id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
18890	Crash in event loop	chimerax-bug-report@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x000000020bb860c0 (most recent call first):
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 368 in event_loop
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1057 in init
  File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1220 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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, chimerax.surface._surface, 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.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imaging, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PIL._webp (total: 53)


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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=6.5G written=24.9M(0%) resident=3775K(0%) swapped_out=21.2M(0%) unallocated=6.5G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework              1024K        8 \nActivity Tracing                   256K        1 \nCG image                          2912K       72 \nColorSync                          704K       38 \nCoreAnimation                     18.9M      153 \nCoreGraphics                        64K        4 \nCoreImage                          160K        5 \nCoreServices                       624K        2 \nCoreUI image data                 5408K       34 \nFoundation                          64K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                             5.9G      107 \nMALLOC guard page                  288K       18 \nMach message                        64K        4 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        672K       42 \nStack                            202.4M       43 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      211.4M      203 \nVM_ALLOCATE (reserved)           128.0M        2         reserved VM address space (unallocated)\n__AUTH                            5521K      697 \n__AUTH_CONST                      77.4M      944 \n__CTF                               824        1 \n__DATA                            37.1M     1082 \n__DATA_CONST                      37.1M     1099 \n__DATA_DIRTY                      2777K      342 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       646.9M      149 \n__OBJC_RO                         61.4M        1 \n__OBJC_RW                         2396K        1 \n__TEXT                             1.3G     1116 \n__TEXT (graphics)                 3232K        3 \n__TPRO_CONST                       128K        2 \ndyld private memory               1584K       14 \nmapped file                      687.2M      115 \npage table in kernel              3775K        1 \nshared memory                     3216K       26 \n===========                     =======  ======= \nTOTAL                              9.4G     6340 \nTOTAL, minus reserved VM space     9.2G     6340 \n"",
  ""legacyInfo"" : {
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    ""queue"" : ""com.apple.main-thread""
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},
  ""logWritingSignature"" : ""b62b37a900551375c9ec9924b781513a3bd352b9"",
  ""trialInfo"" : {
  ""rollouts"" : [
    {
      ""rolloutId"" : ""64b21a7351cbb02ce3442e4e"",
      ""factorPackIds"" : {
        ""REMINDERS_GROCERY"" : ""6647f0f7b6a75d3dc32993e7""
      },
      ""deploymentId"" : 240000042
    },
    {
      ""rolloutId"" : ""6297d96be2c9387df974efa4"",
      ""factorPackIds"" : {

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}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/muzi/Desktop/center_49ns.pdb

Summary of feedback from opening /Users/muzi/Desktop/center_49ns.pdb  
---  
warning | Ignored bad PDB record found on line 2  
REMARK THIS IS A SIMULATION BOX  
  
center_49ns.pdb title:  
Title in water t= 49000.00000 step= 2450 [more info...]  
  
Chain information for center_49ns.pdb #1  
---  
Chain | Description  
? | No description available  
  
Non-standard residues in center_49ns.pdb #1  
---  
HSP — (HSP)  
LIG — (LIG)  
  
Computing secondary structure  

> ui mousemode right select

> select clear

> select protein

8188 atoms, 8270 bonds, 526 residues, 1 model selected  

> rainbow sel

> select ~sel & ##selected

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> hide sel atoms

> select main

8188 atoms, 8270 bonds, 526 residues, 1 model selected  

> hide sel atoms

> select clear

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> show sel atoms

> color sel byelement

> select clear

Drag select of 1 residues  
Drag select of 1152 atoms, 18 residues, 1131 bonds  

> color sel red

> color sel byelement

> color sel orange red

> color sel byhetero

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> color sel red

> color sel byhetero

> color sel byelement

> select H

9974 atoms, 726 residues, 1 model selected  

> hide sel atoms

> select clear

> select add /?:120

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

> select add /?:121

66 atoms, 64 bonds, 4 residues, 1 model selected  

> select add /?:122

86 atoms, 82 bonds, 6 residues, 1 model selected  

> select up

914 atoms, 920 bonds, 58 residues, 1 model selected  

> select add /?:90

948 atoms, 952 bonds, 60 residues, 1 model selected  

> select up

1324 atoms, 1330 bonds, 83 residues, 1 model selected  

> select clear

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> hide sel atoms

Drag select of 261 residues  
Drag select of 20 residues  
Drag select of 19 residues  

> select up

4123 atoms, 4163 bonds, 265 residues, 1 model selected  

> select down

4048 atoms, 260 residues, 1 model selected  

> select up

4123 atoms, 4163 bonds, 265 residues, 1 model selected  

> select down

4048 atoms, 260 residues, 1 model selected  

> select up

4123 atoms, 4163 bonds, 265 residues, 1 model selected  

> select down

4048 atoms, 260 residues, 1 model selected  

> select up

4123 atoms, 4163 bonds, 265 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel #ededecff

> select clear

> undo

> select up

8188 atoms, 8270 bonds, 526 residues, 1 model selected  

> select down

4123 atoms, 4163 bonds, 265 residues, 1 model selected  

> select down

4123 atoms, 4163 bonds, 265 residues, 1 model selected  

> select down

4123 atoms, 4163 bonds, 265 residues, 1 model selected  

> select down

4123 atoms, 4163 bonds, 265 residues, 1 model selected  

> select down

4123 atoms, 4163 bonds, 265 residues, 1 model selected  

> select clear

Drag select of 263 residues  

> ui tool show ""Color Actions""

