#15964 closed defect (nonchimerax)

Graphics crash, macOS 14.6.1, Intel Iris Plus Graphics 655

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

Description

The following bug report has been submitted:
Platform:        macOS-14.6.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Current thread 0x00007ff84699fdc0 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 556 in swap_buffers
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 202 in draw
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 288 in render
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 113 in _redraw
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 100 in draw_new_frame
  File "/Applications/ChimeraX-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 60)


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{
  "uptime" : 870000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro15,2",
  "coalitionID" : 122465,
  "osVersion" : {
    "train" : "macOS 14.6.1",
    "build" : "23G93",
    "releaseType" : "User"
  },
  "captureTime" : "2024-09-18 16:20:32.7602 +0200",
  "codeSigningMonitor" : 0,
  "incident" : "C9238B6C-0C10-41CB-927B-9C64F7767EFD",
  "pid" : 19657,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-09-18 11:48:25.5600 +0200",
  "procStartAbsTime" : 856502835302723,
  "procExitAbsTime" : 872829728241986,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"2D1D3C45-E2CD-50DC-B3E4-890A9DF5387C","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "C9E08316-F481-AE51-0088-DBB74F890D4B",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "wakeTime" : 17015,
  "bridgeVersion" : {"build":"21P6074","train":"8.6"},
  "sleepWakeUUID" : "4E90044D-30F0-461D-949D-8EDEC89765CC",
  "sip" : "enabled",
  "exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
  "termination" : {"flags":0,"code":6,"namespace":"SIGNAL","indicator":"Abort trap: 6","byProc":"ChimeraX","byPid":19657},
  "ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
  "asi" : {"libsystem_c.dylib":["abort() called"]},
  "asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000002\n"],
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : 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    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_bisect.cpython-311-darwin.so",
    "name" : "_bisect.cpython-311-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4481310720,
    "size" : 196608,
    "uuid" : "0fa75f51-66bf-3a60-a393-65ceea03012e",
    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_lzma.cpython-311-darwin.so",
    "name" : "_lzma.cpython-311-darwin.so"
  },
  {
    "source" : "P",
    "arch" : "x86_64",
    "base" : 4481245184,
    "size" : 16384,
    "uuid" : "4921b552-b90a-39c6-b791-14028366f5a0",
    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_bz2.cpython-311-darwin.so",
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    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/zlib.cpython-311-darwin.so",
    "name" : "zlib.cpython-311-darwin.so"
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    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_typing.cpython-311-darwin.so",
    "name" : "_typing.cpython-311-darwin.so"
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    "size" : 65536,
    "uuid" : "ce1cdda7-c310-3834-8656-4829f8b0fa2a",
    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_datetime.cpython-311-darwin.so",
    "name" : "_datetime.cpython-311-darwin.so"
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    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/math.cpython-311-darwin.so",
    "name" : "math.cpython-311-darwin.so"
  },
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    "arch" : "x86_64",
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    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python",
    "name" : "Python",
    "CFBundleVersion" : "3.11.4"
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    "arch" : "x86_64",
    "base" : 4477214720,
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    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
    "size" : 16384,
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    "path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
    "name" : "ChimeraX",
    "CFBundleVersion" : "1.8.0.0"
  },
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    "arch" : "x86_64",
    "base" : 140703183253504,
    "size" : 241656,
    "uuid" : "54b50613-cc4b-3ace-a9ec-919ea83d5e5f",
    "path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
    "name" : "libsystem_kernel.dylib"
  },
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    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703183495168,
    "size" : 49144,
    "uuid" : "d70de43a-2804-340a-804c-5d316c1e013b",
    "path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
    "name" : "libsystem_pthread.dylib"
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    "source" : "P",
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    "size" : 557048,
    "uuid" : "d7acdb03-4453-3d57-9b53-9f338bca635d",
    "path" : "\/usr\/lib\/system\/libsystem_c.dylib",
    "name" : "libsystem_c.dylib"
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    "size" : 45048,
    "uuid" : "4ea5bbf7-8ce1-37ab-916b-d14ffd7d2b4b",
    "path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
    "name" : "libsystem_platform.dylib"
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    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
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    "base" : 140707801870336,
    "size" : 45048,
    "uuid" : "6addefce-1267-354e-9b00-da1e792d8b05",
    "path" : "\/System\/Library\/PrivateFrameworks\/GPUSupport.framework\/Versions\/A\/Libraries\/libGPUSupportMercury.dylib",
    "name" : "libGPUSupportMercury.dylib"
  },
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    "base" : 140712168173568,
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    "CFBundleIdentifier" : "com.apple.driver.AppleIntelKBLGraphicsGLDriver",
    "size" : 15536112,
    "uuid" : "88669d3b-bec7-32df-ae76-1828c7fb2cc4",
    "path" : "\/System\/Library\/Extensions\/AppleIntelKBLGraphicsGLDriver.bundle\/Contents\/MacOS\/AppleIntelKBLGraphicsGLDriver",
    "name" : "AppleIntelKBLGraphicsGLDriver",
    "CFBundleVersion" : "22.0.5"
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    "base" : 140712254091264,
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    "uuid" : "28530138-4bfd-3e68-930b-a672e2466119",
    "path" : "\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/Resources\/GLEngine.bundle\/GLEngine",
    "name" : "GLEngine"
  },
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    "source" : "P",
    "arch" : "x86_64",
    "base" : 140712251887616,
    "CFBundleShortVersionString" : "21.0.19",
    "CFBundleIdentifier" : "com.apple.opengl",
    "size" : 65528,
    "uuid" : "b83396be-2df7-3619-ada6-3a265ff880e2",
    "path" : "\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/OpenGL",
    "name" : "OpenGL",
    "CFBundleVersion" : "21.0.19"
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    "arch" : "x86_64",
    "base" : 140703241240576,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 21172216,
    "uuid" : "d0e19a37-f677-32b5-b3d2-005e60b90f7f",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2487.70.105"
  },
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    "arch" : "x86_64h",
    "base" : 140703183917056,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 4829181,
    "uuid" : "c5e5acb6-9e44-3aa3-bd21-0a5b4a2eee5e",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "2602"
  },
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    "source" : "P",
    "arch" : "x86_64",
    "base" : 140703362613248,
    "CFBundleShortVersionString" : "2.1.1",
    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 2732020,
    "uuid" : "2aa738bf-9f72-3227-8bba-7eae7b9f080b",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
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    "arch" : "x86_64",
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    "size" : 591904,
    "uuid" : "18f658dd-20f3-324d-b7ac-8a9c60b574b3",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
  },
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    "arch" : "x86_64",
    "base" : 140703182659584,
    "size" : 503796,
    "uuid" : "69eca28c-bfb7-35bf-ad4f-1bece712d239",
    "path" : "\/usr\/lib\/libc++.1.dylib",
    "name" : "libc++.1.dylib"
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],
  "sharedCache" : {
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  "size" : 25769803776,
  "uuid" : "b8509d0f-c366-3716-9a03-efa00b40318a"
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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=3.6G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.6G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               512K        4 \nActivity Tracing                   256K        1 \nCG image                           968K       64 \nCG raster data                       8K        1 \nColorSync                          252K       31 \nCoreAnimation                     1272K       91 \nCoreGraphics                        20K        4 \nCoreUI image data                 5320K       43 \nFoundation                          52K        2 \nIOKit                             23.3M        3 \nKernel Alloc Once                    8K        1 \nMALLOC                             3.0G     2662 \nMALLOC guard page                   32K        8 \nMALLOC_LARGE (reserved)            384K        1         reserved VM address space (unallocated)\nMach message                        16K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        120K       30 \nStack                            150.7M       31 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      504.6M      577 \nVM_ALLOCATE (reserved)            32.0M        1         reserved VM address space (unallocated)\n__CTF                               824        1 \n__DATA                            45.1M      796 \n__DATA_CONST                      53.3M      461 \n__DATA_DIRTY                      1842K      230 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       212.1M      155 \n__OBJC_RO                         71.9M        1 \n__OBJC_RW                         2201K        2 \n__TEXT                             1.0G      801 \ndyld private memory                 32K        1 \nmapped file                      559.0M       91 \nshared memory                     2996K       28 \n===========                     =======  ======= \nTOTAL                              5.7G     6133 \nTOTAL, minus reserved VM space     5.6G     6133 \n",
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  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
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},
  "logWritingSignature" : "e26d78a86743188f24c9d735493ecf4d8c2ab04d",
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/lau/Documentos/Ongoing/COP1/ChimeraX/COP!_open&closed&hy5ed.cxs

Log from Tue Sep 17 20:22:45 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/lau/Documentos/Ongoing/COP1/full_data_session.cxs format session

Log from Mon Sep 16 20:24:56 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/Users/lau/Wigge Lab Dropbox/Wigge Lab's shared workspace/Lab
> Info/Manuscripts/COP1/COP1 2024/COP1-HY5 animation/ChimeraX/COP1_closed.cxs"

Log from Sat Sep 14 13:54:22 2024 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Volumes/LAU_32GB/COP1-HY5 Alphafold/fold_cop1/fold_cop1_model_0.cif"

Chain information for fold_cop1_model_0.cif #1  
---  
Chain | Description  
A | .  
  

