B_1_2m_curated_SR-
> VP_9_9_2021_87_5B_1_2m_2___656871___657014___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/Ruby_pdb/FINAL-
> manually_curated_Ruby-bin53_Illumina_curated_808_Ruby_Borg_SR-
> VP_9_9_2021_75_5A_0_95m_2_SR-VP_9_9_2021_87_5B_1_2m_curated_SR-
> VP_9_9_2021_87_5B_1_2m_2___657268___657909___1_relaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/Ruby_pdb/FINAL-
> manually_curated_Ruby-bin53_Illumina_curated_809_Ruby_Borg_SR-
> VP_9_9_2021_75_5A_0_95m_2_SR-VP_9_9_2021_87_5B_1_2m_curated_SR-
> VP_9_9_2021_87_5B_1_2m_2___657998___658708___1_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/Ruby_pdb/FINAL-
> manually_curated_Ruby-bin53_Illumina_curated_810_Ruby_Borg_SR-
> VP_9_9_2021_75_5A_0_95m_2_SR-VP_9_9_2021_87_5B_1_2m_curated_SR-
> VP_9_9_2021_87_5B_1_2m_2___658747___659142___1_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/Ruby_pdb/FINAL-
> manually_curated_Ruby-bin53_Illumina_curated_811_Ruby_Borg_SR-
> VP_9_9_2021_75_5A_0_95m_2_SR-VP_9_9_2021_87_5B_1_2m_curated_SR-
> VP_9_9_2021_87_5B_1_2m_2___659174___659746___1_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/Ruby_pdb/FINAL-
> manually_curated_Ruby-bin53_Illumina_curated_813_Ruby_Borg_SR-
> VP_9_9_2021_75_5A_0_95m_2_SR-VP_9_9_2021_87_5B_1_2m_curated_SR-
> VP_9_9_2021_87_5B_1_2m_2___660170___660562___1_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/Ruby_pdb/FINAL-
> manually_curated_Ruby-bin53_Illumina_curated_814_Ruby_Borg_SR-
> VP_9_9_2021_75_5A_0_95m_2_SR-VP_9_9_2021_87_5B_1_2m_curated_SR-
> VP_9_9_2021_87_5B_1_2m_2___660585___660857___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/Ruby_pdb/FINAL-
> manually_curated_Ruby-bin53_Illumina_curated_815_Ruby_Borg_SR-
> VP_9_9_2021_75_5A_0_95m_2_SR-VP_9_9_2021_87_5B_1_2m_curated_SR-
> VP_9_9_2021_87_5B_1_2m_2___660854___661540___1_relaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/Ruby_pdb/FINAL-
> manually_curated_Ruby-bin53_Illumina_curated_816_Ruby_Borg_SR-
> VP_9_9_2021_75_5A_0_95m_2_SR-VP_9_9_2021_87_5B_1_2m_curated_SR-
> VP_9_9_2021_87_5B_1_2m_2___661671___661766___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/Ruby_pdb/FINAL-
> manually_curated_Ruby-bin53_Illumina_curated_818_Ruby_Borg_SR-
> VP_9_9_2021_75_5A_0_95m_2_SR-VP_9_9_2021_87_5B_1_2m_curated_SR-
> VP_9_9_2021_87_5B_1_2m_2___661823___662236___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/Ruby_pdb/FINAL-
> manually_curated_Ruby-bin53_Illumina_curated_819_Ruby_Borg_SR-
> VP_9_9_2021_75_5A_0_95m_2_SR-VP_9_9_2021_87_5B_1_2m_curated_SR-
> VP_9_9_2021_87_5B_1_2m_2___662329___662631___1_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/Ruby_pdb/FINAL-
> manually_curated_Ruby-bin53_Illumina_curated_820_Ruby_Borg_SR-
> VP_9_9_2021_75_5A_0_95m_2_SR-VP_9_9_2021_87_5B_1_2m_curated_SR-
> VP_9_9_2021_87_5B_1_2m_2___662694___662996___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/Ruby_pdb/FINAL-
> manually_curated_Ruby-bin53_Illumina_curated_821_Ruby_Borg_SR-
> VP_9_9_2021_75_5A_0_95m_2_SR-VP_9_9_2021_87_5B_1_2m_curated_SR-
> VP_9_9_2021_87_5B_1_2m_2___663095___663463___1_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/Ruby_pdb/FINAL-
> manually_curated_Ruby-bin53_Illumina_curated_823_Ruby_Borg_SR-
> VP_9_9_2021_75_5A_0_95m_2_SR-VP_9_9_2021_87_5B_1_2m_curated_SR-
> VP_9_9_2021_87_5B_1_2m_2___664002___664226___1_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/Ruby_pdb/FINAL-
> manually_curated_Ruby-bin53_Illumina_curated_824_Ruby_Borg_SR-
> VP_9_9_2021_75_5A_0_95m_2_SR-VP_9_9_2021_87_5B_1_2m_curated_SR-
> VP_9_9_2021_87_5B_1_2m_2___664273___664896___1_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/Ruby_pdb/FINAL-
> manually_curated_Ruby-bin53_Illumina_curated_825_Ruby_Borg_SR-
> VP_9_9_2021_75_5A_0_95m_2_SR-VP_9_9_2021_87_5B_1_2m_curated_SR-
> VP_9_9_2021_87_5B_1_2m_2___665250___665369___1_relaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
> /Users/jill/Documents/Borg_multi_copy_gene_AP2/Ruby_pdb/FINAL-
> manually_curated_Ruby-bin53_Illumina_curated_826_Ruby_Borg_SR-
> VP_9_9_2021_75_5A_0_95m_2_SR-VP_9_9_2021_87_5B_1_2m_curated_SR-
> VP_9_9_2021_87_5B_1_2m_2___665458___665568___1_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb

Chain information for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_805_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___656632___656853___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#2  
---  
Chain | Description  
A | No description available  
  
Chain information for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_806_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___656871___657014___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#3  
---  
Chain | Description  
A | No description available  
  
Chain information for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_808_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___657268___657909___1_relaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
#4  
---  
Chain | Description  
A | No description available  
  
Chain information for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_809_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___657998___658708___1_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#5  
---  
Chain | Description  
A | No description available  
  
Chain information for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_810_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___658747___659142___1_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#6  
---  
Chain | Description  
A | No description available  
  
Chain information for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_811_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___659174___659746___1_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#7  
---  
Chain | Description  
A | No description available  
  
Chain information for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_813_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___660170___660562___1_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#8  
---  
Chain | Description  
A | No description available  
  
Chain information for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_814_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___660585___660857___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#9  
---  
Chain | Description  
A | No description available  
  
Chain information for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_815_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___660854___661540___1_relaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
#10  
---  
Chain | Description  
A | No description available  
  
Chain information for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_816_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___661671___661766___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#11  
---  
Chain | Description  
A | No description available  
  
Chain information for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_818_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___661823___662236___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#12  
---  
Chain | Description  
A | No description available  
  
Chain information for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_819_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___662329___662631___1_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
#13  
---  
Chain | Description  
A | No description available  
  
Chain information for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_820_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___662694___662996___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#14  
---  
Chain | Description  
A | No description available  
  
Chain information for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_821_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___663095___663463___1_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
#15  
---  
Chain | Description  
A | No description available  
  
Chain information for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_823_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___664002___664226___1_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb
#16  
---  
Chain | Description  
A | No description available  
  
Chain information for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_824_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___664273___664896___1_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
#17  
---  
Chain | Description  
A | No description available  
  
Chain information for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_825_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___665250___665369___1_relaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb
#18  
---  
Chain | Description  
A | No description available  
  
Chain information for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_826_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___665458___665568___1_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb
#19  
---  
Chain | Description  
A | No description available  
  

> close #1

> hide #3-19 target m

> hide #2 models

> close #2

> show #3 models

> close #3

> show #4 models

> select ::name="CYS"

262 atoms, 239 bonds, 24 residues, 8 models selected  

> show sel & #4 atoms

> color sel & #4 byhetero

> select clear

> coulombic #4

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_808_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___657268___657909___1_relaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb_A
SES surface #4.1: minimum, -15.40, mean -0.40, maximum 20.33  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp #!4

Map values for surface "FINAL-manually_curated_Ruby-
bin53_Illumina_curated_808_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___657268___657909___1_relaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb_A
SES surface": minimum -27.73, mean -3.579, maximum 23.21  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide #!4 surfaces