> color sel #7aa4a4ff

> color sel #aeececff

> color sel #aeededff

> color sel #afeeeeff

> color sel #b0efefff

> color sel #b0f0f0ff

> color sel #b1f0f0ff

> color sel #b1f1f1ff

> color sel #b2f2f2ff

> select clear

Drag select of 15 residues  
Drag select of 263 residues  

> ui tool show ""Color Actions""

> color sel #b6f48aff

> select clear

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> show sel atoms

> select clear

Drag select of 7 atoms, 6 bonds  

> select H

9974 atoms, 726 residues, 1 model selected  

> hide sel atoms

> select clear

> set bgColor white

> lighting soft

> lighting flat

> lighting soft

> lighting full

> lighting simple

> lighting soft

> graphics silhouettes false

> lighting full

> graphics silhouettes true

> graphics silhouettes false

> lighting soft

> graphics silhouettes true

> lighting flat

> lighting full

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> camera ortho

> select clear

> camera ortho

> view

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

Drag select of 120 atoms, 120 bonds  

> select up

140 atoms, 121 bonds, 17 residues, 1 model selected  

> select clear

> select /?:58

34 atoms, 32 bonds, 2 residues, 1 model selected  

> select up

618 atoms, 620 bonds, 40 residues, 1 model selected  

> select up

8188 atoms, 8270 bonds, 526 residues, 1 model selected  

> graphics silhouettes true

> graphics silhouettes false

> lighting full

> lighting flat

> lighting full

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> select clear

> select /?:152

32 atoms, 30 bonds, 2 residues, 1 model selected  

> select up

273 atoms, 275 bonds, 17 residues, 1 model selected  

> select up

8188 atoms, 8270 bonds, 526 residues, 1 model selected  

> graphics silhouettes true

> graphics silhouettes false

> lighting soft

> lighting full

> lighting soft

> lighting full

> select clear

> lighting full

> graphics silhouettes true

> lighting full

> lighting soft

> lighting full

> graphics silhouettes false

> lighting full

> camera

Camera parameters:  
type: orthographic  
position: -100.06 104.54 97.943  
view direction: 0.97574 -0.17415 -0.13269  
field width: 157.14  

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting simple

> lighting full

> graphics silhouettes true

> lighting soft

> select clear

Drag select of 1 atoms, 2 bonds  

> select clear

> select /?:270@C9

1 atom, 1 residue, 1 model selected  

> select clear

Drag select of 165 atoms, 155 bonds  

> select up

182 atoms, 156 bonds, 22 residues, 1 model selected  

> select up

1056 atoms, 1034 bonds, 22 residues, 1 model selected  

> select up

17788 atoms, 17670 bonds, 726 residues, 1 model selected  

> select down

1056 atoms, 1034 bonds, 22 residues, 1 model selected  

> select up

17788 atoms, 17670 bonds, 726 residues, 1 model selected  

> select down

1056 atoms, 1034 bonds, 22 residues, 1 model selected  

> select clear

> select C

5596 atoms, 4484 bonds, 726 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel dark gray

> color sel light gray

> undo

> select clear

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> select C

5596 atoms, 4484 bonds, 726 residues, 1 model selected  

> select clear

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel light gray

> color sel byhetero

> select clear

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel gainsboro

> color sel byhetero

> select clear

> lighting soft

> lighting full

> lighting soft

Drag select of 18 atoms, 19 bonds  

> select clear

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> select clear

> graphics silhouettes false

> lighting soft

> lighting full

> transparency 50 target a

> transparency 30 target a

> lighting full

> lighting soft

> lighting full

> transparency 10 target a

> select /?:136

34 atoms, 32 bonds, 2 residues, 1 model selected  

> select up

914 atoms, 920 bonds, 58 residues, 1 model selected  

> select up

8188 atoms, 8270 bonds, 526 residues, 1 model selected  

> select clear

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> hide sel atoms

Drag select of 262 residues  
Drag select of 3 residues  

> select up

4123 atoms, 4163 bonds, 265 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel light sky blue

> color sel cornflower blue

Drag select of 5 residues  
Drag select of 266 residues  

> select down

4136 atoms, 266 residues, 1 model selected  
Drag select of 5 residues  
Drag select of 218 residues  

> select clear

Drag select of 50 residues  

> select up

1205 atoms, 1213 bonds, 77 residues, 1 model selected  

> select up

4094 atoms, 4135 bonds, 263 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel forest green

> color sel medium sea green

> color sel dark sea green

> color sel yellow green

> color sel lime

> color sel green

> color sel chartreuse

> color sel lawn green

> color sel spring green

> color sel lime green

> color sel forest green

> color sel sea green

> color sel medium sea green

> select clear

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> show sel atoms

> select clear

> select H

9974 atoms, 726 residues, 1 model selected  

> hide sel atoms

> select clear

> transparency 30 target a

> transparency 50 target a

> transparency 5 target a

Drag select of 1 atoms, 3 residues  

> select clear

> lighting soft

> lighting full

> lighting soft

> lighting full

> ui tool show ""Color Actions""