> open "/Volumes/LAU_32GB/COP1-HY5 Alphafold/fold_cop1/fold_cop1_model_0.cif"

Chain information for fold_cop1_model_0.cif #2  
---  
Chain | Description  
A | .  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #2/A

Alignment identifier is 1  

> select #1/A:10 #2/A:10

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

> select #1/A:10-11 #2/A:10-11

28 atoms, 28 bonds, 4 residues, 2 models selected  
. [ID: 1] region 2 chains [10-11] RMSD: 0.000  
  

> color sel red

> select #1/A:1 #2/A:1

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/A:1-9 #2/A:1-9

138 atoms, 138 bonds, 18 residues, 2 models selected  
. [ID: 1] region 2 chains [1-9] RMSD: 0.000  
  

> color sel orange

> select #1/A:12 #2/A:12

10 atoms, 8 bonds, 2 residues, 2 models selected  

> select #1/A:12-19 #2/A:12-19

122 atoms, 124 bonds, 16 residues, 2 models selected  
. [ID: 1] region 2 chains [12-19] RMSD: 0.000  
  

> color sel orange

> select #1/A:20 #2/A:20

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select #1/A:20-675 #2/A:20-675

10396 atoms, 10588 bonds, 1312 residues, 2 models selected  
. [ID: 1] region 2 chains [20-675] RMSD: 0.000  
  

> color sel medium blue

> color sel #8aacffff

[Repeated 1 time(s)]

> color sel #89abffff

> color sel #88aaffff

> color sel #86a9ffff

> color sel #84a8ffff

> color sel #82a8ffff

> color sel #81a8ffff

> color sel #80a8ffff

[Repeated 1 time(s)]

> color sel #80a9ffff

> color sel #80abffff

> color sel #80acffff

> color sel #81aeffff

> color sel #81afffff

> color sel #81b0ffff

> color sel #81b1ffff

> color sel #82b2ffff

> color sel #83b3ffff

> color sel #83b4ffff

> color sel #84b5ffff

> color sel #84b6ffff

> color sel #84b7ffff

> color sel #85b8ffff

[Repeated 1 time(s)]

> color sel #86b9ffff

> color sel #87baffff

> color sel #88bbffff

> color sel #88bcffff

> color sel #89bdffff

> color sel #8bbeffff

> color sel #8dbeffff

> color sel #8fbfffff

> color sel #90c0ffff

[Repeated 1 time(s)]

> color sel #91c0ffff

> color sel #92c0ffff

> color sel #92bfffff

> color sel #94bfffff

[Repeated 1 time(s)]

> color sel #95bfffff

[Repeated 1 time(s)]

> color sel #97c0ffff

[Repeated 1 time(s)]

> color sel #98c0ffff

> color sel #99c0ffff

[Repeated 1 time(s)]

> color sel #9ac0ffff

[Repeated 1 time(s)]

> color sel #9bc0ffff

> color sel #9cbfffff

[Repeated 1 time(s)]

> color sel #9dbfffff

[Repeated 1 time(s)]

> color sel #9ebfffff

> color sel #9fbfffff

> color sel #a0bfffff

[Repeated 1 time(s)]

> color sel #a1bfffff

[Repeated 1 time(s)]

> color sel #a2bfffff

> color sel #a3beffff

> color sel #a4bdffff

[Repeated 1 time(s)]

> color sel #a4bcffff

> color sel #a7baffff

> color sel #acb6ffff

> color sel #aeb3ffff

> color sel #afb2ffff

> color sel #aeb1ffff

> color sel #adafffff

> color sel #adadffff

> color sel #acacffff

> color sel #acabffff

[Repeated 1 time(s)]

> color sel #acaaffff

[Repeated 1 time(s)]

> color sel #aba9ffff

> color sel #aba8ffff

[Repeated 1 time(s)]

> color sel #aaa7ffff

> color sel #aaa6ffff

> color sel #a9a4ffff

> color sel #a8a2ffff

> color sel #a7a1ffff

> color sel #a6a0ffff

> color sel #a59fffff

> color sel #a59effff

> color sel #a59dffff

> color sel #a49cffff

[Repeated 1 time(s)]

> color sel #a49bffff

> color sel #a49affff

> color sel #a39affff

[Repeated 2 time(s)]

> select clear

> set bgColor white

> select #1/A:12 #2/A:12

10 atoms, 8 bonds, 2 residues, 2 models selected  

> select #1/A:12-24 #2/A:12-24

186 atoms, 188 bonds, 26 residues, 2 models selected  
. [ID: 1] region 2 chains [12-24] RMSD: 0.000  
  

> color sel cornflower blue

> select #1/A:1 #2/A:1

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/A:1-39 #2/A:1-39

550 atoms, 558 bonds, 78 residues, 2 models selected  
. [ID: 1] region 2 chains [1-39] RMSD: 0.000  
  

> select #1/A:40-41 #2/A:40-41

34 atoms, 32 bonds, 4 residues, 2 models selected  

> select #1/A:8-41 #2/A:8-41

474 atoms, 482 bonds, 68 residues, 2 models selected  
. [ID: 1] region 2 chains [8-41] RMSD: 0.000  
  

> select #1/A:1 #2/A:1

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #1/A:1-40 #2/A:1-40

568 atoms, 576 bonds, 80 residues, 2 models selected  
. [ID: 1] region 2 chains [1-40] RMSD: 0.000  
  

> ui tool show "Color Actions"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> color sel pink

[Repeated 2 time(s)]

> select clear

> select /A:1-40

568 atoms, 576 bonds, 80 residues, 2 models selected  

> set bgColor black

> select clear

> select A/:1-40

Expected an objects specifier or a keyword  

> select /A:1-40

568 atoms, 576 bonds, 80 residues, 2 models selected  

> color sel yellow

> select clear

> select #1/A:1-40 #2/A:1-40

568 atoms, 576 bonds, 80 residues, 2 models selected  

> select #1/A:10 #2/A:10

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

> select #1/A:10-11 #2/A:10-11

28 atoms, 28 bonds, 4 residues, 2 models selected  
. [ID: 1] region 2 chains [10-11] RMSD: 0.000  
  

> color sel red

> select clear

> surface

> transparency 60

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #1.1 models

> hide #!2 models

> show #!2 models

> hide #2.1 models

> show #2.1 models

> select /A:1-40

568 atoms, 576 bonds, 80 residues, 2 models selected  

> color (#!2 & sel) #f4e90d66

[Repeated 1 time(s)]

> color (#!2 & sel) #f4e90e66

> color (#!2 & sel) #f4ea1266

> color (#!2 & sel) #f4ea1566

> color (#!2 & sel) #f4ea1866

> color (#!2 & sel) #f4ea1e66

> color (#!2 & sel) #f4ea2166

> color (#!2 & sel) #f4eb2466

> color (#!2 & sel) #f4ef2d66

> color (#!2 & sel) #f4f43e66

> color (#!2 & sel) #f0f44866

> color (#!2 & sel) #eff44a66

> color (#!2 & sel) #f0f44c66

> color (#!2 & sel) #f0f44d66

> color (#!2 & sel) #eff44f66

> color (#!2 & sel) #ebf45d66

> color (#!2 & sel) #e6f47066

> color (#!2 & sel) #e6f47366

> color (#!2 & sel) #e6f47466

[Repeated 1 time(s)]

> color (#!2 & sel) #e7f47666

> color (#!2 & sel) #ebf48366

> color (#!2 & sel) #edf49366

> color (#!2 & sel) #eef49a66

> color (#!2 & sel) #eff49b66

> color (#!2 & sel) #eff49c66

> color (#!2 & sel) #f0f49d66

> color (#!2 & sel) #f0f49e66

> color (#!2 & sel) #f2f4a166

> color (#!2 & sel) #f3f4a366

> color (#!2 & sel) #f4f4a666

> color (#!2 & sel) #f4f3a766

> color (#!2 & sel) #f4f2a966

> color (#!2 & sel) #f4f0ad66

> color (#!2 & sel) #f4efaf66

> color (#!2 & sel) #f4efb066

> color (#!2 & sel) #f4edb266

> color (#!2 & sel) #f4ecb666

> color (#!2 & sel) #f4ebba66

> color (#!2 & sel) #f4ebbb66

[Repeated 1 time(s)]

> color (#!2 & sel) #f4e9bd66

> color (#!2 & sel) #f4e9c066

> color (#!2 & sel) #f4e9c166

> color (#!2 & sel) #f4e8c466

> color (#!2 & sel) #f4e9c866

[Repeated 1 time(s)]

> color (#!2 & sel) #f4e9c766

> color (#!2 & sel) #f4eac666

> color (#!2 & sel) #f4ebc366

> color (#!2 & sel) #f4e9be66

> color (#!2 & sel) #f4e8b966

> color (#!2 & sel) #f4e7b566

> color (#!2 & sel) #f4e7b366

> color (#!2 & sel) #f4e6b066

> color (#!2 & sel) #f4e7ab66

> color (#!2 & sel) #f4e8a666

> color (#!2 & sel) #f4e89566

> color (#!2 & sel) #f4e57966

> color (#!2 & sel) #f4e46566

> color (#!2 & sel) #f4e46066

[Repeated 1 time(s)]

> color (#!2 & sel) #f4e45f66

> color (#!2 & sel) #f4e55f66

> color (#!2 & sel) #f4e65f66

[Repeated 1 time(s)]

> color (#!2 & sel) #f4e75f66

[Repeated 1 time(s)]

> color (#!2 & sel) #f4e85f66

> color (#!2 & sel) #f4e95f66

> color (#!2 & sel) #f4ea5f66

> color (#!2 & sel) #f4eb5f66

> color (#!2 & sel) #f4ec6066

> color (#!2 & sel) #f4ed6066

> color (#!2 & sel) #f4ed6166

> color (#!2 & sel) #f4ee6166

> color (#!2 & sel) #f4ef6266

> color (#!2 & sel) #f4f06366

> color (#!2 & sel) #f4f16366

> color (#!2 & sel) #f4f06666

> color (#!2 & sel) #f4ef6866

> color (#!2 & sel) #f4ee6a66

> color (#!2 & sel) #f4ed6c66

> color (#!2 & sel) #f4ed6d66

> color (#!2 & sel) #f4ed6f66

> color (#!2 & sel) #f4ee6f66

> color (#!2 & sel) #f4ef7166

> color (#!2 & sel) #f4ef7366

> color (#!2 & sel) #f4ef7466

> color (#!2 & sel) #f4ee7766

> color (#!2 & sel) #f4ee7966

> color (#!2 & sel) #f4ed7c66

> color (#!2 & sel) #f4ee8266

> color (#!2 & sel) #f4ee8666

> color (#!2 & sel) #f4ef8a66

> color (#!2 & sel) #f4ef8b66

> color (#!2 & sel) #f4ef8c66

> color (#!2 & sel) #f4ee8d66

> color (#!2 & sel) #f4ef8e66

[Repeated 1 time(s)]

> color (#!2 & sel) #f4ef9066

> color (#!2 & sel) #f4ef9266

[Repeated 1 time(s)]

> color (#!2 & sel) #f4f09366

[Repeated 1 time(s)]

> color (#!2 & sel) #f4f09466

> color (#!2 & sel) #f4f09566

[Repeated 1 time(s)]

> color (#!2 & sel) #f4f19666

[Repeated 1 time(s)]

> color (#!2 & sel) #f4f19766

> color (#!2 & sel) #f4f09966

> color (#!2 & sel) #f4f19966

> color (#!2 & sel) #f4f19a66

> color (#!2 & sel) #f4f19b66

> color (#!2 & sel) #f4f19c66

> color (#!2 & sel) #f4f19d66

> color (#!2 & sel) #f4f19e66

> color (#!2 & sel) #f4f19f66

> color (#!2 & sel) #f4f2a166

> color (#!2 & sel) #f4f3a266

> color (#!2 & sel) #f4f3a366

> color (#!2 & sel) #f4f3a466

> color (#!2 & sel) #f4f4a466

> color (#!2 & sel) #f4f4a566

> color (#!2 & sel) #f3f4a566

> color (#!2 & sel) #f2f4a266

> color (#!2 & sel) #f1f4a066

> color (#!2 & sel) #f1f49d66

> color (#!2 & sel) #f1f49c66

> color (#!2 & sel) #f1f49b66

> color (#!2 & sel) #f0f49966

> color (#!2 & sel) #f0f49866

> color (#!2 & sel) #eff49666

> color (#!2 & sel) #edf49366

> color (#!2 & sel) #ecf49166

> color (#!2 & sel) #ecf49066

[Repeated 3 time(s)]

