Opened 19 months ago

Closed 19 months ago

#14892 closed defect (duplicate)

Crash in garbage collection

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

Description 

The following bug report has been submitted:
Platform:        macOS-14.0-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000000032521e000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000032421b000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000323218000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000322215000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000321212000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000032020f000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031f20c000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031e209000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031d206000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031c203000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031b200000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031a1fd000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003191fa000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x0000000205093240 (most recent call first):
  Garbage-collecting
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 157 in asArray
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 146 in 
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 145 in asArray
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 146 in 
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py", line 145 in asArray
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2828 in set_matrix
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 817 in set_projection_matrix
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 725 in _use_shader
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 801 in _opengl_shader
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 698 in shader
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 818 in _draw_geometry
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 787 in draw_self
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 780 in draw
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1567 in _draw_multiple
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1554 in draw_opaque
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 258 in _draw_scene
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
  File "/Applications/ChimeraX-1.7.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.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.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.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, 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.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 62)


{"app_name":"ChimeraX","timestamp":"2024-04-03 08:59:38.00 -0500","app_version":"1.7.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.7.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.0 (23A344)","roots_installed":0,"name":"ChimeraX","incident_id":"40AB6C73-0735-44B8-A987-A804CF0B51E3"}
{
  "uptime" : 140000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,3",
  "coalitionID" : 26441,
  "osVersion" : {
    "train" : "macOS 14.0",
    "build" : "23A344",
    "releaseType" : "User"
  },
  "captureTime" : "2024-04-03 08:58:04.5071 -0500",
  "codeSigningMonitor" : 1,
  "incident" : "40AB6C73-0735-44B8-A987-A804CF0B51E3",
  "pid" : 60030,
  "translated" : true,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-04-01 15:26:50.7089 -0500",
  "procStartAbsTime" : 1803712739761,
  "procExitAbsTime" : 3510229654792,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"E7645B00-7015-5C35-8B97-5BFF52D821FD","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "F5D56411-1169-49D5-5797-B94C04536BCA",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "wakeTime" : 2176,
  "sleepWakeUUID" : "474FEBFB-BE5D-4ED0-B20A-BA8BB61AC3B3",
  "sip" : "enabled",
  "vmRegionInfo" : "0xa9 is not in any region.  Bytes before following region: 140722963070807\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffc9e39c000-7ffcc3abc000 [599.1M] r-x\/r-x SM=COW  ...t_id=5584839f",
  "exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":60030},
  "vmregioninfo" : "0xa9 is not in any region.  Bytes before following region: 140722963070807\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffc9e39c000-7ffcc3abc000 [599.1M] r-x\/r-x SM=COW  ...t_id=5584839f",
  "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,
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    "uuid" : "33c43114-85f0-3f32-86d7-8e6a2403d38c",
    "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    "name" : "libsystem_pthread.dylib"
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    "uuid" : "3e9a5bfa-50c0-3a96-9291-4826c62d1182",
    "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
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    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
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  "logWritingSignature" : "c411e6e116106bef96d3327097f4cf80b7dc8e97",
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},
  "reportNotes" : [
  "PC register does not match crashing frame (0x0 vs 0x7FF899D3EA78)"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/jonathanmartin/Downloads/AF-Q825Z7-F1-model_v4.pdb

AF-Q825Z7-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for lysine--TRNA ligase (Q825Z7) [more
info...]  
  
Chain information for AF-Q825Z7-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | lysine--TRNA ligase | Q825Z7_STRAW 1-1093  
  

> select /A:249:548

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

> select /A:2490548

Nothing selected  

> select /A:249-548

2339 atoms, 2390 bonds, 300 residues, 1 model selected  

> select ~sel & ##selected

6057 atoms, 6192 bonds, 793 residues, 1 model selected  

> color sel seafoam

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel seafoam green

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel green

> color list

No custom colors.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> color sel olivedrab

> lighting flat

> set bgColor white

> lighting simple

> lighting soft

> lighting full

> lighting flat

> ui mousemode right select

> select clear

> open /Users/jonathanmartin/code/mprf_figures/fullmprf.cxs

opened ChimeraX session  

> open /Users/jonathanmartin/Downloads/AF-Q825Z7-F1-model_v4.pdb

AF-Q825Z7-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for lysine--TRNA ligase (Q825Z7) [more
info...]  
  