> color #b6f48aff

> color #aee984ff

> color #abe682ff

> color #abe582ff

> color #aae481ff

> color #a9e380ff

> color #a9e280ff

> color #a7e07fff

> color #a5dd7dff

> color #a4dc7dff

> color #a3da7cff

> color #a2d97bff

> color #a1d87bff

> color #a0d679ff

> color #9fd579ff

> color #9fd578ff

> color #9ed478ff

> color #9ed378ff

> color #9dd377ff

> color #9cd277ff

> color #9bcf76ff

> color #9acf75ff

> color #9ace75ff

> color #98cb73ff

> color #97cb73ff

> color #97ca73ff

> color #97ca72ff

> color #95c871ff

> color #95c771ff

> undo

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> hide sel atoms

Drag select of 90 residues  

> select up

1879 atoms, 1894 bonds, 120 residues, 1 model selected  

> select up

4094 atoms, 4135 bonds, 263 residues, 1 model selected  

> select clear

> show atoms

> hide atoms

> lighting full

> lighting soft

> lighting full

> lighting soft

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> show sel atoms

> select clear

> lighting full

> lighting soft

Drag select of 37 atoms, 37 bonds  

> select clear

> lighting flat

> lighting full

> graphics silhouettes false

> lighting soft

> lighting full

> graphics silhouettes true

> graphics silhouettes false

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> hide sel atoms

Drag select of 90 residues  

> select up

1916 atoms, 1931 bonds, 122 residues, 1 model selected  

> select up

4094 atoms, 4135 bonds, 263 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel #b2f2f2ff