> color (#!2 & sel) #ecf48f66

> color (#!2 & sel) #edf48f66

> color (#!2 & sel) #eef48e66

> color (#!2 & sel) #eff48e66

> color (#!2 & sel) #f0f48e66

[Repeated 1 time(s)]

> color (#!2 & sel) #f1f48e66

> color (#!2 & sel) #f2f48e66

> color (#!2 & sel) #f3f48e66

> color (#!2 & sel) #f4f48f66

> color (#!2 & sel) #f4f38e66

[Repeated 1 time(s)]

> color (#!2 & sel) #f4f28e66

[Repeated 1 time(s)]

> color (#!2 & sel) #f4f28f66

> select /A:1-40

568 atoms, 576 bonds, 80 residues, 2 models selected  

> select #1/A:10 #2/A:10

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

> select #1/A:10-11 #2/A:10-11

28 atoms, 28 bonds, 4 residues, 2 models selected  
. [ID: 1] region 2 chains [10-11] RMSD: 0.000  
  

> color (#!2 & sel) #f4452d66

[Repeated 1 time(s)]

> color (#!2 & sel) #f4472b66

[Repeated 1 time(s)]

> color (#!2 & sel) #f4482b66

> color (#!2 & sel) #f44a2b66

> color (#!2 & sel) #f4572e66

> color (#!2 & sel) #f4643166

> color (#!2 & sel) #f4663266

> color (#!2 & sel) #f4673166

> color (#!2 & sel) #f4693066

> color (#!2 & sel) #f4682c66

> color (#!2 & sel) #f4672966

> color (#!2 & sel) #f4662866

> color (#!2 & sel) #f4652766

> color (#!2 & sel) #f4642666

> color (#!2 & sel) #f4632566

> color (#!2 & sel) #f4622466

> color (#!2 & sel) #f4602266

> color (#!2 & sel) #f45f2066

> color (#!2 & sel) #f45e2066

> color (#!2 & sel) #f45d1f66

[Repeated 1 time(s)]

> color (#!2 & sel) #f45c1e66

> color (#!2 & sel) #f45b1d66

> select clear

> transparency #2 30

> transparency #2 90

> transparency #2 30

> transparency #2 40

> select /A:368-619

4014 atoms, 4106 bonds, 504 residues, 2 models selected  

> select /A:368-675

4858 atoms, 4968 bonds, 616 residues, 2 models selected  

> color (#!2 & sel) #f45b1a66

> color (#!2 & sel) #f45c1b66

> color (#!2 & sel) #f4723166

> color (#!2 & sel) #f48f4e66

> color (#!2 & sel) #f4935266

> color (#!2 & sel) #f4945366

> color (#!2 & sel) #f4995e66

> color (#!2 & sel) #f49e6b66

> color (#!2 & sel) #f49d6c66

> color (#!2 & sel) #f49c6d66

> color (#!2 & sel) #f49d7b66

> color (#!2 & sel) #f4a09266

> color (#!2 & sel) #f49d9466

> color (#!2 & sel) #f49b9466

> color (#!2 & sel) #f4999466

> color (#!2 & sel) #f4a3ad66

> color (#!2 & sel) #f4b0e066

> color (#!2 & sel) #f4afe766

> color (#!2 & sel) #f4aee866

> color (#!2 & sel) #f4adea66

> color (#!2 & sel) #e6a4f466

> color (#!2 & sel) #c58ef466

> color (#!2 & sel) #c089f466

> color (#!2 & sel) #bf88f466

> color (#!2 & sel) #be86f466

> color (#!2 & sel) #b07af466

> color (#!2 & sel) #8f60f466

> color (#!2 & sel) #8b5cf466

> color (#!2 & sel) #895af466

> color (#!2 & sel) #885af466

> color (#!2 & sel) #7042f466

> color (#!2 & sel) #6033f466

> color (#!2 & sel) #6032f466

> color (#!2 & sel) #6033f466

> color (#!2 & sel) #6435f466

> color (#!2 & sel) #6637f466

> color (#!2 & sel) #6b39f466

> color (#!2 & sel) #6c3af466

> color (#!2 & sel) #6d3bf466

> color (#!2 & sel) #6e3cf466

> color (#!2 & sel) #6f3cf466

> color (#!2 & sel) #713ff466

> color (#!2 & sel) #7541f466

> color (#!2 & sel) #7943f466

> color (#!2 & sel) #7c44f466

> color (#!2 & sel) #7e44f466

> color (#!2 & sel) #8145f466

> color (#!2 & sel) #8346f466

> color (#!2 & sel) #914ff466

> color (#!2 & sel) #9350f466

> color (#!2 & sel) #9551f466

> color (#!2 & sel) #9751f466

> color (#!2 & sel) #9851f466

> color (#!2 & sel) #9a51f466

> color (#!2 & sel) #9d51f466

> color (#!2 & sel) #9f51f466

> color (#!2 & sel) #a051f466

[Repeated 1 time(s)]

> color (#!2 & sel) #9456f466

> color (#!2 & sel) #7a5ef466

> color (#!2 & sel) #5a5af466

> color (#!2 & sel) #4e66f466

> color (#!2 & sel) #3c75f466

> color (#!2 & sel) #307ff466

> color (#!2 & sel) #248cf466

> color (#!2 & sel) #1c95f466

> color (#!2 & sel) #199bf466

> color (#!2 & sel) #1a9df466

> color (#!2 & sel) #1a9ef466

> color (#!2 & sel) #1b9ff466

> color (#!2 & sel) #1f9ff466

> color (#!2 & sel) #229ef466

> color (#!2 & sel) #259af466

> color (#!2 & sel) #2697f466

> color (#!2 & sel) #2794f466

> color (#!2 & sel) #2893f466

> color (#!2 & sel) #2891f466

> color (#!2 & sel) #2990f466

> color (#!2 & sel) #298ff466

> color (#!2 & sel) #298ef466

> color (#!2 & sel) #298cf466

> color (#!2 & sel) #298bf466

> color (#!2 & sel) #298af466

> color (#!2 & sel) #2b89f466

> color (#!2 & sel) #2c87f466

> color (#!2 & sel) #2e86f466

> color (#!2 & sel) #2f85f466

> color (#!2 & sel) #3084f466

> color (#!2 & sel) #3c81f466

> color (#!2 & sel) #4e78f466

> color (#!2 & sel) #586df466

> color (#!2 & sel) #6a63f466

> color (#!2 & sel) #8366f466

> color (#!2 & sel) #8e67f466

> color (#!2 & sel) #9566f466

> color (#!2 & sel) #9666f466

> color (#!2 & sel) #9964f466

> color (#!2 & sel) #9a62f466

> color (#!2 & sel) #9d5ff466

> color (#!2 & sel) #9f5df466

> color (#!2 & sel) #a05bf466

> color (#!2 & sel) #a059f466

> color (#!2 & sel) #a159f466

> color (#!2 & sel) #a158f466

> color (#!2 & sel) #a255f466

[Repeated 1 time(s)]

> color (#!2 & sel) #a253f466

> color (#!2 & sel) #a450f466

> color (#!2 & sel) #a64bf466

> color (#!2 & sel) #a848f466

> color (#!2 & sel) #a846f466

> color (#!2 & sel) #a945f466

> color (#!2 & sel) #a944f466

> color (#!2 & sel) #a841f466

> color (#!2 & sel) #a93ff466

> color (#!2 & sel) #aa3df466

> color (#!2 & sel) #aa38f466

> color (#!2 & sel) #ad33f466

> color (#!2 & sel) #ac32f466

[Repeated 1 time(s)]

> color (#!2 & sel) #ac31f466

> color (#!2 & sel) #ab30f466

[Repeated 1 time(s)]

> color (#!2 & sel) #ab2ff466

> color (#!2 & sel) #aa2ef466

> color (#!2 & sel) #a92df466

[Repeated 1 time(s)]

> color (#!2 & sel) #a92cf466

> color (#!2 & sel) #a82bf466

> color (#!2 & sel) #a729f466

> color (#!2 & sel) #a627f466

> color (#!2 & sel) #a525f466

> color (#!2 & sel) #a524f466

> color (#!2 & sel) #a424f466

> color (#!2 & sel) #a222f466

> color (#!2 & sel) #a01ff466

> color (#!2 & sel) #9e1df466

> color (#!2 & sel) #9d1cf466

> color (#!2 & sel) #9b1bf466

> color (#!2 & sel) #9818f466

> color (#!2 & sel) #9617f466

> color (#!2 & sel) #9516f466

> color (#!2 & sel) #9316f466

> color (#!2 & sel) #9214f466

> color (#!2 & sel) #8e13f466

> color (#!2 & sel) #8910f466

> color (#!2 & sel) #870ff466

[Repeated 1 time(s)]

> color (#!2 & sel) #860ff466

> color (#!2 & sel) #7f0cf466

> color (#!2 & sel) #7a08f466

> color (#!2 & sel) #7907f466

> color (#!2 & sel) #7502f466

> color (#!2 & sel) #7400f466

> color (#!2 & sel) #7100f466

> color (#!2 & sel) #6e00f466

> color (#!2 & sel) #6500f466

> color (#!2 & sel) #6200f466

> color (#!2 & sel) #5f00f466

> color (#!2 & sel) #5300f466

> color (#!2 & sel) #4700f466

> color (#!2 & sel) #4400f466

> color (#!2 & sel) #4100f466

> color (#!2 & sel) #3e00f466

> color (#!2 & sel) #3b00f466

> color (#!2 & sel) #3800f466

> color (#!2 & sel) #3500f466

> color (#!2 & sel) #3200f466

[Repeated 1 time(s)]