Chain information for AF-Q825Z7-F1-model_v4.pdb #2  
---  
Chain | Description | UniProt  
A | lysine--TRNA ligase | Q825Z7_STRAW 1-1093  
  

> ui tool show "Modeller Comparative"

> ui tool show Matchmaker

> matchmaker #2 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 7duw.pdb, chain A (#1) with AF-Q825Z7-F1-model_v4.pdb, chain A
(#2), sequence alignment score = 677.4  
RMSD between 132 pruned atom pairs is 1.288 angstroms; (across all 503 pairs:
24.592)  
  

> select clear

> ui mousemode right translate

> select /B:249-548

2156 atoms, 2205 bonds, 2 pseudobonds, 283 residues, 2 models selected  

> select /A:249-548

4495 atoms, 4595 bonds, 2 pseudobonds, 583 residues, 3 models selected  

> ui tool show Matchmaker

> matchmaker #2 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 7duw.pdb, chain A (#1) with AF-Q825Z7-F1-model_v4.pdb, chain A
(#2), sequence alignment score = 677.4  
RMSD between 132 pruned atom pairs is 1.288 angstroms; (across all 503 pairs:
24.592)  
  

> matchmaker #2 & sel 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 7duw.pdb, chain A (#1) with AF-Q825Z7-F1-model_v4.pdb, chain A
(#2), sequence alignment score = 474  
RMSD between 131 pruned atom pairs is 1.170 angstroms; (across all 292 pairs:
4.377)  
  

> matchmaker #2 to #1 & sel

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 7duw.pdb, chain A (#1) with AF-Q825Z7-F1-model_v4.pdb, chain A
(#2), sequence alignment score = 209.4  
RMSD between 18 pruned atom pairs is 1.402 angstroms; (across all 198 pairs:
12.849)  
  

> ui mousemode right "translate selected models"

> view matrix models
> #1,1,0,0,14.656,0,1,0,-1.6416,0,0,1,-2.3523,#2,-0.008061,-0.749,-0.66252,135.31,-0.65721,0.50332,-0.56103,129.34,0.75367,0.43089,-0.49631,124.07

> view matrix models
> #1,1,0,0,-14.026,0,1,0,1.415,0,0,1,0.22615,#2,-0.008061,-0.749,-0.66252,106.63,-0.65721,0.50332,-0.56103,132.39,0.75367,0.43089,-0.49631,126.64

> view matrix models
> #1,1,0,0,-0.75215,0,1,0,0.062859,0,0,1,-0.15683,#2,-0.008061,-0.749,-0.66252,119.9,-0.65721,0.50332,-0.56103,131.04,0.75367,0.43089,-0.49631,126.26

> ui mousemode right "translate selected models"

> ui mousemode right select

> select clear

> select add #2

8396 atoms, 8582 bonds, 1093 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.008061,-0.749,-0.66252,195.64,-0.65721,0.50332,-0.56103,123.03,0.75367,0.43089,-0.49631,120.21

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.40268,-0.44748,-0.7985,192.87,-0.49401,0.62816,-0.60114,122.13,0.77059,0.63653,0.031887,127.85

> view matrix models
> #2,0.096323,-0.98146,0.16569,209.78,0.91194,0.02031,-0.40983,129.12,0.39887,0.19058,0.89699,142.78

> close session

> open /Users/jonathanmartin/Downloads/AF-O69916-F1-model_v4.pdb

AF-O69916-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for putative integral membrane lysyl-TRNA
synthetase (O69916) [more info...]  
  