> close #4

> show #5 models

> color bfactor #5

3917 atoms, 236 residues, atom bfactor range 25 to 94  

> coulombic #5

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_809_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___657998___658708___1_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb_A
SES surface #5.1: minimum, -12.96, mean 1.76, maximum 15.95  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp #!5

Map values for surface "FINAL-manually_curated_Ruby-
bin53_Illumina_curated_809_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___657998___658708___1_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb_A
SES surface": minimum -25.84, mean -4.038, maximum 26.43  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide #!5 surfaces

> close #5

> show #6 models

> close #6

> show #7 models

> color bfactor #7

2938 atoms, 190 residues, atom bfactor range 49.2 to 98.2  

> select ::name="CYS"

207 atoms, 189 bonds, 19 residues, 7 models selected  

> show sel & #7 atoms

> color sel & #7 byhetero

> close #7

> select add #12

2280 atoms, 2292 bonds, 150 residues, 6 models selected  

> select add #11

2795 atoms, 2810 bonds, 181 residues, 7 models selected  

> select subtract #12

658 atoms, 649 bonds, 44 residues, 6 models selected  

> select subtract #11

143 atoms, 131 bonds, 13 residues, 5 models selected  

> select add #14

1613 atoms, 1616 bonds, 106 residues, 5 models selected  

> select subtract #14

66 atoms, 60 bonds, 6 residues, 4 models selected  

> select add #16

1314 atoms, 1321 bonds, 78 residues, 4 models selected  

> select subtract #16

44 atoms, 40 bonds, 4 residues, 3 models selected  

> select add #17

3465 atoms, 3492 bonds, 210 residues, 3 models selected  

> select subtract #17

33 atoms, 30 bonds, 3 residues, 2 models selected  

> select add #18

670 atoms, 671 bonds, 40 residues, 2 models selected  

> select subtract #18

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

> select add #19

592 atoms, 596 bonds, 36 residues, 1 model selected  

> select subtract #19

Nothing selected  

> show #8 models

> close #8

> show #9 models

> close #9

> show #10 models

> coulombic #10

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_815_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___660854___661540___1_relaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb_A
SES surface #10.1: minimum, -27.18, mean -0.87, maximum 16.09  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp #!10

Map values for surface "FINAL-manually_curated_Ruby-
bin53_Illumina_curated_815_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___660854___661540___1_relaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb_A
SES surface": minimum -31.65, mean -4.16, maximum 23  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide #!10 surfaces

> select ::name="CYS"

176 atoms, 161 bonds, 16 residues, 6 models selected  

> show #!10 atoms

> hide #!10 atoms

> select ::name="CYS"

176 atoms, 161 bonds, 16 residues, 6 models selected  

> show #!10 atoms

> select H

8895 atoms, 1074 residues, 10 models selected  

> hide (#!10 & sel) target a

> select clear

> color #!10 byhetero

> color #10 #374f8eff

> color #10 #577de0ff

> color #10 #e0c93cff

> color #10 #e0b431ff

> color #10 #c9a12cff

> set bgColor white

> color #!10 byhetero

> select ::name="LYS"

2688 atoms, 2583 bonds, 122 residues, 10 models selected  

> color (#!10 & sel) lime

> select ::name="PRO"

434 atoms, 435 bonds, 31 residues, 7 models selected  

> show sel & #!10 atoms

> color (#!10 & sel) cyan

> open 7mh7

Summary of feedback from opening 7mh7 fetched from pdb  
---  
note | Fetching compressed mmCIF 7mh7 from
http://files.rcsb.org/download/7mh7.cif  
  
7mh7 title:  
crystal structure of NAD kinase from Pseudomonas aeruginosa PAO1 [more
info...]  
  
Chain information for 7mh7 #1  
---  
Chain | Description | UniProt  
A | NAD kinase | NADK_PSEAE 1-295  
  
Non-standard residues in 7mh7 #1  
---  
NAP — nadp nicotinamide-adenine-dinucleotide phosphate
(2'-monophosphoadenosine 5'-diphosphoribose)  
  
7mh7 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> view clip false

> hide sel & #!10 atoms

> select clear

> hide #1#!10 atoms

> ui tool show Matchmaker

> matchmaker #!10 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7mh7, chain A (#1) with FINAL-manually_curated_Ruby-
bin53_Illumina_curated_815_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___660854___661540___1_relaxed_rank_001_alphafold2_ptm_model_5_seed_000.pdb,
chain A (#10), sequence alignment score = 349.6  
RMSD between 143 pruned atom pairs is 1.030 angstroms; (across all 224 pairs:
3.474)  
  

> color #1 #7c97d7ff

> close #1#10

> show #11 models

> view clip false

> close #11

> show #12 models

> open 2kvq

Summary of feedback from opening 2kvq fetched from pdb  
---  
note | Fetching compressed mmCIF 2kvq from
http://files.rcsb.org/download/2kvq.cif  
  
2kvq title:  
Solution structure of NusE:NusG-CTD complex [more info...]  
  