> color (#!2 & sel) #3300f466

> color (#!2 & sel) #3400f466

> color (#!2 & sel) #3700f466

> color (#!2 & sel) #3b00f466

> color (#!2 & sel) #3e00f466

> color (#!2 & sel) #4200f466

> color (#!2 & sel) #4700f466

> color (#!2 & sel) #5100f466

> color (#!2 & sel) #5900f466

> color (#!2 & sel) #6201f466

> color (#!2 & sel) #6a02f466

> color (#!2 & sel) #6f02f466

> color (#!2 & sel) #7502f466

> color (#!2 & sel) #7a04f466

> color (#!2 & sel) #7c06f466

> color (#!2 & sel) #7f0af466

> color (#!2 & sel) #850ff466

> color (#!2 & sel) #8a14f466

> color (#!2 & sel) #961df466

> color (#!2 & sel) #9b21f466

> color (#!2 & sel) #9d22f466

> color (#!2 & sel) #9d23f466

> color (#!2 & sel) #9e25f466

> color (#!2 & sel) #a22df466

> color (#!2 & sel) #a32ff466

> color (#!2 & sel) #a532f466

> color (#!2 & sel) #a83af466

> color (#!2 & sel) #ab41f466

> color (#!2 & sel) #ad45f466

> color (#!2 & sel) #b04bf466

> color (#!2 & sel) #b24ef466

> color (#!2 & sel) #b350f466

> color (#!2 & sel) #b656f466

> color (#!2 & sel) #b758f466

> color (#!2 & sel) #b85af466

> color (#!2 & sel) #b95ff466

> color (#!2 & sel) #b860f466

> color (#!2 & sel) #b963f466

> color (#!2 & sel) #b967f466

> color (#!2 & sel) #b96af466

> color (#!2 & sel) #ba6df466

> color (#!2 & sel) #b96ef466

> color (#!2 & sel) #b96ff466

> color (#!2 & sel) #bb72f466

> color (#!2 & sel) #bc75f466

> color (#!2 & sel) #bd76f466

> color (#!2 & sel) #be78f466

> color (#!2 & sel) #bf7bf466

> color (#!2 & sel) #c080f466

> color (#!2 & sel) #c082f466

> color (#!2 & sel) #c185f466

> color (#!2 & sel) #c288f466

> color (#!2 & sel) #c289f466

> color (#!2 & sel) #c28af466

> color (#!2 & sel) #c38cf466

> color (#!2 & sel) #c48ef466

[Repeated 1 time(s)]

> color (#!2 & sel) #c58ff466

> color (#!2 & sel) #c691f466

> color (#!2 & sel) #c692f466

> color (#!2 & sel) #c795f466

> color (#!2 & sel) #c798f466

> color (#!2 & sel) #c899f466

[Repeated 1 time(s)]

> color (#!2 & sel) #c89bf466

> color (#!2 & sel) #c99ef466

> color (#!2 & sel) #ca9ff466

> color (#!2 & sel) #caa0f466

[Repeated 1 time(s)]

> color (#!2 & sel) #caa1f466

> color (#!2 & sel) #cba2f466

> color (#!2 & sel) #cba3f466

> color (#!2 & sel) #cca4f466

> color (#!2 & sel) #cca5f466

> color (#!2 & sel) #cda6f466

> color (#!2 & sel) #cda7f466

> color (#!2 & sel) #cda8f466

> color (#!2 & sel) #cea9f466

[Repeated 1 time(s)]

> color (#!2 & sel) #cdaaf466

> color (#!2 & sel) #cbaaf466

> color (#!2 & sel) #cba9f466

> color (#!2 & sel) #c9a9f466

> color (#!2 & sel) #c7a8f466

> color (#!2 & sel) #c5a8f466

> color (#!2 & sel) #c3a8f466

> color (#!2 & sel) #c2a8f466

> color (#!2 & sel) #c0a7f466

> color (#!2 & sel) #bda6f466

> color (#!2 & sel) #bba6f466

> color (#!2 & sel) #b8a5f466

> color (#!2 & sel) #b7a5f466

[Repeated 1 time(s)]

> color (#!2 & sel) #b6a4f466

> color (#!2 & sel) #b5a4f466

> color (#!2 & sel) #b4a4f466

> color (#!2 & sel) #b2a4f466

> color (#!2 & sel) #b2a3f466

> color (#!2 & sel) #b1a3f466

> color (#!2 & sel) #b0a3f466

> color (#!2 & sel) #afa3f466

> color (#!2 & sel) #ada2f466

> color (#!2 & sel) #aba2f466

> color (#!2 & sel) #aaa1f466

> color (#!2 & sel) #a8a0f466

> color (#!2 & sel) #a7a0f466

> color (#!2 & sel) #a59ff466

> color (#!2 & sel) #a49ff466

> color (#!2 & sel) #a29ef466

> color (#!2 & sel) #a19ef466

> color (#!2 & sel) #9e9df466

> color (#!2 & sel) #9c9cf466

> color (#!2 & sel) #9b9bf466

> color (#!2 & sel) #999cf466

> color (#!2 & sel) #979cf466

> color (#!2 & sel) #979bf466

> color (#!2 & sel) #969bf466

> color (#!2 & sel) #959cf466

> color (#!2 & sel) #919af466

> color (#!2 & sel) #8e99f466

> color (#!2 & sel) #8c98f466

> color (#!2 & sel) #8a97f466

> color (#!2 & sel) #8897f466

> color (#!2 & sel) #8797f466

> color (#!2 & sel) #8696f466

> color (#!2 & sel) #8596f466

[Repeated 1 time(s)]

> color (#!2 & sel) #8495f466

> color (#!2 & sel) #8395f466

> color (#!2 & sel) #8195f466

> color (#!2 & sel) #8094f466

> color (#!2 & sel) #7f94f466

> color (#!2 & sel) #7e94f466

> color (#!2 & sel) #7d94f466

[Repeated 1 time(s)]

> color (#!2 & sel) #7b94f466

> color (#!2 & sel) #7a94f466

> color (#!2 & sel) #7994f466

> color (#!2 & sel) #7893f466

> color (#!2 & sel) #7793f466

> color (#!2 & sel) #7693f466

> color (#!2 & sel) #7593f466

[Repeated 2 time(s)]

> color (#!2 & sel) #7592f366

> color (#!2 & sel) #7492f266

> color (#!2 & sel) #7491f166

[Repeated 1 time(s)]

> color (#!2 & sel) #7391f066

[Repeated 1 time(s)]

> color (#!2 & sel) #7390ef66

[Repeated 1 time(s)]

> color (#!2 & sel) #7290ee66

> color (#!2 & sel) #728fed66

[Repeated 1 time(s)]

> color (#!2 & sel) #728eec66

> color (#!2 & sel) #718eec66

[Repeated 1 time(s)]

> color (#!2 & sel) #718eeb66

> color (#!2 & sel) #718deb66

> color (#!2 & sel) #708ce866

> color (#!2 & sel) #6e8be666

> color (#!2 & sel) #6d89e466

> color (#!2 & sel) #6d88e266

> color (#!2 & sel) #6984db66

> color (#!2 & sel) #657fd266

> color (#!2 & sel) #617aca66

> color (#!2 & sel) #5f77c566

> color (#!2 & sel) #5e76c466

> color (#!2 & sel) #5e76c366

> color (#!2 & sel) #5c73bf66

> color (#!2 & sel) #5a71bc66

> color (#!2 & sel) #586eb666

> color (#!2 & sel) #566bb266

> color (#!2 & sel) #556bb266

[Repeated 1 time(s)]

> color (#!2 & sel) #566cb366

> color (#!2 & sel) #576eb666

> color (#!2 & sel) #596fb966

> color (#!2 & sel) #5a71bb66

> color (#!2 & sel) #5b72be66

> color (#!2 & sel) #5c73bf66

> color (#!2 & sel) #5d74c166

> color (#!2 & sel) #5d75c266

> color (#!2 & sel) #5e76c566

> color (#!2 & sel) #5f78c666

> color (#!2 & sel) #617aca66

> color (#!2 & sel) #637ccd66

> color (#!2 & sel) #637cce66

> color (#!2 & sel) #647dcf66

> color (#!2 & sel) #6680d466

> color (#!2 & sel) #6782d766

> color (#!2 & sel) #6882d866

[Repeated 1 time(s)]

> color (#!2 & sel) #6983da66

> color (#!2 & sel) #6a84dc66

> color (#!2 & sel) #6a85dc66

> color (#!2 & sel) #6b86de66

> color (#!2 & sel) #6b87e066

> color (#!2 & sel) #6c87e066

[Repeated 1 time(s)]

> color (#!2 & sel) #6c87e166

> color (#!2 & sel) #6c88e166

> color (#!2 & sel) #6c88e266

> color (#!2 & sel) #6d88e266

> color (#!2 & sel) #6d89e366

> select clear

> set bgColor white

> hide #!2 cartoons

[Repeated 1 time(s)]

> show #!2 cartoons

> transparency #2 60

> transparency #2 20

> select /A 368-675

Expected a keyword  

> select /A:368-675

4858 atoms, 4968 bonds, 616 residues, 2 models selected  

> color (#!2 & sel) #698ae366

[Repeated 1 time(s)]

> color (#!2 & sel) #6787e366

> color (#!2 & sel) #6786e366

> color (#!2 & sel) #6785e366

> color (#!2 & sel) #6684e366

> color (#!2 & sel) #6582e366

> color (#!2 & sel) #6079e366

> color (#!2 & sel) #5868e366

> color (#!2 & sel) #545ee366

> color (#!2 & sel) #545de366

> color (#!2 & sel) #545ce366

> color (#!2 & sel) #5356e366

> color (#!2 & sel) #5350e366

[Repeated 1 time(s)]

> color (#!2 & sel) #544fe366

> color (#!2 & sel) #534ee366

> color (#!2 & sel) #534de366

> color (#!2 & sel) #554be366

> color (#!2 & sel) #584ae366

> color (#!2 & sel) #5b49e366

> color (#!2 & sel) #5f48e366

> color (#!2 & sel) #6246e366

> color (#!2 & sel) #6444e366

> color (#!2 & sel) #6743e366

> color (#!2 & sel) #6842e366

> color (#!2 & sel) #6941e366

> color (#!2 & sel) #6b3fe366

> color (#!2 & sel) #703de366

> color (#!2 & sel) #723ce366

> color (#!2 & sel) #723be366

> color (#!2 & sel) #713ae366

> color (#!2 & sel) #6d37e366

> color (#!2 & sel) #6a35e366

> color (#!2 & sel) #6432e366

> color (#!2 & sel) #5d2ee366

> color (#!2 & sel) #4c25e366

> color (#!2 & sel) #4321e366

> color (#!2 & sel) #4121e366

> color (#!2 & sel) #3b1fe366

> color (#!2 & sel) #2516e366

> color (#!2 & sel) #1e13e366

> color (#!2 & sel) #1c12e366

> color (#!2 & sel) #1b13e366

> color (#!2 & sel) #1410e366

> color (#!2 & sel) #0b0fe366

> color (#!2 & sel) #0a10e366

> color (#!2 & sel) #0b13e366

> color (#!2 & sel) #0717e366

> color (#!2 & sel) #0518e366

> color (#!2 & sel) #0619e366

> color (#!2 & sel) #061ae366

> color (#!2 & sel) #041ce366

> color (#!2 & sel) #0024e366

> color (#!2 & sel) #0029e366

> color (#!2 & sel) #002be366

> color (#!2 & sel) #002de366

> color (#!2 & sel) #0031e366

> color (#!2 & sel) #0035e366

> color (#!2 & sel) #0038e366

> color (#!2 & sel) #003ce366

> color (#!2 & sel) #003de366

> color (#!2 & sel) #003fe366

> color (#!2 & sel) #0040e366

> color (#!2 & sel) #0041e366

> color (#!2 & sel) #0042e366

> color (#!2 & sel) #0043e366

> color (#!2 & sel) #0545e366

> color (#!2 & sel) #0a47e366

> color (#!2 & sel) #104be366

> color (#!2 & sel) #144de366

> color (#!2 & sel) #1a51e366

> color (#!2 & sel) #2053e366

> color (#!2 & sel) #2a56e366

> color (#!2 & sel) #3259e366

> color (#!2 & sel) #355ae366

[Repeated 1 time(s)]