Chain information for AF-O69916-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | putative integral membrane lysyl-TRNA synthetase | O69916_STRCO 1-589  
  

> select /A:250-547

2397 atoms, 2454 bonds, 298 residues, 1 model selected  

> select ~sel & ##selected

2293 atoms, 2353 bonds, 291 residues, 1 model selected  

> color sel olivedrab

> ui mousemode right select

> select clear

> undo

> select /A:250-600

2733 atoms, 2798 bonds, 340 residues, 1 model selected  

> select ~sel & ##selected

1957 atoms, 2009 bonds, 249 residues, 1 model selected  

> select up

1958 atoms, 2009 bonds, 250 residues, 1 model selected  

> select up

1968 atoms, 2019 bonds, 250 residues, 1 model selected  

> color sel olivedrab

> select clear

> undo

> redo

> undo

> redo

> color sel olivedrab

> select clear

Drag select of 11 residues  

> ui mousemode right "translate selected models"

> ui mousemode right select

> ui mousemode right translate

> ui mousemode right select

> select clear

> ui mousemode right translate

> close session

> open /Users/jonathanmartin/Downloads/1a01.pdb

1a01.pdb title:  
Hemoglobin (val Β1 met, TRP Β37 ala) mutant [more info...]  
  
Chain information for 1a01.pdb #1  
---  
Chain | Description | UniProt  
A C | hemoglobin (α chain) | HBA_HUMAN 1-141  
B D | hemoglobin (β chain) | HBB_HUMAN 2-146  
  
Non-standard residues in 1a01.pdb #1  
---  
HEM — protoporphyrin IX containing Fe (HEME)  
  

> open /Users/jonathanmartin/Downloads/AF-P04078-F1-model_v4.pdb

AF-P04078-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for glutamine synthetase cytosolic isozyme
(P04078) [more info...]  
  
Chain information for AF-P04078-F1-model_v4.pdb #2  
---  
Chain | Description | UniProt  
A | glutamine synthetase cytosolic isozyme | GLNA1_MEDSA 1-356  
  

> close session

> open /Users/jonathanmartin/Downloads/AF-P04078-F1-model_v4.pdb

AF-P04078-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for glutamine synthetase cytosolic isozyme
(P04078) [more info...]  
  
Chain information for AF-P04078-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | glutamine synthetase cytosolic isozyme | GLNA1_MEDSA 1-356  
  

> select /A:151-254

780 atoms, 803 bonds, 104 residues, 1 model selected  

> color sel tomato

> lighting soft

> select

2762 atoms, 2837 bonds, 356 residues, 1 model selected  

> ui mousemode right select

> select clear

> open /Users/jonathanmartin/Downloads/AF-P04771-F1-model_v4.pdb

AF-P04771-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for glutamine synthetase Pr-2 (P04771) [more
info...]  
  
Chain information for AF-P04771-F1-model_v4.pdb #2  
---  
Chain | Description | UniProt  
A | glutamine synthetase Pr-2 | GLNA2_PHAVU 1-356  
  

> select add #2

2769 atoms, 2845 bonds, 356 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-29.088,0,1,0,18.961,0,0,1,40.47

> ui mousemode right translate

> select #2/A:1-356

2769 atoms, 2845 bonds, 356 residues, 1 model selected  

> select /A

5531 atoms, 5682 bonds, 712 residues, 2 models selected  

> select /A1

Nothing selected  

> select /1

Nothing selected  

> select /#2

Expected an objects specifier or a keyword  

> select /A#2

5531 atoms, 5682 bonds, 712 residues, 2 models selected  

> select #2

2769 atoms, 2845 bonds, 356 residues, 1 model selected  

> select #2:164-347

1424 atoms, 1456 bonds, 184 residues, 1 model selected  

> color sel olivedrab

> ui mousemode right select

> select clear

> select #1

2762 atoms, 2837 bonds, 356 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.75335,-0.6371,0.16299,1.9557,0.35283,0.18243,-0.91773,2.4313,0.55495,0.74888,0.36222,-2.3299

> view matrix models
> #1,0.71594,-0.62008,0.32083,2.3394,0.34448,-0.085953,-0.93485,3.611,0.60726,0.77982,0.15207,-3.0863

> ui mousemode right select

> select clear

> select #1

2762 atoms, 2837 bonds, 356 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.60695,-0.76715,0.20757,1.631,-0.18272,-0.38889,-0.90298,0.99208,0.77345,0.51014,-0.37621,-2.983