Chain information for 2kvq  
---  
Chain | Description | UniProt  
1.1/E 1.2/E 1.3/E 1.4/E 1.5/E 1.6/E 1.7/E 1.8/E 1.9/E 1.10/E 1.11/E 1.12/E
1.13/E 1.14/E 1.15/E 1.16/E 1.17/E 1.18/E | NusE | RS10_ECOLI 1-45 47-82  
1.1/G 1.2/G 1.3/G 1.4/G 1.5/G 1.6/G 1.7/G 1.8/G 1.9/G 1.10/G 1.11/G 1.12/G
1.13/G 1.14/G 1.15/G 1.16/G 1.17/G 1.18/G | Transcription antitermination
protein nusG | NUSG_ECOLI 123-181  
  

> ui tool show Matchmaker

> matchmaker #12 to #1.1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 2kvq, chain E (#1.1) with FINAL-manually_curated_Ruby-
bin53_Illumina_curated_818_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___661823___662236___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb,
chain A (#12), sequence alignment score = 66.3  
RMSD between 38 pruned atom pairs is 1.238 angstroms; (across all 77 pairs:
8.444)  
  

> close #1

> select ::name="CYS"

176 atoms, 161 bonds, 16 residues, 6 models selected  

> show sel & #12 atoms

> color sel & #12 byhetero

> coulombic sel & #12

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_818_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___661823___662236___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb_A
SES surface #12.1: minimum, -17.67, mean -0.79, maximum 10.50  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select clear

> coulombic #!12

Coulombic values for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_818_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___661823___662236___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb_A
SES surface #12.1: minimum, -17.67, mean -0.79, maximum 10.50  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp #!12

Map values for surface "FINAL-manually_curated_Ruby-
bin53_Illumina_curated_818_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___661823___662236___1_relaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb_A
SES surface": minimum -27.85, mean -3.385, maximum 24.7  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide #!12 surfaces

> color bfactor #!12

2137 atoms, 137 residues, 1 surfaces, atom bfactor range 27 to 98.6  

> close #12

> show #13 models

> select ::name="CYS"

143 atoms, 131 bonds, 13 residues, 5 models selected  

> show #13 atoms

> hide #13 atoms

> select :CYS,ASP,HIS

783 atoms, 733 bonds, 63 residues, 7 models selected  

> show sel & #13 atoms

> select clear

> coulombic #13

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_819_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___662329___662631___1_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A
SES surface #13.1: minimum, -15.92, mean 0.75, maximum 13.46  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp #!13

Map values for surface "FINAL-manually_curated_Ruby-
bin53_Illumina_curated_819_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___662329___662631___1_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A
SES surface": minimum -24.78, mean -3.698, maximum 22.55  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide #!13 surfaces

> open 5dy9

Summary of feedback from opening 5dy9 fetched from pdb  
---  
note | Fetching compressed mmCIF 5dy9 from
http://files.rcsb.org/download/5dy9.cif  
  
5dy9 title:  
Y68T Hfq from Methanococcus jannaschii in complex with AMP [more info...]  
  
Chain information for 5dy9 #1  
---  
Chain | Description | UniProt  
A B C D E F G H I J K L | Hfq-like protein | Y1435_METJA 1-71  
  
Non-standard residues in 5dy9 #1  
---  
AMP — adenosine monophosphate  
CL — chloride ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
NA — sodium ion  
PEG — di(hydroxyethyl)ether  
SO4 — sulfate ion  
TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer)  
  
5dy9 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> ui tool show Matchmaker

> matchmaker #!13 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5dy9, chain E (#1) with FINAL-manually_curated_Ruby-
bin53_Illumina_curated_819_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___662329___662631___1_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb,
chain A (#13), sequence alignment score = 161.1  
RMSD between 50 pruned atom pairs is 0.795 angstroms; (across all 60 pairs:
4.784)  
  