> color (#!2 & sel) #385ae366

> color (#!2 & sel) #3e5ae366

[Repeated 3 time(s)]

> color (#!2 & sel) #3e5be366

> color (#!2 & sel) #405de366

> color (#!2 & sel) #425fe366

> color (#!2 & sel) #4360e366

> color (#!2 & sel) #4862e366

> color (#!2 & sel) #4b63e366

> color (#!2 & sel) #4d63e366

[Repeated 1 time(s)]

> color (#!2 & sel) #4e63e366

[Repeated 2 time(s)]

> color (#!2 & sel) #4f63e366

> color (#!2 & sel) #5062e366

> color (#!2 & sel) #5261e366

> color (#!2 & sel) #5361e366

> color (#!2 & sel) #5461e366

> color (#!2 & sel) #5560e366

> color (#!2 & sel) #5660e366

> color (#!2 & sel) #585fe366

> color (#!2 & sel) #585ee366

> color (#!2 & sel) #595ee366

> color (#!2 & sel) #5a5de366

> color (#!2 & sel) #5b5de366

> color (#!2 & sel) #5c5de366

> color (#!2 & sel) #5d5ce366

> color (#!2 & sel) #635fe366

> color (#!2 & sel) #6560e366

> color (#!2 & sel) #6760e366

> color (#!2 & sel) #6961e366

> color (#!2 & sel) #6b61e366

> color (#!2 & sel) #7063e366

> color (#!2 & sel) #7665e366

> color (#!2 & sel) #7966e366

> color (#!2 & sel) #7a66e366

[Repeated 2 time(s)]

> color (#!2 & sel) #847fe366

> color (#!2 & sel) #837fe366

> color (#!2 & sel) #837ee366

[Repeated 1 time(s)]

> color (#!2 & sel) #837de366

> color (#!2 & sel) #827ce366

> color (#!2 & sel) #827be366

> color (#!2 & sel) #8279e366

[Repeated 1 time(s)]

> color (#!2 & sel) #8378e366

> color (#!2 & sel) #8478e366

> color (#!2 & sel) #8678e366

> color (#!2 & sel) #8777e366

> color (#!2 & sel) #8877e366

> color (#!2 & sel) #8a76e366

> color (#!2 & sel) #8b76e366

> color (#!2 & sel) #8b75e366

> color (#!2 & sel) #8b74e366

> color (#!2 & sel) #8c74e366

> color (#!2 & sel) #8b73e366

> color (#!2 & sel) #8b72e366

> color (#!2 & sel) #8a71e366

> color (#!2 & sel) #8a70e366

> color (#!2 & sel) #8970e366

> color (#!2 & sel) #896fe366

> color (#!2 & sel) #896ee366

> color (#!2 & sel) #886ee366

> color (#!2 & sel) #886de366

> color (#!2 & sel) #886ce366

> color (#!2 & sel) #876ce366

> color (#!2 & sel) #876be366

> color (#!2 & sel) #876ae366

> color (#!2 & sel) #8669e366

[Repeated 1 time(s)]

> color (#!2 & sel) #8568e366

> color (#!2 & sel) #8468e366

> color (#!2 & sel) #8368e366

> color (#!2 & sel) #8367e366

> color (#!2 & sel) #8364e366

> color (#!2 & sel) #8363e366

[Repeated 1 time(s)]

> color (#!2 & sel) #8261e366

[Repeated 1 time(s)]

> color (#!2 & sel) #815fe366

[Repeated 1 time(s)]

> color (#!2 & sel) #805de366

> color (#!2 & sel) #7f5ce366

> color (#!2 & sel) #7d5be366

> color (#!2 & sel) #755be366

> color (#!2 & sel) #725ee366

> color (#!2 & sel) #7264e366

> color (#!2 & sel) #7267e366

[Repeated 2 time(s)]

> color (#!2 & sel) #6d66e366

> color (#!2 & sel) #6c65e366

> color (#!2 & sel) #6663e366

> color (#!2 & sel) #6362e366

> color (#!2 & sel) #6262e366

> color (#!2 & sel) #5e63e366

> color (#!2 & sel) #5d64e366

> color (#!2 & sel) #5c64e366

[Repeated 1 time(s)]

> color (#!2 & sel) #5b65e366

> color (#!2 & sel) #5966e366

> color (#!2 & sel) #5867e366

[Repeated 2 time(s)]

> select clear

> set bgColor black

> set bgColor white

> lighting simple

> lighting soft

> lighting full

> lighting simple

> lighting full

> lighting simple

> lighting full

> lighting simple

> lighting soft

> lighting simple

> lighting full

> select A/:368-675

Expected an objects specifier or a keyword  

> select /A:368-675

4858 atoms, 4968 bonds, 616 residues, 2 models selected  

> transparency (#!2 & sel) 40

> lighting soft

> lighting simple

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting simple

> lighting soft

> lighting full

> select /A:1:40

34 atoms, 30 bonds, 4 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel gold

> select /A:1-40

568 atoms, 576 bonds, 80 residues, 2 models selected  

> color sel gold

> color sel yellow

> color sel khaki

> color sel goldenrod

> color sel green yellow

> color sel yellow green

> color sel dark khaki

> color sel light salmon

> color sel sandy brown

> color sel wheat

> color sel khaki

> color sel goldenrod

> select #1/A:10 #2/A:10

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

> select #1/A:10-11 #2/A:10-11

28 atoms, 28 bonds, 4 residues, 2 models selected  
. [ID: 1] region 2 chains [10-11] RMSD: 0.000  
  

> color sel red

> color sel dark red

> color sel maroon

> color sel coral

> color sel indian red

> color sel tomato

> select /A:41-675

10116 atoms, 10306 bonds, 1270 residues, 2 models selected  

> color sel medium purple

> select /A:368-675

4858 atoms, 4968 bonds, 616 residues, 2 models selected  

> color sel royal blue

> color sel slate blue

> color sel dark slate blue

> color sel medium blue

> color sel blue violet

> color sel dark violet

> color sel rebecca purple

> color sel dodger blue

> color sel cornflower blue

> color sel blue

> color sel royal blue

> color sel medium slate blue

> color sel slate blue

> color sel dark slate blue

> color sel rebecca purple

> color sel cornflower blue

> color sel slate blue

> color sel medium slate blue

> color sel royal blue

> color sel medium slate blue

> color sel royal blue

> select clear

> ui tool show "Side View"

> lighting simple

> lighting soft

> lighting full

> view orient

> select A/

Expected an objects specifier or a keyword  

> select /A

10684 atoms, 10884 bonds, 1350 residues, 2 models selected  

> show sel & #!2 cartoons

[Repeated 3 time(s)]

> transparency (#!2 & sel) 40

> select /A:368-675

4858 atoms, 4968 bonds, 616 residues, 2 models selected  

> show sel & #!2 cartoons

[Repeated 2 time(s)]

> show sel & #!2 atoms

[Repeated 1 time(s)]

> show sel & #!2 cartoons

> hide sel & #!2 surfaces

> hide sel & #!2 atoms

> show sel & #!2 surfaces

> select clear

> save /Users/lau/Desktop/COP1_colored.tif width 1616 height 1023 supersample
> 3 transparentBackground true

> select all

10684 atoms, 10884 bonds, 1350 residues, 2 models selected  

> transparency (#!2 & sel) 10

> select A/

Expected an objects specifier or a keyword  

> select /A

10684 atoms, 10884 bonds, 1350 residues, 2 models selected  

> transparency (#!2 & sel) 30

> save /Users/lau/Desktop/COP1_colored.tif width 1616 height 1023 supersample
> 3

> select clear

> save /Users/lau/Desktop/COP1_colored.tif width 1616 height 1023 supersample
> 3

> select A/:6-13

Expected an objects specifier or a keyword  

> select /A:6-13

110 atoms, 112 bonds, 16 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel tomato

> select clear

> save /Users/lau/Desktop/COP1_colored_2.tif width 1616 height 1023
> supersample 3

> open "/Volumes/LAU_32GB/COP1-HY5 Alphafold/fold_hy5/fold_hy5_model_0.cif"

Chain information for fold_hy5_model_0.cif #3  
---  
Chain | Description  
A | .  
  

> close #3

> save "/Users/lau/Wigge Lab Dropbox/Wigge Lab's shared workspace/Lab
> Info/Manuscripts/COP1/COP1 2024/COP1-HY5 animation/COP1_closed.cxs"

——— End of log from Sat Sep 14 13:54:22 2024 ———

opened ChimeraX session  

> close #1

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

Cell requested for row 0 is out of bounds for table with 2 rows! Resizing
table model.  

> ui tool show Angles/Torsions

> select /A: 22

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

> cofr sel

> ui mousemode right "rotate slab"

> ui tool show "Model Panel"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> ~hbonds

> hbonds sel reveal true

0 hydrogen bonds found  
Exactly two atoms must be selected!  