> ui mousemode right select

> select clear

> select #1

2762 atoms, 2837 bonds, 356 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.61072,0.58022,0.53886,-13.312,0.48226,0.81228,-0.32807,3.2399,-0.62805,0.059512,-0.77589,-14.072

> view matrix models
> #1,-0.61803,0.60119,0.50658,-13.633,0.509,0.79707,-0.32495,3.5475,-0.59913,0.057018,-0.79862,-13.936

> view matrix models
> #1,-0.67063,0.60563,-0.42833,-18.652,-0.5727,-0.78971,-0.21992,3.1554,-0.47145,0.097818,0.87645,-4.9141

> view matrix models
> #1,-0.11492,-0.4338,-0.89365,-11.263,0.61598,-0.73689,0.27849,14.974,-0.77933,-0.51847,0.3519,-6.9196

> view matrix models
> #1,0.042998,-0.50957,-0.85936,-9.4379,0.6923,-0.60497,0.39336,15.5,-0.72033,-0.61185,0.32676,-6.1006

> ui mousemode right select

> select clear

> select #1

2762 atoms, 2837 bonds, 356 residues, 1 model selected  

> select clear

> select #1

2762 atoms, 2837 bonds, 356 residues, 1 model selected  
Drag select of 4 residues  

> select #1

2762 atoms, 2837 bonds, 356 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.042998,-0.50957,-0.85936,-8.3937,0.6923,-0.60497,0.39336,3.5469,-0.72033,-0.61185,0.32676,-7.6078

> ui mousemode right select

> select clear

> ui mousemode right translate

> color #1 olivedrab

> color #2 tomato

> select #1:106-356

1957 atoms, 2012 bonds, 251 residues, 1 model selected  

> color sel tan

> select #2:103-356

1983 atoms, 2040 bonds, 254 residues, 1 model selected  

> color sel tan

> ui mousemode right select

> select clear

> open /Users/jonathanmartin/Downloads/P04771.fa

Summary of feedback from opening /Users/jonathanmartin/Downloads/P04771.fa  
---  
notes | Alignment identifier is P04771.fa  
Associated AF-P04771-F1-model_v4.pdb chain A to P04771 1-356 with 0 mismatches  
  
Opened 1 sequences from P04771.fa  

> open /Users/jonathanmartin/Downloads/AF-P38094-F1-model_v4.pdb

AF-P38094-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for protein flug (P38094) [more info...]  
  
Chain information for AF-P38094-F1-model_v4.pdb #3  
---  
Chain | Description | UniProt  
A | protein flug | FLUG_EMENI 1-865  
  

> select #3

6808 atoms, 6964 bonds, 865 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,-8.5042,0,1,0,8.6919,0,0,1,14.886

> view matrix models #3,1,0,0,-31.618,0,1,0,70.496,0,0,1,77.299

> select #3:540-865

2538 atoms, 2597 bonds, 326 residues, 1 model selected  

> select #3:540-865

2538 atoms, 2597 bonds, 326 residues, 1 model selected  

> color sel tan

> view matrix models #3,1,0,0,-31.557,0,1,0,70.549,0,0,1,77.282

> ui mousemode right select

> select #3/A:840

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

> select clear

> ui mousemode right translate

> select #3

6808 atoms, 6964 bonds, 865 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,-59.876,0,1,0,62.086,0,0,1,82.026

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.94483,-0.25099,-0.21049,-57.833,0.22636,0.96474,-0.13434,62.549,0.23678,0.079283,0.96832,81.546

> view matrix models
> #3,-0.36897,-0.88309,0.28985,-56.815,0.27874,0.19236,0.9409,57.296,-0.88666,0.42796,0.17517,88.228

> view matrix models
> #3,-0.53216,-0.54558,0.64742,-59.538,0.38946,0.52124,0.75936,57.475,-0.75175,0.65625,-0.064898,88.962

> view matrix models
> #3,-0.34396,-0.55936,0.75419,-60.592,0.51221,0.5614,0.64998,57.826,-0.78697,0.60987,0.093415,88.126

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.34396,-0.55936,0.75419,-29.283,0.51221,0.5614,0.64998,64.042,-0.78697,0.60987,0.093415,87.213