> color sel #aff2f2ff

> color sel #aff1f1ff

> color sel #aef1f1ff

> color sel #aef0f0ff

> color sel #aeefefff

> color sel #adeeeeff

> color sel #abececff

> color sel #abebebff

> color sel #aaeaeaff

> color sel #a9e9e9ff

> color sel #a8e8e8ff

> color sel #a8e7e7ff

> color sel #a7e7e7ff

> color sel #a7e6e6ff

> color sel #a6e5e5ff

> color sel #a5e4e4ff

> color sel #a5e3e3ff

> color sel #a4e2e2ff

> color sel #a2e0e0ff

> color sel #9fdbdbff

> color sel #9edadaff

> color sel #9ed9d9ff

> color sel #9dd8d8ff

> color sel #9cd8d8ff

> color sel #9cd7d7ff

> color sel #9bd6d6ff

> color sel #9cd7d7ff

> color sel #9dd8d8ff

> color sel #9dd9d9ff

> color sel #9fdbdbff

> color sel #9fdcdcff

> color sel #a0dcdcff

> color sel #a0ddddff

> color sel #a1ddddff

> color sel #a1dedeff

> color sel #a2dfdfff

> color sel #a1dedeff

> color sel #a1ddddff

> color sel #a0ddddff

> color sel #9fdbdbff

> color sel #9dd9d9ff

> color sel #9dd8d8ff

> color sel #9bd5d5ff

> color sel #9ad5d5ff

> color sel #9ad4d4ff

> color sel #98d2d2ff

> color sel #98d1d1ff

> color sel #97d1d1ff

> color sel #97d0d0ff

> color sel #96cfcfff

> color sel #94cdcdff

> color sel #93cbcbff

> color sel #93cacaff

> color sel #92cacaff

> color sel #91c8c8ff

> color sel #90c6c6ff

> color sel #8fc6c6ff

> color sel #8fc5c5ff

> color sel #8ec3c3ff

> color sel #7cababff

> color sel #5c7e7eff

> color sel #5b7e7eff

> color sel #5a7c7cff

> color sel #638888ff

> color sel #6f9999ff

> color sel #77a4a4ff

> color sel #79a7a7ff

> color sel #7ba9a9ff

> color sel #7cababff

> color sel #7dadadff

> color sel #7faeaeff

> color sel #7fafafff

> color sel #7fb0b0ff

> color sel #84b6b6ff

> color sel #87babaff

> color sel #8abebeff

> color sel #8abfbfff

> color sel #8abebeff

> color sel #88bbbbff

> color sel #87babaff

> color sel #86b8b8ff

> color sel #85b8b8ff

> color sel #85b7b7ff

> color sel #83b5b5ff

> color sel #82b4b4ff

> color sel #82b3b3ff

> color sel #83b4b4ff

> color sel #8abebeff

> color sel #97d0d0ff

> color sel #9ad4d4ff

> color sel #9bd6d6ff

> color sel #9cd7d7ff

> color sel #9edadaff

> color sel #a1ddddff

> color sel #a7e6e6ff

> color sel #aaebebff

> color sel #b1f4f4ff

> color sel #b3f7f7ff

> color sel #b4f8f8ff

> color sel #b5f9f9ff

> color sel #b4f9f9ff

> color sel #b2f5f5ff

> color sel #adefefff

> color sel #a5e4e4ff

> color sel #a4e2e2ff

> color sel #a1dedeff

> color sel #9fdcdcff

> color sel #9edadaff

> color sel #9ed9d9ff

> color sel #9bd6d6ff

> color sel #9ad4d4ff

> color sel #99d3d3ff

> color sel #97d1d1ff

> color sel #95ceceff

> color sel #91c8c8ff

> color sel #91c7c7ff

> color sel #8fc6c6ff

> color sel #8ec4c4ff

> color sel #8dc2c2ff

> color sel #8bc0c0ff

> color sel #8bbfbfff

> color sel #89bdbdff

> color sel #88bbbbff

> color sel #87babaff

> color sel #85b8b8ff

> color sel #83b5b5ff

> color sel #83b4b4ff

> color sel #81b2b2ff

> color sel #80b0b0ff

> color sel #7fb0b0ff

> color sel #80b0b0ff

> color sel #80b1b1ff

> color sel #81b2b2ff

> color sel #82b3b3ff

> color sel #82b4b4ff

> color sel #83b4b4ff

> color sel #84b5b5ff

> color sel #84b6b6ff

> color sel #85b8b8ff

> color sel #86b8b8ff

> color sel #87babaff

> color sel #88bbbbff

> color sel #88bcbcff

> color sel #88bbbbff

> color sel #87babaff

> color sel #86b9b9ff

> color sel #86b8b8ff

> color sel #85b8b8ff

> color sel #84b7b7ff

> color sel #84b6b6ff

> color sel #84b5b5ff

> color sel #83b5b5ff

> color sel #82b4b4ff

> color sel #82b3b3ff

Drag select of 92 residues  

> select up

2162 atoms, 2182 bonds, 138 residues, 1 model selected  

> select up

4094 atoms, 4135 bonds, 263 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel #b6f48aff

> color sel #b3f088ff

> color sel #a9e280ff

> color sel #a8e180ff

> color sel #a8e17fff

> color sel #a5dd7dff

> color sel #a4dc7dff

> color sel #a3db7cff

> color sel #a1d87aff

> color sel #a0d67aff

> color sel #9ed478ff

> color sel #9dd377ff

> color sel #9cd277ff

> color sel #9cd176ff

> color sel #9acf75ff

> color sel #9ace75ff

> color sel #98cc74ff

> color sel #97ca72ff

> color sel #95c871ff

> color sel #94c771ff

> color sel #94c670ff

> color sel #93c670ff

> color sel #92c46fff

> color sel #92c36fff

> color sel #91c36eff

> color sel #91c26eff

> color sel #90c26eff

> color sel #90c16eff

> color sel #90c16dff

> color sel #8fc06dff

> color sel #8fbf6cff

> color sel #8ebe6cff

> color sel #8cbc6bff

> color sel #8cbb6aff

> color sel #8bbb6aff

> color sel #8bba6aff

> color sel #8bba69ff

> color sel #8ab969ff

> color sel #89b868ff

> color sel #89b768ff

> color sel #88b667ff

> color sel #87b567ff

> color sel #87b566ff

> color sel #86b466ff

> color sel #85b265ff

> color sel #84b164ff

> color sel #83b064ff

> color sel #82af63ff

> color sel #82ae63ff

> color sel #82ae62ff

> color sel #81ad62ff

> color sel #81ac62ff

> color sel #80ac62ff

> color sel #80ac61ff

> color sel #80ab61ff

> color sel #7fab61ff

> color sel #7aa45dff

> color sel #79a25cff

> color sel #78a15bff

> color sel #769f5aff

> color sel #769e5aff

> color sel #759d59ff

> color sel #749b58ff

> color sel #739a57ff

> color sel #749b58ff

> color sel #77a05bff

> color sel #7aa35cff

> color sel #7ea960ff

> color sel #81ad62ff

> color sel #82af63ff

> color sel #83b064ff

> color sel #84b265ff

> color sel #87b466ff

> color sel #87b567ff

> color sel #88b667ff

> color sel #89b768ff

> color sel #8ab969ff

> color sel #8bba69ff

> color sel #8bba6aff

> color sel #8cbc6aff

> color sel #8dbc6bff

> color sel #8dbd6bff

> color sel #8dbe6bff

> color sel #8fc06dff

> color sel #90c16dff

> color sel #90c16eff

> color sel #90c26eff

> color sel #91c26eff

> color sel #92c46fff

> color sel #93c570ff

> color sel #92c36fff

> color sel #91c26eff

> color sel #90c26eff

> color sel #90c16eff

> color sel #8ebe6cff

> color sel #8cbc6bff

> color sel #8cbc6aff

> color sel #8cbb6aff

> color sel #8bba6aff

> color sel #8bba69ff

> color sel #8ab969ff

> color sel #89b868ff

> select clear

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> show sel atoms

> select H

9974 atoms, 726 residues, 1 model selected  

> hide sel atoms

> color sel byelement

> select clear

Drag select of 43 atoms, 41 bonds  

> select up

50 atoms, 41 bonds, 8 residues, 1 model selected  

> select up

384 atoms, 376 bonds, 8 residues, 1 model selected  

> select up

17788 atoms, 17670 bonds, 726 residues, 1 model selected  

> select down

384 atoms, 376 bonds, 8 residues, 1 model selected  

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> color sel byelement

> ui tool show ""Color Actions""

> color sel white smoke

> color sel byhetero

> select clear

> transparency 0 target a

> camera mono

> save /Users/muzi/Desktop/zein/ph=2/double_zein/double_zein_ph2.cxs

No map chosen to save  

> select add #1

17788 atoms, 17670 bonds, 726 residues, 1 model selected  
No map chosen to save  

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

> select clear

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

> select add #1

17788 atoms, 17670 bonds, 726 residues, 1 model selected  

> select clear

> select #1

17788 atoms, 17670 bonds, 726 residues, 1 model selected  

> save /Users/muzi/Desktop/zein/ph=2/double_zein/double_zein_ph2.tif width 936
> height 768 supersample 3


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

Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/muzi/Desktop/zein/ph=2/double_zein/double_zein_ph2.cxs

Log from Sat Sep 27 18:52:14 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/muzi/Desktop/center_49ns.pdb

Summary of feedback from opening /Users/muzi/Desktop/center_49ns.pdb  
---  
warning | Ignored bad PDB record found on line 2  
REMARK THIS IS A SIMULATION BOX  
  
center_49ns.pdb title:  
Title in water t= 49000.00000 step= 2450 [more info...]  
  