> show sel atoms

> hide sel cartoons

[Repeated 4 time(s)]

> close #2.2

> hide sel surfaces

> show sel atoms

> hide sel atoms

> show sel atoms

> distance style symbol false

[Repeated 2 time(s)]

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> show (#!2 & sel) target ab

> style (#!2 & sel) stick

Changed 7 atom styles  

> ui tool show Rotamers

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 3 time(s)]

> swapaa interactive sel VAL rotLib Dunbrack

/A VAL 22: phi -58.5, psi 130.4 trans  
Changed 12 bond radii  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> hide sel atoms

> show sel cartoons

> hide sel surfaces

> select /A

5357 atoms, 5454 bonds, 678 residues, 4 models selected  

> hide sel surfaces

> hide sel atoms

> select /A: 22

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

> swapaa interactive sel VAL rotLib Dynameomics

fold_cop1_model_0.cif #!2/A VAL 22: phi -58.5, psi 130.4 trans  
Changed 12 bond radii  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> swapaa interactive sel VAL rotLib Dynameomics

fold_cop1_model_0.cif #!2/A VAL 22: phi -58.5, psi 130.4 trans  
Changed 12 bond radii  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> swapaa interactive sel VAL rotLib Dynameomics

fold_cop1_model_0.cif #!2/A VAL 22: phi -58.5, psi 130.4 trans  
Changed 12 bond radii  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> swapaa interactive sel VAL rotLib Richardson.mode

fold_cop1_model_0.cif #!2/A VAL 22: phi -58.5, psi 130.4 trans  
Changed 12 bond radii  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> swapaa #!2/A:22 VAL criteria 2 rotLib Dynameomics retain false

Using Dynameomics library  
fold_cop1_model_0.cif #!2/A VAL 22: phi -58.5, psi 130.4 trans  
Applying VAL rotamer (chi angles: -72.1) to fold_cop1_model_0.cif #!2/A VAL 22  

> swapaa interactive sel VAL rotLib Richardson.mode

fold_cop1_model_0.cif #!2/A VAL 22: phi -58.5, psi 130.4 trans  
Changed 12 bond radii  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> swapaa #!2/A:22 VAL criteria 3 rotLib Dynameomics retain false

Using Dynameomics library  
fold_cop1_model_0.cif #!2/A VAL 22: phi -58.5, psi 130.4 trans  
Applying VAL rotamer (chi angles: 60.7) to fold_cop1_model_0.cif #!2/A VAL 22  
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.  

> swapaa #!2/A:22 VAL criteria 2 rotLib Dynameomics retain false

Using Dynameomics library  
fold_cop1_model_0.cif #!2/A VAL 22: phi -58.5, psi 130.4 trans  
Applying VAL rotamer (chi angles: -72.1) to fold_cop1_model_0.cif #!2/A VAL 22  

> select subtract #2.1

1 model selected  

> select add #2.2

15 atoms, 12 bonds, 3 residues, 4 models selected  

> select add #2.6

30 atoms, 24 bonds, 6 residues, 8 models selected  

> select subtract #2.2

15 atoms, 12 bonds, 3 residues, 4 models selected  

> swapaa interactive sel VAL rotLib Richardson.mode

No amino acid residues specified for swapping  

> hide #!2.2 models

> close #2.2

> close #2.6

> view #2.1 clip false

No displayed objects specified.  

> select /A: 22

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

> ui tool show Rotamers

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 1 time(s)]

> select /A: 21

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

> select /A: 20

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

> select /A: 20

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

> select /A: 19

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

> select /A: 19

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

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> ui tool show "Show Sequence Viewer"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> sequence chain /A

Alignment identifier is 2/A  

> select /A:15

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

> select /A:15

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

> swapaa interactive sel THR rotLib Dunbrack

/A PRO 15: phi -66.4, psi 131.0 trans  
Changed 12 bond radii  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 1 time(s)]

> hbonds #!2 & ~#!2/A:15 & ~solvent reveal true restrict #2.2 & ~@c,ca,n

0 hydrogen bonds found  
No rotamers selected  

> swapaa #!2/A:15 THR criteria 2 rotLib Dunbrack

Using Dunbrack library  
fold_cop1_model_0.cif #!2/A PRO 15: phi -66.4, psi 131.0 trans  
Applying THR rotamer (chi angles: 58.0) to fold_cop1_model_0.cif #!2/A THR 15  

> swapaa interactive sel THR rotLib Dunbrack

/A THR 15: phi -66.4, psi 131.0 trans  
Changed 12 bond radii  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> swapaa interactive sel THR rotLib Dunbrack

fold_cop1_model_0.cif #!2/A THR 15: phi -66.4, psi 131.0 trans  
Changed 12 bond radii  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> swapaa interactive sel THR rotLib Dunbrack

fold_cop1_model_0.cif #!2/A THR 15: phi -66.4, psi 131.0 trans  
Changed 12 bond radii  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> hide #2.1 models

> hide #!2 models

> show #!2 models

> hide #1 models

> close #1

> hide #!2.2 models

> show #!2.2 models

> hide #!2.3 models

> show #!2.3 models

> hide #!2.4 models

> show #!2.4 models

> swapaa #!2/A:15 THR criteria 3 rotLib Dunbrack retain false

Using Dunbrack library  
fold_cop1_model_0.cif #!2/A THR 15: phi -66.4, psi 131.0 trans  
Applying THR rotamer (chi angles: -177.1) to fold_cop1_model_0.cif #!2/A THR
15  

> view #2.3 clip false

> ui tool show Rotamers

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> swapaa interactive sel THR rotLib Dunbrack

fold_cop1_model_0.cif #!2/A THR 15: phi -66.4, psi 131.0 trans  
Changed 12 bond radii  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 1 time(s)]

> swapaa interactive sel CYH rotLib Dunbrack

fold_cop1_model_0.cif #!2/A THR 15: phi -66.4, psi 131.0 trans  
Changed 9 bond radii  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1/fold_cop1_summary_confidences_0.json"

JSON file "/Volumes/LAU_32GB/COP1-HY5
Alphafold/fold_cop1/fold_cop1_summary_confidences_0.json" is not AlphaFold
predicted aligned error data, expected a top level list  

> preset "overall look" interactive

Using preset: Overall Look / Interactive  
Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f
    lighting depthCue t

  

> color bfactor sel

4 atoms, 1 residues, 1 surfaces, atom bfactor range 34.6 to 38  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1/fold_cop1_full_data_0.json"

Opened AlphaFold PAE with values for 675 residues and atoms  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> ui windowfill toggle

[Repeated 1 time(s)]

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae

Opened AlphaFold PAE with values for 675 residues and atoms  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae

Opened AlphaFold PAE with values for 675 residues and atoms  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae

Opened AlphaFold PAE with values for 675 residues and atoms  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae

Opened AlphaFold PAE with values for 675 residues and atoms  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae

Opened AlphaFold PAE with values for 675 residues and atoms  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae

Opened AlphaFold PAE with values for 675 residues and atoms  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae

Opened AlphaFold PAE with values for 675 residues and atoms  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae

Opened AlphaFold PAE with values for 675 residues and atoms  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae

Opened AlphaFold PAE with values for 675 residues and atoms  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae

Opened AlphaFold PAE with values for 675 residues and atoms  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae

Opened AlphaFold PAE with values for 675 residues and atoms  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae

Opened AlphaFold PAE with values for 675 residues and atoms  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae

Opened AlphaFold PAE with values for 675 residues and atoms  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae

Opened AlphaFold PAE with values for 675 residues and atoms  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae

Opened AlphaFold PAE with values for 675 residues and atoms  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae

Opened AlphaFold PAE with values for 675 residues and atoms  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae

Opened AlphaFold PAE with values for 675 residues and atoms  

> alphafold pae #2 colorDomains true

> show #2.1 models

> show #!2 target m

[Repeated 5 time(s)]

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> alphafold pae #2 colorDomains true

[Repeated 3 time(s)]

> select clear

> color /A:27-230 lime

> alphafold pae #2 colorDomains true

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1/fold_cop1_full_data_0.json" format pae

Opened AlphaFold PAE with values for 675 residues and atoms  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> view #2.1 clip false

No displayed objects specified.  

> hide #2.1 models

> show #2.1 models

> open "/Volumes/LAU_32GB/COP1-HY5 Alphafold/fold_cop1/fold_cop1_model_0.cif"

Chain information for fold_cop1_model_0.cif #1  
---  
Chain | Description  
A | .  
  

> color #2/A:40 lime

> color #2/A:66 magenta

> color #2/A:26-239 lime

> color #2/A:178 lime

> color #2/A:152 magenta

> alphafold pae #2 colorDomains true

[Repeated 5 time(s)]

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> select all

10684 atoms, 10883 bonds, 1350 residues, 2 models selected  

> alphafold pae #2 colorDomains true

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> alphafold pae #2 colorDomains true

[Repeated 1 time(s)]

> show sel surfaces

[Repeated 1 time(s)]

> alphafold pae #2 colorDomains true

> color #2/A:288-674 lime

> color #2/A:1-18 magenta

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> alphafold pae #2 colorDomains true

[Repeated 1 time(s)]

> color #2/A:2-35 lime

> color #2/A:48-675 magenta

> alphafold pae #2 colorDomains true

[Repeated 4 time(s)]

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> color bfactor #2 palette alphafold

5342 atoms, 675 residues, 1 surfaces, atom bfactor range 17.2 to 97.8  

> preset "molecular surfaces" "atomic coloring (transparent)"

Using preset: Molecular Surfaces / Atomic Coloring (Transparent)  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> hide sel surfaces

> hide sel atoms

> show sel atoms

> hide sel cartoons

[Repeated 1 time(s)]

> hide sel atoms

> show sel cartoons

> alphafold pae #2 colorDomains true

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> hide #1.1 target m

> select subtract #1.1

5342 atoms, 5441 bonds, 675 residues, 3 models selected  

> hide #!1 models

> select clear

> close #1

> color /A:118 lime

> color /A:183 magenta

> color /A:42-231 lime

> color /A:7-99 lime

> color /A:286-669 magenta

> color /A:99 lime

> color /A:669 magenta

> color /A:1-48 lime

> color /A:19 lime

> color /A:6 magenta

> color /A:272-675 lime

> color /A:1-26 magenta

> color /A:1-20 lime

> color /A:286-675 magenta

> alphafold pae #2 colorDomains true

Alignment identifier is 2/A  

> select /A:10

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

> select /A:10-11

14 atoms, 14 bonds, 2 residues, 1 model selected  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1_hy5_complex/fold_cop1_hy5_complex_full_data_0.json"

Opening an AlphaFold PAE file requires specifying the structure to associate.
Did not find an open structure from the same directory. To specify the
structure use menu  
  
Tools / Structure Prediction / AlphaFold Error Plot  
  
or use the open command, for example  
  
open /Volumes/LAU_32GB/COP1-HY5
Alphafold/fold_cop1_hy5_complex/fold_cop1_hy5_complex_full_data_0.json format
pae structure #1  

> open "/Volumes/LAU_32GB/COP1-HY5 Alphafold/fold_cop1/fold_cop1_model_0.cif"

Chain information for fold_cop1_model_0.cif #1  
---  
Chain | Description  
A | .  
  

> open "/Volumes/LAU_32GB/COP1-HY5 Alphafold/fold_cop1/fold_cop1_model_1.cif"

Chain information for fold_cop1_model_1.cif #3  
---  
Chain | Description  
A | .  
  

> open "/Volumes/LAU_32GB/COP1-HY5 Alphafold/fold_cop1/fold_cop1_model_2.cif"

Chain information for fold_cop1_model_2.cif #4  
---  
Chain | Description  
A | .  
  

> open "/Volumes/LAU_32GB/COP1-HY5 Alphafold/fold_cop1/fold_cop1_model_3.cif"

Chain information for fold_cop1_model_3.cif #5  
---  
Chain | Description  
A | .  
  