> view matrix models
> #3,-0.34396,-0.55936,0.75419,-28.401,0.51221,0.5614,0.64998,64.468,-0.78697,0.60987,0.093415,87.415

> view matrix models
> #3,-0.34396,-0.55936,0.75419,-27.658,0.51221,0.5614,0.64998,68.664,-0.78697,0.60987,0.093415,85.388

> ui mousemode right select

Drag select of 1 residues  

> select clear

> select #3

6808 atoms, 6964 bonds, 865 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.74679,-0.65488,-0.11588,-24.164,0.30283,0.17971,0.93595,68.143,-0.59211,-0.73405,0.33252,86.511

> view matrix models
> #3,0.6004,0.77247,-0.20692,-26.531,0.56706,-0.22879,0.79126,69.446,0.56388,-0.59241,-0.5754,89.568

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.6004,0.77247,-0.20692,-60.443,0.56706,-0.22879,0.79126,84.09,0.56388,-0.59241,-0.5754,63.161

> ui mousemode right translate

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.6004,0.77247,-0.20692,-50.161,0.56706,-0.22879,0.79126,69.568,0.56388,-0.59241,-0.5754,54.328

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.58861,0.74608,-0.3113,-49.406,0.52286,-0.057652,0.85047,68.89,0.61657,-0.66336,-0.42403,53.406

> view matrix models
> #3,0.60186,0.77392,-0.19701,-50.232,0.57067,-0.24421,0.78403,69.642,0.55866,-0.58431,-0.58863,54.405

> view matrix models
> #3,0.68915,0.71427,-0.12204,-50.762,0.6097,-0.48055,0.63035,71.087,0.39159,-0.50881,-0.76666,55.731

> view matrix models
> #3,0.62945,0.69811,-0.34124,-49.19,0.73922,-0.40263,0.53986,71.216,0.23949,-0.59206,-0.76948,56.262

> view matrix models
> #3,0.76622,0.60702,-0.2108,-50.11,0.64255,-0.7267,0.24295,74.069,-0.0057148,-0.32161,-0.94686,57.303

> view matrix models
> #3,0.81102,0.55706,-0.17868,-50.297,0.57986,-0.80592,0.11941,75.177,-0.077481,-0.20045,-0.97664,57.37

> view matrix models
> #3,0.83388,0.52676,-0.16482,-50.365,0.54045,-0.83988,0.050089,75.784,-0.11205,-0.13085,-0.98505,57.338

> view matrix models
> #3,0.88663,0.44027,-0.14159,-50.429,0.42396,-0.89608,-0.1315,77.326,-0.18477,0.056567,-0.98115,57.039

> view matrix models
> #3,0.77568,0.59741,-0.20352,-50.155,0.63076,-0.7447,0.21808,74.295,-0.021276,-0.29754,-0.95447,57.33

> ui mousemode right select

> select clear

> ui tool show Matchmaker

> matchmaker #3 to #2

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 AF-P04771-F1-model_v4.pdb, chain A (#2) with
AF-P38094-F1-model_v4.pdb, chain A (#3), sequence alignment score = 336.2  
RMSD between 116 pruned atom pairs is 1.034 angstroms; (across all 325 pairs:
7.930)  
  

> select #3

6808 atoms, 6964 bonds, 865 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.73034,-0.14093,-0.66838,-65.677,0.45373,-0.63135,0.62891,57.235,-0.51062,-0.76258,-0.39716,86.07

> ui mousemode right select

> select clear

> undo

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.73034,-0.14093,-0.66838,-69.499,0.45373,-0.63135,0.62891,62.81,-0.51062,-0.76258,-0.39716,93.721

> ui mousemode right select

> select clear

> hide #2 models

> show #2 models

> hide #2 models

> hide #3 models

> ui mousemode right translate

> hide #1 models

> show #2 models

> hide #2 models

> show #3 models

> show #2 models

> show #1 models

> save /Users/jonathanmartin/Downloads/test.cxs

> ui tool show Matchmaker

> matchmaker #2-3 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 AF-P04078-F1-model_v4.pdb, chain A (#1) with
AF-P04771-F1-model_v4.pdb, chain A (#2), sequence alignment score = 1774.1  
RMSD between 355 pruned atom pairs is 0.145 angstroms; (across all 356 pairs:
0.297)  
  