Chain information for center_49ns.pdb #1  
---  
Chain | Description  
? | No description available  
  
Non-standard residues in center_49ns.pdb #1  
---  
HSP — (HSP)  
LIG — (LIG)  
  
Computing secondary structure  

> ui mousemode right select

> select clear

> select protein

8188 atoms, 8270 bonds, 526 residues, 1 model selected  

> rainbow sel

> select ~sel & ##selected

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> hide sel atoms

> select main

8188 atoms, 8270 bonds, 526 residues, 1 model selected  

> hide sel atoms

> select clear

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> show sel atoms

> color sel byelement

> select clear

Drag select of 1 residues  
Drag select of 1152 atoms, 18 residues, 1131 bonds  

> color sel red

> color sel byelement

> color sel orange red

> color sel byhetero

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> color sel red

> color sel byhetero

> color sel byelement

> select H

9974 atoms, 726 residues, 1 model selected  

> hide sel atoms

> select clear

> select add /?:120

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

> select add /?:121

66 atoms, 64 bonds, 4 residues, 1 model selected  

> select add /?:122

86 atoms, 82 bonds, 6 residues, 1 model selected  

> select up

914 atoms, 920 bonds, 58 residues, 1 model selected  

> select add /?:90

948 atoms, 952 bonds, 60 residues, 1 model selected  

> select up

1324 atoms, 1330 bonds, 83 residues, 1 model selected  

> select clear

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> hide sel atoms

Drag select of 261 residues  
Drag select of 20 residues  
Drag select of 19 residues  

> select up

4123 atoms, 4163 bonds, 265 residues, 1 model selected  

> select down

4048 atoms, 260 residues, 1 model selected  

> select up

4123 atoms, 4163 bonds, 265 residues, 1 model selected  

> select down

4048 atoms, 260 residues, 1 model selected  

> select up

4123 atoms, 4163 bonds, 265 residues, 1 model selected  

> select down

4048 atoms, 260 residues, 1 model selected  

> select up

4123 atoms, 4163 bonds, 265 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel #ededecff

> select clear

[Repeated 1 time(s)]

> undo

[Repeated 3 time(s)]

> select up

8188 atoms, 8270 bonds, 526 residues, 1 model selected  

> select down

4123 atoms, 4163 bonds, 265 residues, 1 model selected  

> select down

4123 atoms, 4163 bonds, 265 residues, 1 model selected  

> select down

4123 atoms, 4163 bonds, 265 residues, 1 model selected  

> select down

4123 atoms, 4163 bonds, 265 residues, 1 model selected  

> select down

4123 atoms, 4163 bonds, 265 residues, 1 model selected  

> select clear

Drag select of 263 residues  

> ui tool show ""Color Actions""

> color sel #7aa4a4ff

> color sel #aeececff

> color sel #aeededff

[Repeated 1 time(s)]

> color sel #afeeeeff

> color sel #b0efefff

[Repeated 1 time(s)]

> color sel #b0f0f0ff

> color sel #b1f0f0ff

> color sel #b1f1f1ff

[Repeated 1 time(s)]

> color sel #b2f2f2ff

[Repeated 1 time(s)]

> select clear

Drag select of 15 residues  
Drag select of 263 residues  

> ui tool show ""Color Actions""

> color sel #b6f48aff

> select clear

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> show sel atoms

> select clear

Drag select of 7 atoms, 6 bonds  

> select H

9974 atoms, 726 residues, 1 model selected  

> hide sel atoms

> select clear

> set bgColor white

> lighting soft

> lighting flat

> lighting soft

> lighting full

> lighting simple

> lighting soft

> graphics silhouettes false

> lighting full

> graphics silhouettes true

> graphics silhouettes false

> lighting soft

> graphics silhouettes true

> lighting flat

> lighting full

> lighting soft

[Repeated 1 time(s)]

> graphics silhouettes false

> graphics silhouettes true

> camera ortho

> select clear

> camera ortho

> view

[Repeated 1 time(s)]

> lighting soft

[Repeated 1 time(s)]

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

Drag select of 120 atoms, 120 bonds  

> select up

140 atoms, 121 bonds, 17 residues, 1 model selected  

> select clear

> select /?:58

34 atoms, 32 bonds, 2 residues, 1 model selected  

> select up

618 atoms, 620 bonds, 40 residues, 1 model selected  

> select up

8188 atoms, 8270 bonds, 526 residues, 1 model selected  

> graphics silhouettes true

> graphics silhouettes false

> lighting full

> lighting flat

> lighting full

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> select clear

> select /?:152

32 atoms, 30 bonds, 2 residues, 1 model selected  

> select up

273 atoms, 275 bonds, 17 residues, 1 model selected  

> select up

8188 atoms, 8270 bonds, 526 residues, 1 model selected  

> graphics silhouettes true

> graphics silhouettes false

> lighting soft

> lighting full

> lighting soft

> lighting full

> select clear

> lighting full

> graphics silhouettes true

> lighting full

> lighting soft

> lighting full

> graphics silhouettes false

> lighting full

> camera

Camera parameters:  
type: orthographic  
position: -100.06 104.54 97.943  
view direction: 0.97574 -0.17415 -0.13269  
field width: 157.14  