> open "/Volumes/LAU_32GB/COP1-HY5 Alphafold/fold_cop1/fold_cop1_model_4.cif"

Chain information for fold_cop1_model_4.cif #6  
---  
Chain | Description  
A | .  
  

> hide #!2 models

> hide #2.1 models

> show #!2 models

> show #2.1 models

> hide #1 models

> hide #3 models

> hide #4 models

> hide #5 models

> hide #6 models

> show #1 models

> hide #1 models

> show #1 models

> hide #!2 models

> hide #2.1 models

> close #2.1

> hide #1 models

> select add #2

5342 atoms, 5441 bonds, 675 residues, 1 model selected  

> select subtract #2

Nothing selected  

> show #1 models

> close #2

> show #3 models

> hide #1 models

> show #1 models

> hide #1 models

> hide #3 models

> show #4 models

> show #1 models

> hide #4 models

> show #4 models

> hide #4 models

> hide #1 models

> show #3 models

> hide #3 models

> show #5 models

> hide #5 models

> show #6 models

> hide #6 models

> show #5 models

> hide #5 models

> show #4 models

> hide #4 models

> show #3 models

> show #1 models

> select /1

Nothing selected  

> select /A

26710 atoms, 27210 bonds, 3375 residues, 5 models selected  

> show #4 models

> show #5 models

> show #6 models

> select subtract #3

21368 atoms, 21768 bonds, 2700 residues, 4 models selected  

> select subtract #4

16026 atoms, 16326 bonds, 2025 residues, 3 models selected  

> select subtract #5

10684 atoms, 10884 bonds, 1350 residues, 2 models selected  

> select subtract #6

5342 atoms, 5442 bonds, 675 residues, 1 model selected  

> hide #3 models

> hide #4 models

> hide #5 models

> hide #6 models

> show #3 models

> select subtract #1

Nothing selected  

> select add #3

5342 atoms, 5442 bonds, 675 residues, 1 model selected  

> hide #1 models

> show #1 models

> ui mousemode right "translate selected models"

> ui mousemode right rotate

> select subtract #3

Nothing selected  

> select 1/

Expected an objects specifier or a keyword  

> select /1:A

Nothing selected  

> select /1

Nothing selected  

> show #4 models

> show #5 models

> show #6 models

> select add #1

5342 atoms, 5442 bonds, 675 residues, 1 model selected  

> select add #3

10684 atoms, 10884 bonds, 1350 residues, 2 models selected  

> select add #4

16026 atoms, 16326 bonds, 2025 residues, 3 models selected  

> select add #5

21368 atoms, 21768 bonds, 2700 residues, 4 models selected  

> select add #6

26710 atoms, 27210 bonds, 3375 residues, 5 models selected  

> ui tool show "Modeller Comparative"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

No alignments chosen for modeling  

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> matchmaker #3-6 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 fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_1.cif,
chain A (#3), sequence alignment score = 3505.1  
RMSD between 480 pruned atom pairs is 0.710 angstroms; (across all 675 pairs:
5.895)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_2.cif,
chain A (#4), sequence alignment score = 3502.7  
RMSD between 489 pruned atom pairs is 0.647 angstroms; (across all 675 pairs:
4.976)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_3.cif,
chain A (#5), sequence alignment score = 3506.3  
RMSD between 459 pruned atom pairs is 0.556 angstroms; (across all 675 pairs:
7.536)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_4.cif,
chain A (#6), sequence alignment score = 3498.5  
RMSD between 426 pruned atom pairs is 0.617 angstroms; (across all 675 pairs:
8.497)  
  

> select subtract #1

21368 atoms, 21768 bonds, 2700 residues, 4 models selected  

> select subtract #3

16026 atoms, 16326 bonds, 2025 residues, 3 models selected  

> select subtract #4

10684 atoms, 10884 bonds, 1350 residues, 2 models selected  

> select subtract #5

5342 atoms, 5442 bonds, 675 residues, 1 model selected  

> select subtract #6

Nothing selected  

> hide #3 models

> hide #4 models

> hide #5 models

> hide #6 models

> show #3 models

> hide #3 models

> show #4 models

> show #3 models

> hide #1 models

> show #5 models

> hide #4 models

> hide #3 models

> hide #5 models

> show #1 models

> show #5 models

> hide #1 models

> show #6 models

> hide #5 models

> show #5 models

> show #4 models

> show #3 models

> show #1 models

> hide #3 models

> hide #4 models

> hide #5 models

> hide #6 models

> show #6 models

> hide #6 models

> show #3 models

> show #4 models

> show #5 models

> show #6 models

> ui mousemode right "play coordinates"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> save /Users/lau/Documentos/Ongoing/COP1/COP1_alone.cxs

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1_hy5_complex/fold_cop1_hy5_complex_model_0.cif"

Chain information for fold_cop1_hy5_complex_model_0.cif #2  
---  
Chain | Description  
A | .  
B | .  
  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1_hy5_complex/fold_cop1_hy5_complex_model_1.cif"

Chain information for fold_cop1_hy5_complex_model_1.cif #7  
---  
Chain | Description  
A | .  
B | .  
  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1_hy5_complex/fold_cop1_hy5_complex_model_2.cif"

Chain information for fold_cop1_hy5_complex_model_2.cif #8  
---  
Chain | Description  
A | .  
B | .  
  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1_hy5_complex/fold_cop1_hy5_complex_model_3.cif"

Chain information for fold_cop1_hy5_complex_model_3.cif #9  
---  
Chain | Description  
A | .  
B | .  
  

> open "/Volumes/LAU_32GB/COP1-HY5
> Alphafold/fold_cop1_hy5_complex/fold_cop1_hy5_complex_model_4.cif"

Chain information for fold_cop1_hy5_complex_model_4.cif #10  
---  
Chain | Description  
A | .  
B | .  
  

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> matchmaker #2 to #8/A pairing bs

Parameters  
---  
Chain pairing | bs  
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 fold_cop1_hy5_complex_model_2.cif, chain A (#8) with
fold_cop1_hy5_complex_model_0.cif, chain A (#2), sequence alignment score =
3442.1  
RMSD between 451 pruned atom pairs is 0.580 angstroms; (across all 675 pairs:
14.410)  
  

> hide #1 models

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> hide #6 models

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

[Repeated 1 time(s)]

> matchmaker #2,8-10 & sel to #7/A & sel pairing bs

No 'to' chains specified  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 72, in refresh  
self._items_change()  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 169, in _items_change  
item_names = self._item_names()  
^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in _item_names  
values = [v for v in self.list_func() if self.filter_func(v)]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in   
values = [v for v in self.list_func() if self.filter_func(v)]  
^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 22, in   
filter_func = lambda x, ff=filter_func, cf=class_filter: ff(x) and
isinstance(x, cf)  
^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 328, in _filter_bring_models  
ref_structures = [ref_value.structure]  
^^^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'structure'  
  
AttributeError: 'NoneType' object has no attribute 'structure'  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 328, in _filter_bring_models  
ref_structures = [ref_value.structure]  
^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> matchmaker #2-10 & sel to #1 & sel

No 'to' model specified  

> matchmaker #2-10 & sel to #1 & sel

No 'to' model specified  

> matchmaker #3-10 & sel to #2 & sel

No 'to' model specified  

> hide #7 models

> hide #8 models

> hide #9 models

> hide #10 models

> show #9 models

> hide #9 models

> show #8 models

> hide #8 models

> show #7 models

> hide #7 models

> show #6 models

> show #7 models

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> matchmaker #2-10 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with
fold_cop1_hy5_complex_model_0.cif, chain A (#2), sequence alignment score =
3442.7  
RMSD between 431 pruned atom pairs is 0.644 angstroms; (across all 675 pairs:
20.990)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_1.cif,
chain A (#3), sequence alignment score = 3505.1  
RMSD between 480 pruned atom pairs is 0.710 angstroms; (across all 675 pairs:
5.895)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_2.cif,
chain A (#4), sequence alignment score = 3502.7  
RMSD between 489 pruned atom pairs is 0.647 angstroms; (across all 675 pairs:
4.976)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_3.cif,
chain A (#5), sequence alignment score = 3506.3  
RMSD between 459 pruned atom pairs is 0.556 angstroms; (across all 675 pairs:
7.536)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_4.cif,
chain A (#6), sequence alignment score = 3498.5  
RMSD between 426 pruned atom pairs is 0.617 angstroms; (across all 675 pairs:
8.497)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with
fold_cop1_hy5_complex_model_1.cif, chain A (#7), sequence alignment score =
3452.9  
RMSD between 413 pruned atom pairs is 0.685 angstroms; (across all 675 pairs:
21.616)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with
fold_cop1_hy5_complex_model_2.cif, chain A (#8), sequence alignment score =
3432.5  
RMSD between 452 pruned atom pairs is 0.784 angstroms; (across all 675 pairs:
21.495)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with
fold_cop1_hy5_complex_model_3.cif, chain A (#9), sequence alignment score =
3462.5  
RMSD between 455 pruned atom pairs is 0.601 angstroms; (across all 675 pairs:
22.545)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with
fold_cop1_hy5_complex_model_4.cif, chain A (#10), sequence alignment score =
3448.1  
RMSD between 460 pruned atom pairs is 0.796 angstroms; (across all 675 pairs:
22.634)  
  

> hide #6 models

> show #1 models

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select /1

Nothing selected  

> matchmaker #2-10 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with
fold_cop1_hy5_complex_model_0.cif, chain A (#2), sequence alignment score =
3442.7  
RMSD between 431 pruned atom pairs is 0.644 angstroms; (across all 675 pairs:
20.990)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_1.cif,
chain A (#3), sequence alignment score = 3505.1  
RMSD between 480 pruned atom pairs is 0.710 angstroms; (across all 675 pairs:
5.895)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_2.cif,
chain A (#4), sequence alignment score = 3502.7  
RMSD between 489 pruned atom pairs is 0.647 angstroms; (across all 675 pairs:
4.976)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_3.cif,
chain A (#5), sequence alignment score = 3506.3  
RMSD between 459 pruned atom pairs is 0.556 angstroms; (across all 675 pairs:
7.536)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_4.cif,
chain A (#6), sequence alignment score = 3498.5  
RMSD between 426 pruned atom pairs is 0.617 angstroms; (across all 675 pairs:
8.497)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with
fold_cop1_hy5_complex_model_1.cif, chain A (#7), sequence alignment score =
3452.9  
RMSD between 413 pruned atom pairs is 0.685 angstroms; (across all 675 pairs:
21.616)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with
fold_cop1_hy5_complex_model_2.cif, chain A (#8), sequence alignment score =
3432.5  
RMSD between 452 pruned atom pairs is 0.784 angstroms; (across all 675 pairs:
21.495)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with
fold_cop1_hy5_complex_model_3.cif, chain A (#9), sequence alignment score =
3462.5  
RMSD between 455 pruned atom pairs is 0.601 angstroms; (across all 675 pairs:
22.545)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with
fold_cop1_hy5_complex_model_4.cif, chain A (#10), sequence alignment score =
3448.1  
RMSD between 460 pruned atom pairs is 0.796 angstroms; (across all 675 pairs:
22.634)  
  