Matchmaker AF-P04078-F1-model_v4.pdb, chain A (#1) with
AF-P38094-F1-model_v4.pdb, chain A (#3), sequence alignment score = 314.9  
RMSD between 117 pruned atom pairs is 1.048 angstroms; (across all 328 pairs:
8.385)  
  

> hide #2 models

> show #2 models

> ui tool show Matchmaker

> ui tool show "Modeller Comparative"

> hide #1 models

> hide #2 models

> show #2 models

> show #1 models

> ui mousemode right select

Drag select of 1074 residues  

> select subtract #3/A:1

8380 atoms, 1073 residues, 3 models selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> save /Users/jonathanmartin/Downloads/flug_selection.fasta format fasta
> alignment 3/A

> select clear

> close session

> open /Users/jonathanmartin/Downloads/1a01.pdb format pdb

1a01.pdb title:  
Hemoglobin (val Β1 met, TRP Β37 ala) mutant [more info...]  
  
Chain information for 1a01.pdb #1  
---  
Chain | Description | UniProt  
A C | hemoglobin (α chain) | HBA_HUMAN 1-141  
B D | hemoglobin (β chain) | HBB_HUMAN 2-146  
  
Non-standard residues in 1a01.pdb #1  
---  
HEM — protoporphyrin IX containing Fe (HEME)  
  

> select

4738 atoms, 4664 bonds, 20 pseudobonds, 776 residues, 2 models selected  

> hide sel atoms

> select clear

> select /B,D

2410 atoms, 2378 bonds, 10 pseudobonds, 388 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> select /A

1160 atoms, 1143 bonds, 5 pseudobonds, 190 residues, 2 models selected  

> hide sel cartoons

Drag select of 11 residues  

> select clear

> ui mousemode right translate

> color aqua green

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color /A green

> color /B green

> color /C green

> lighting flat

> lighting soft

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting flat

> color /C olive

> color /C gray

> select ~sel & ##selected

Nothing selected  

> color /C maroon

> color list

No custom colors.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> color /C orchid

> color /C medium purple

> color /C slate blue

> color /C violet

> color /C blue violet

> color /C darkred

> select /B

1208 atoms, 1189 bonds, 5 pseudobonds, 197 residues, 2 models selected  

> show sel atoms

> hide sel atoms

> show sel cartoons

> select /C

1168 atoms, 1143 bonds, 5 pseudobonds, 198 residues, 2 models selected  

> hide sel cartoons

> color /B cobalt

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color /B dodger blue

> close session

> open /Users/jonathanmartin/Downloads/test.cxs format session

opened ChimeraX session  

> ui tool show Matchmaker

> matchmaker #2-3 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 AF-P04078-F1-model_v4.pdb, chain A (#1) with
AF-P04771-F1-model_v4.pdb, chain A (#2), sequence alignment score = 1774.1  
RMSD between 355 pruned atom pairs is 0.145 angstroms; (across all 356 pairs:
0.297)  
  
Matchmaker AF-P04078-F1-model_v4.pdb, chain A (#1) with
AF-P38094-F1-model_v4.pdb, chain A (#3), sequence alignment score = 314.9  
RMSD between 117 pruned atom pairs is 1.048 angstroms; (across all 328 pairs:
8.385)  
  


===== 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 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M1 Pro
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: MacBookPro18,3
      Model Number: MKGT3LL/A
      Chip: Unknown
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.1.1
      OS Loader Version: 10151.1.1

Software:

    System Software Overview:

      System Version: macOS 14.0 (23A344)
      Kernel Version: Darwin 23.0.0
      Time since boot: 3 days, 22 hours, 59 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    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: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    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
    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
    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: 1.5.13
    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: 1.0.3
    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: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    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: 1.33.2
    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: 0.2.0
    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: 4.47.0
    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: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    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: 10.0.1
    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: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    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: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by Eric Pettersen, 19 months ago

Cc: Tom Goddard added
Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in garbage collection

comment:2 by Eric Pettersen, 19 months ago

Resolution: → duplicate
Status: accepted → closed
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