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting simple

[Repeated 1 time(s)]

> lighting full

> graphics silhouettes true

> lighting soft

> select clear

Drag select of 1 atoms, 2 bonds  

> select clear

> select /?:270@C9

1 atom, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]Drag select of 165 atoms, 155 bonds  

> select up

182 atoms, 156 bonds, 22 residues, 1 model selected  

> select up

1056 atoms, 1034 bonds, 22 residues, 1 model selected  

> select up

17788 atoms, 17670 bonds, 726 residues, 1 model selected  

> select down

1056 atoms, 1034 bonds, 22 residues, 1 model selected  

> select up

17788 atoms, 17670 bonds, 726 residues, 1 model selected  

> select down

1056 atoms, 1034 bonds, 22 residues, 1 model selected  

> select clear

> select C

5596 atoms, 4484 bonds, 726 residues, 1 model selected  

> ui tool show ""Color Actions""

[Repeated 1 time(s)]

> color sel dark gray

> color sel light gray

> undo

[Repeated 1 time(s)]

> select clear

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> select C

5596 atoms, 4484 bonds, 726 residues, 1 model selected  

> select clear

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel light gray

> color sel byhetero

> select clear

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel gainsboro

> color sel byhetero

> select clear

> lighting soft

> lighting full

> lighting soft

Drag select of 18 atoms, 19 bonds  

> select clear

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> select clear

> graphics silhouettes false

> lighting soft

> lighting full

> transparency 50 target a

> transparency 30 target a

> lighting full

> lighting soft

> lighting full

> transparency 10 target a

> select /?:136

34 atoms, 32 bonds, 2 residues, 1 model selected  

> select up

914 atoms, 920 bonds, 58 residues, 1 model selected  

> select up

8188 atoms, 8270 bonds, 526 residues, 1 model selected  

> select clear

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> hide sel atoms

Drag select of 262 residues  
Drag select of 3 residues  

> select up

4123 atoms, 4163 bonds, 265 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel light sky blue

> color sel cornflower blue

Drag select of 5 residues  
[Repeated 1 time(s)]Drag select of 266 residues  

> select down

4136 atoms, 266 residues, 1 model selected  
Drag select of 5 residues  
Drag select of 218 residues  

> select clear

Drag select of 50 residues  

> select up

1205 atoms, 1213 bonds, 77 residues, 1 model selected  

> select up

4094 atoms, 4135 bonds, 263 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel forest green

> color sel medium sea green

> color sel dark sea green

[Repeated 1 time(s)]

> color sel yellow green

> color sel lime

> color sel green

> color sel chartreuse

> color sel lawn green

> color sel spring green

> color sel lime green

> color sel forest green

> color sel sea green

> color sel medium sea green

> select clear

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> show sel atoms

> select clear

[Repeated 1 time(s)]

> select H

9974 atoms, 726 residues, 1 model selected  

> hide sel atoms

> select clear

> transparency 30 target a

> transparency 50 target a

> transparency 5 target a

Drag select of 1 atoms, 3 residues  

> select clear

> lighting soft

> lighting full

> lighting soft

> lighting full

> ui tool show ""Color Actions""

> color #b6f48aff

[Repeated 1 time(s)]

> color #aee984ff

> color #abe682ff

> color #abe582ff

> color #aae481ff

> color #a9e380ff

> color #a9e280ff

> color #a7e07fff

> color #a5dd7dff

> color #a4dc7dff

> color #a3da7cff

> color #a2d97bff

> color #a1d87bff

> color #a0d679ff

> color #9fd579ff

[Repeated 1 time(s)]

> color #9fd578ff

> color #9ed478ff

> color #9ed378ff

> color #9dd377ff

> color #9cd277ff

> color #9bcf76ff

> color #9acf75ff

> color #9ace75ff

> color #98cb73ff

> color #97cb73ff

> color #97ca73ff

> color #97ca72ff

> color #95c871ff

> color #95c771ff

> undo

[Repeated 9 time(s)]

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> hide sel atoms

Drag select of 90 residues  

> select up

1879 atoms, 1894 bonds, 120 residues, 1 model selected  

> select up

4094 atoms, 4135 bonds, 263 residues, 1 model selected  

> select clear

> show atoms

> hide atoms

> lighting full

> lighting soft

> lighting full

> lighting soft

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> show sel atoms

> select clear

> lighting full

> lighting soft

Drag select of 37 atoms, 37 bonds  

> select clear

> lighting flat

> lighting full

> graphics silhouettes false

> lighting soft

> lighting full

> graphics silhouettes true

> graphics silhouettes false

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> hide sel atoms

Drag select of 90 residues  

> select up

1916 atoms, 1931 bonds, 122 residues, 1 model selected  

> select up

4094 atoms, 4135 bonds, 263 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel #b2f2f2ff

> color sel #aff2f2ff

> color sel #aff1f1ff

> color sel #aef1f1ff

> color sel #aef0f0ff

[Repeated 1 time(s)]