> view clip false

> hide #!1,13 atoms

> show #!1,13 cartoons

> coulombic #!1,13

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:  
5dy9 #1/G ASN 16 ND2  
5dy9 #1/G ASN 16 OD1  
5dy9 #1/G ASN 16 CG  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 5dy9_A SES surface #1.2: minimum, -10.37, mean -0.60,
maximum 8.68  
Coulombic values for 5dy9_B SES surface #1.3: minimum, -10.64, mean -0.63,
maximum 8.78  
Coulombic values for 5dy9_C SES surface #1.4: minimum, -10.32, mean -0.72,
maximum 8.15  
Coulombic values for 5dy9_D SES surface #1.5: minimum, -12.34, mean -0.09,
maximum 10.51  
Coulombic values for 5dy9_E SES surface #1.6: minimum, -10.60, mean -0.26,
maximum 8.80  
Coulombic values for 5dy9_F SES surface #1.7: minimum, -10.01, mean -0.23,
maximum 11.19  
Coulombic values for 5dy9_G SES surface #1.8: minimum, -10.92, mean -0.76,
maximum 8.62  
Coulombic values for 5dy9_H SES surface #1.9: minimum, -9.99, mean -0.61,
maximum 10.35  
Coulombic values for 5dy9_I SES surface #1.10: minimum, -10.37, mean -0.65,
maximum 9.55  
Coulombic values for 5dy9_J SES surface #1.11: minimum, -10.58, mean -0.74,
maximum 8.31  
Coulombic values for 5dy9_K SES surface #1.12: minimum, -10.90, mean -0.58,
maximum 9.12  
Coulombic values for 5dy9_L SES surface #1.13: minimum, -10.79, mean -0.74,
maximum 8.22  
Coulombic values for FINAL-manually_curated_Ruby-
bin53_Illumina_curated_819_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___662329___662631___1_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A
SES surface #13.1: minimum, -15.92, mean 0.75, maximum 13.46  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp #!1,13

Map values for surface "5dy9_A SES surface": minimum -26.37, mean -4.012,
maximum 24.48  
Map values for surface "5dy9_B SES surface": minimum -26.83, mean -3.831,
maximum 23.22  
Map values for surface "5dy9_C SES surface": minimum -26.3, mean -3.907,
maximum 22.34  
Map values for surface "5dy9_D SES surface": minimum -25.91, mean -4.12,
maximum 23.03  
Map values for surface "5dy9_E SES surface": minimum -26.25, mean -3.511,
maximum 24.09  
Map values for surface "5dy9_F SES surface": minimum -27.27, mean -3.88,
maximum 22.68  
Map values for surface "5dy9_G SES surface": minimum -23.66, mean -4.053,
maximum 21.96  
Map values for surface "5dy9_H SES surface": minimum -26.2, mean -4.209,
maximum 22.37  
Map values for surface "5dy9_I SES surface": minimum -26.06, mean -3.978,
maximum 23.02  
Map values for surface "5dy9_J SES surface": minimum -25.54, mean -4.108,
maximum 22.47  
Map values for surface "5dy9_K SES surface": minimum -27.25, mean -4.024,
maximum 24.21  
Map values for surface "5dy9_L SES surface": minimum -23.59, mean -4, maximum
22.43  
Map values for surface "FINAL-manually_curated_Ruby-
bin53_Illumina_curated_819_Ruby_Borg_SR-VP_9_9_2021_75_5A_0_95m_2_SR-
VP_9_9_2021_87_5B_1_2m_curated_SR-
VP_9_9_2021_87_5B_1_2m_2___662329___662631___1_relaxed_rank_001_alphafold2_ptm_model_1_seed_000.pdb_A
SES surface": minimum -25.12, mean -3.702, maximum 22.42  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide #!1,13 surfaces

> close #1,13

> show #14 models

> view clip false

> color bfactor #14

1547 atoms, 100 residues, atom bfactor range 42.5 to 98  

> coulombic #14


===== 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: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




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

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 10
      L2 Cache: 20 MB
      Memory: 64 GB

Software:

    System Software Overview:

      System Version: macOS 12.6.1 (21G217)
      Kernel Version: Darwin 21.6.0
      Time since boot: 5 days 6:43

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9