> color sel #aeefefff

> color sel #adeeeeff

> color sel #abececff

[Repeated 1 time(s)]

> color sel #abebebff

> color sel #aaeaeaff

> color sel #a9e9e9ff

[Repeated 2 time(s)]

> color sel #a8e8e8ff

[Repeated 1 time(s)]

> color sel #a8e7e7ff

> color sel #a7e7e7ff

> color sel #a7e6e6ff

[Repeated 1 time(s)]

> color sel #a6e5e5ff

> color sel #a5e4e4ff

> color sel #a5e3e3ff

[Repeated 1 time(s)]

> color sel #a4e2e2ff

> color sel #a2e0e0ff

> color sel #9fdbdbff

> color sel #9edadaff

> color sel #9ed9d9ff

> color sel #9dd8d8ff

> color sel #9cd8d8ff

> color sel #9cd7d7ff

[Repeated 2 time(s)]

> color sel #9bd6d6ff

> color sel #9cd7d7ff

[Repeated 1 time(s)]

> color sel #9dd8d8ff

> color sel #9dd9d9ff

> color sel #9fdbdbff

> color sel #9fdcdcff

> color sel #a0dcdcff

[Repeated 1 time(s)]

> color sel #a0ddddff

> color sel #a1ddddff

> color sel #a1dedeff

[Repeated 2 time(s)]

> color sel #a2dfdfff

> color sel #a1dedeff

[Repeated 2 time(s)]

> color sel #a1ddddff

> color sel #a0ddddff

> color sel #9fdbdbff

[Repeated 1 time(s)]

> color sel #9dd9d9ff

> color sel #9dd8d8ff

> color sel #9bd5d5ff

> color sel #9ad5d5ff

> color sel #9ad4d4ff

> color sel #98d2d2ff

> color sel #98d1d1ff

[Repeated 1 time(s)]

> color sel #97d1d1ff

> color sel #97d0d0ff

[Repeated 1 time(s)]

> color sel #96cfcfff

> color sel #94cdcdff

> color sel #93cbcbff

> color sel #93cacaff

> color sel #92cacaff

> color sel #91c8c8ff

> color sel #90c6c6ff

> color sel #8fc6c6ff

> color sel #8fc5c5ff

> color sel #8ec3c3ff

> color sel #7cababff

> color sel #5c7e7eff

> color sel #5b7e7eff

> color sel #5a7c7cff

[Repeated 2 time(s)]

> color sel #638888ff

> color sel #6f9999ff

> color sel #77a4a4ff

> color sel #79a7a7ff

> color sel #7ba9a9ff

> color sel #7cababff

> color sel #7dadadff

> color sel #7faeaeff

> color sel #7fafafff

[Repeated 1 time(s)]

> color sel #7fb0b0ff

> color sel #84b6b6ff

> color sel #87babaff

> color sel #8abebeff

> color sel #8abfbfff

> color sel #8abebeff

> color sel #88bbbbff

> color sel #87babaff

[Repeated 1 time(s)]

> color sel #86b8b8ff

> color sel #85b8b8ff

> color sel #85b7b7ff

> color sel #83b5b5ff

> color sel #82b4b4ff

> color sel #82b3b3ff

> color sel #83b4b4ff

> color sel #8abebeff

> color sel #97d0d0ff

> color sel #9ad4d4ff

> color sel #9bd6d6ff

> color sel #9cd7d7ff

> color sel #9edadaff

> color sel #a1ddddff

> color sel #a7e6e6ff

> color sel #aaebebff

> color sel #b1f4f4ff

> color sel #b3f7f7ff

[Repeated 1 time(s)]

> color sel #b4f8f8ff

[Repeated 1 time(s)]

> color sel #b5f9f9ff

> color sel #b4f9f9ff

> color sel #b2f5f5ff

> color sel #adefefff

> color sel #a5e4e4ff

> color sel #a4e2e2ff

> color sel #a1dedeff

> color sel #9fdcdcff

> color sel #9edadaff

> color sel #9ed9d9ff

> color sel #9bd6d6ff

> color sel #9ad4d4ff

> color sel #99d3d3ff

> color sel #97d1d1ff

> color sel #95ceceff

> color sel #91c8c8ff

> color sel #91c7c7ff

> color sel #8fc6c6ff

> color sel #8ec4c4ff

> color sel #8dc2c2ff

> color sel #8bc0c0ff

> color sel #8bbfbfff

> color sel #89bdbdff

> color sel #88bbbbff

> color sel #87babaff

> color sel #85b8b8ff

> color sel #83b5b5ff

> color sel #83b4b4ff

[Repeated 1 time(s)]

> color sel #81b2b2ff

> color sel #80b0b0ff

> color sel #7fb0b0ff

> color sel #80b0b0ff

> color sel #80b1b1ff

> color sel #81b2b2ff

[Repeated 1 time(s)]

> color sel #82b3b3ff

> color sel #82b4b4ff

> color sel #83b4b4ff

> color sel #84b5b5ff

> color sel #84b6b6ff

> color sel #85b8b8ff

> color sel #86b8b8ff

> color sel #87babaff

[Repeated 1 time(s)]

> color sel #88bbbbff

[Repeated 1 time(s)]

> color sel #88bcbcff

> color sel #88bbbbff

[Repeated 1 time(s)]

> color sel #87babaff

[Repeated 1 time(s)]

> color sel #86b9b9ff

[Repeated 1 time(s)]

> color sel #86b8b8ff

> color sel #85b8b8ff

> color sel #84b7b7ff

> color sel #84b6b6ff

[Repeated 1 time(s)]

> color sel #84b5b5ff

> color sel #83b5b5ff

[Repeated 1 time(s)]

> color sel #82b4b4ff

> color sel #82b3b3ff

Drag select of 92 residues  

> select up

2162 atoms, 2182 bonds, 138 residues, 1 model selected  

> select up

4094 atoms, 4135 bonds, 263 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel #b6f48aff

[Repeated 2 time(s)]

> color sel #b3f088ff

> color sel #a9e280ff

> color sel #a8e180ff

> color sel #a8e17fff

> color sel #a5dd7dff

> color sel #a4dc7dff

> color sel #a3db7cff

[Repeated 1 time(s)]

> color sel #a1d87aff

> color sel #a0d67aff

> color sel #9ed478ff

> color sel #9dd377ff

> color sel #9cd277ff

> color sel #9cd176ff

> color sel #9acf75ff

> color sel #9ace75ff

> color sel #98cc74ff

> color sel #97ca72ff

> color sel #95c871ff

> color sel #94c771ff

> color sel #94c670ff

> color sel #93c670ff

> color sel #92c46fff

[Repeated 1 time(s)]

> color sel #92c36fff

> color sel #91c36eff

> color sel #91c26eff

> color sel #90c26eff

> color sel #90c16eff

> color sel #90c16dff

> color sel #8fc06dff

> color sel #8fbf6cff

> color sel #8ebe6cff

> color sel #8cbc6bff

> color sel #8cbb6aff

> color sel #8bbb6aff

> color sel #8bba6aff

> color sel #8bba69ff

> color sel #8ab969ff

[Repeated 2 time(s)]

> color sel #89b868ff

[Repeated 1 time(s)]

> color sel #89b768ff

> color sel #88b667ff

> color sel #87b567ff

> color sel #87b566ff

> color sel #86b466ff

> color sel #85b265ff

> color sel #84b164ff

> color sel #83b064ff

> color sel #82af63ff

> color sel #82ae63ff

> color sel #82ae62ff

> color sel #81ad62ff

> color sel #81ac62ff

> color sel #80ac62ff

> color sel #80ac61ff

> color sel #80ab61ff

> color sel #7fab61ff

> color sel #7aa45dff

> color sel #79a25cff

> color sel #78a15bff

> color sel #769f5aff

> color sel #769e5aff

> color sel #759d59ff

> color sel #749b58ff

> color sel #739a57ff

> color sel #749b58ff

> color sel #77a05bff

> color sel #7aa35cff

> color sel #7ea960ff

> color sel #81ad62ff

> color sel #82af63ff

> color sel #83b064ff

> color sel #84b265ff

> color sel #87b466ff

> color sel #87b567ff

> color sel #88b667ff

[Repeated 1 time(s)]

> color sel #89b768ff

> color sel #8ab969ff

[Repeated 1 time(s)]

> color sel #8bba69ff

> color sel #8bba6aff

> color sel #8cbc6aff

> color sel #8dbc6bff

> color sel #8dbd6bff

> color sel #8dbe6bff

> color sel #8fc06dff

> color sel #90c16dff

> color sel #90c16eff

> color sel #90c26eff

> color sel #91c26eff

> color sel #92c46fff

> color sel #93c570ff

[Repeated 1 time(s)]

> color sel #92c36fff

> color sel #91c26eff

> color sel #90c26eff

> color sel #90c16eff

> color sel #8ebe6cff

> color sel #8cbc6bff

> color sel #8cbc6aff

> color sel #8cbb6aff

> color sel #8bba6aff

> color sel #8bba69ff

> color sel #8ab969ff

[Repeated 1 time(s)]

> color sel #89b868ff

> select clear

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> show sel atoms

> select H

9974 atoms, 726 residues, 1 model selected  

> hide sel atoms

> color sel byelement

> select clear

Drag select of 43 atoms, 41 bonds  

> select up

50 atoms, 41 bonds, 8 residues, 1 model selected  

> select up

384 atoms, 376 bonds, 8 residues, 1 model selected  

> select up

17788 atoms, 17670 bonds, 726 residues, 1 model selected  

> select down

384 atoms, 376 bonds, 8 residues, 1 model selected  

> select ligand

9600 atoms, 9400 bonds, 200 residues, 1 model selected  

> color sel byelement

> ui tool show ""Color Actions""

> color sel white smoke

> color sel byhetero

> select clear

> transparency 0 target a

> camera mono

> save /Users/muzi/Desktop/zein/ph=2/double_zein/double_zein_ph2.cxs

——— End of log from Sat Sep 27 18:52:14 2025 ———

> view name session-start

opened ChimeraX session  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGR3CH/A
      Chip: Apple M1 Pro
      Total Number of Cores: 8 (6 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6.1 (24G90)
      Kernel Version: Darwin 24.6.0
      Time since boot: 13天12分钟

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      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: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.4
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.7
    ChimeraX-AtomicLibrary: 14.1.19
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    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-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.3
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.45.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.2
    coverage: 7.10.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.3.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
}}}
"	defect	closed	normal		Core		can't reproduce		Tom Goddard				all	ChimeraX