> show #2 models

> show #3 models

> show #4 models

> show #5 models

> show #6 models

> show #8 models

> show #9 models

> show #10 models

> ui tool show Matchmaker

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> matchmaker #2-10 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with
fold_cop1_hy5_complex_model_0.cif, chain A (#2), sequence alignment score =
3442.7  
RMSD between 431 pruned atom pairs is 0.644 angstroms; (across all 675 pairs:
20.990)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_1.cif,
chain A (#3), sequence alignment score = 3505.1  
RMSD between 480 pruned atom pairs is 0.710 angstroms; (across all 675 pairs:
5.895)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_2.cif,
chain A (#4), sequence alignment score = 3502.7  
RMSD between 489 pruned atom pairs is 0.647 angstroms; (across all 675 pairs:
4.976)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_3.cif,
chain A (#5), sequence alignment score = 3506.3  
RMSD between 459 pruned atom pairs is 0.556 angstroms; (across all 675 pairs:
7.536)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with fold_cop1_model_4.cif,
chain A (#6), sequence alignment score = 3498.5  
RMSD between 426 pruned atom pairs is 0.617 angstroms; (across all 675 pairs:
8.497)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with
fold_cop1_hy5_complex_model_1.cif, chain A (#7), sequence alignment score =
3452.9  
RMSD between 413 pruned atom pairs is 0.685 angstroms; (across all 675 pairs:
21.616)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with
fold_cop1_hy5_complex_model_2.cif, chain A (#8), sequence alignment score =
3432.5  
RMSD between 452 pruned atom pairs is 0.784 angstroms; (across all 675 pairs:
21.495)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with
fold_cop1_hy5_complex_model_3.cif, chain A (#9), sequence alignment score =
3462.5  
RMSD between 455 pruned atom pairs is 0.601 angstroms; (across all 675 pairs:
22.545)  
  
Matchmaker fold_cop1_model_0.cif, chain A (#1) with
fold_cop1_hy5_complex_model_4.cif, chain A (#10), sequence alignment score =
3448.1  
RMSD between 460 pruned atom pairs is 0.796 angstroms; (across all 675 pairs:
22.634)  
  

> ui mousemode right "play coordinates"

> lighting simple

> lighting soft

> lighting full

> hide #3 models

> hide #4 models

> hide #5 models

> hide #6 models

> hide #7 models

> hide #8 models

> hide #9 models

> hide #10 models

> select /A:1-40

2840 atoms, 2880 bonds, 400 residues, 10 models selected  

> color (#1-2 & sel) yellow

> select /B

6465 atoms, 6500 bonds, 840 residues, 5 models selected  

> color (#2 & sel) magenta

> clear all

Unknown command: clear all  

> select clear

> select /a:1-40

2840 atoms, 2880 bonds, 400 residues, 10 models selected  

> ui tool show "Color Actions"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> color sel goldenrod

[Repeated 4 time(s)]

> select /a:368-675

24290 atoms, 24840 bonds, 3080 residues, 10 models selected  

> color sel medium blue

> color sel royal blue

> select /a:41-367

26290 atoms, 26680 bonds, 3270 residues, 10 models selected  

> color sel indigo

> color sel medium slate blue

> ui tool show "Show Sequence Viewer"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select /a:10-11

140 atoms, 140 bonds, 20 residues, 10 models selected  

> color sel tomato

> show sel & #1-2 surfaces

> select all

59885 atoms, 60920 bonds, 7590 residues, 10 models selected  

> show sel & #!1-2 surfaces

> transparency (#!1-2 & sel) 30

> transparency (#!1-2 & sel) 90

> transparency (#!1-2 & sel) 50

> select /A:1-40

2840 atoms, 2880 bonds, 400 residues, 10 models selected  

> color sel goldenrod

> select /A:11-12

120 atoms, 120 bonds, 20 residues, 10 models selected  

> color sel tomato

> select /A:368-675

24290 atoms, 24840 bonds, 3080 residues, 10 models selected  

> color sel royal blue

> select /A:41-367

26290 atoms, 26680 bonds, 3270 residues, 10 models selected  

> color sel medium slate blue

> hide #!1 models

> select /B:1-100

3805 atoms, 3830 bonds, 500 residues, 5 models selected  

> select /B:80-100

905 atoms, 905 bonds, 105 residues, 5 models selected  

> ui tool show "Show Sequence Viewer"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> sequence chain #2/B #7/B #8/B #9/B #10/B

Alignment identifier is 1  

> select #2/B:43 #7/B:43 #8/B:43 #9/B:43 #10/B:43

35 atoms, 30 bonds, 5 residues, 5 models selected  

> select #2/B:43-44 #7/B:43-44 #8/B:43-44 #9/B:43-44 #10/B:43-44

70 atoms, 70 bonds, 10 residues, 5 models selected  
. [ID: 1] region 5 chains [43-44] RMSD: 0.358  
  

> color sel tomato

[Repeated 3 time(s)]

> select /B

6465 atoms, 6500 bonds, 840 residues, 5 models selected  

> color sel deep pink

> transparency (#!2 & sel) 70

> color sel orchid

> transparency (#!2 & sel) 70

> transparency (#!2 & sel) 40

> hide sel & #!2 cartoons

> select /A

53420 atoms, 54420 bonds, 6750 residues, 10 models selected  

> hide sel & #!2 cartoons

> select /b:41-43

145 atoms, 140 bonds, 15 residues, 5 models selected  

> select /b:42-43

90 atoms, 85 bonds, 10 residues, 5 models selected  

> color sel tomato

> set bgColor white

> set bgColor #ffffff00

> show #!1 models

> select add #7

6707 atoms, 6810 bonds, 851 residues, 6 models selected  

> select subtract #7

72 atoms, 68 bonds, 8 residues, 5 models selected  

> select add #8

6689 atoms, 6793 bonds, 849 residues, 5 models selected  

> select subtract #8

54 atoms, 51 bonds, 6 residues, 4 models selected  

> select add #9

6671 atoms, 6776 bonds, 847 residues, 4 models selected  

> select subtract #9

36 atoms, 34 bonds, 4 residues, 3 models selected  

> select add #10

6653 atoms, 6759 bonds, 845 residues, 3 models selected  

> select subtract #10

18 atoms, 17 bonds, 2 residues, 2 models selected  

> select add #2

6635 atoms, 6742 bonds, 843 residues, 2 models selected  

> select subtract #2

2 models selected  

> select all

59885 atoms, 60920 bonds, 7590 residues, 10 models selected  

> show sel & #!1-2 cartoons

> hide #!2 models

> select clear

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #2.2 models

> show #2.2 models

> hide #2.1 models

> show #2.1 models

> show #3 models

> show #4 models

> show #5 models

> show #6 models

> hide #!2 models

> hide #2.1 models

> hide #2.2 models

> hide #!1 models

> hide #1.1 models

> show #!1 models

> hide #6 models

> show #6 models

> hide #6 models

> hide #5 models

> show #5 models

> show #6 models

> show #!2 models

> show #7 models

> show #8 models

> show #9 models

> show #10 models

> hide #10 models

> hide #8 models

> hide #9 models

> hide #7 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> save /Users/lau/Documentos/Ongoing/COP1/full_data_session.cxs

——— End of log from Mon Sep 16 20:24:56 2024 ———

opened ChimeraX session  

> hide #!2 models

> show #3-6#!1 surfaces

> hide #!1,3-6 surfaces

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> show #!1 surfaces

> hide #!1 cartoons

> hide #1.1 models

> hide #3.1 models

> show #3.1 models

> show #!1,3 surfaces

> hide #!1,3 surfaces

> show #!1,3 surfaces

> show #!4 models

> hide #!3 models

> show #!1,4 surfaces

> show #!5 models

> show #!6 models

> hide #!1 models

> show #!1 models

> show #!3 models

> hide #!1,3-6 cartoons

> show #!1,3-6 surfaces

> transparency #1,3-6 50

> select /A1-40

Nothing selected  

> select /A:1-40

2840 atoms, 2880 bonds, 400 residues, 10 models selected  

> color sel goldenrod

> select /A:11-12

120 atoms, 120 bonds, 20 residues, 10 models selected  

> color sel tomato

> select /A:368-675

24290 atoms, 24840 bonds, 3080 residues, 10 models selected  

> color sel royal blue

> select /A:41-367

26290 atoms, 26680 bonds, 3270 residues, 10 models selected  

> color sel indigo

> color sel dark magenta

> select all

59885 atoms, 60920 bonds, 7590 residues, 10 models selected  

> transparency (#!1,3-6 & sel) 40

> lighting soft

> lighting simple

> select clear

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/lau/Desktop/movie1.mp4

Movie saved to /Users/lau/Desktop/movie1.mp4  
  

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

> hide #1.1 models

> show #!3 models

> show #1.1 models

> hide #1.1 models

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/lau/Desktop/movie2.mp4

Movie saved to /Users/lau/Desktop/movie2.mp4  
  

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

> hide #!3 models

> show #!4 models

> hide #!1 models

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/lau/Desktop/movie3.mp4

Movie saved to /Users/lau/Desktop/movie3.mp4  
  

> save /Users/lau/Desktop/image3.png supersample 3

> hide #!4 models

> show #!5 models

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/lau/Desktop/movie4.mp4

Movie saved to /Users/lau/Desktop/movie4.mp4  
  

> save /Users/lau/Desktop/image4.png supersample 3

> show #!6 models

> hide #!5 models

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/lau/Desktop/movie5.mp4

Movie saved to /Users/lau/Desktop/movie5.mp4  
  

> save /Users/lau/Desktop/image5.png supersample 3

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> set bgColor black

> set bgColor transparent

> save /Users/lau/Documentos/Ongoing/COP1/ChimeraX/COP!_open&closed&hy5ed.cxs
> includeMaps true

——— End of log from Tue Sep 17 20:22:45 2024 ———

opened ChimeraX session  

> hide #!6 models

> show #!2 models

> show #!2 surfaces

> hide #!2 cartoons

> transparency #2 60

> set bgColor white

> show #!2 atoms

> select /A:1-367

29130 atoms, 29570 bonds, 3670 residues, 10 models selected  

> hide sel & #!2 atoms

> select /B:1-80

2955 atoms, 2975 bonds, 400 residues, 5 models selected  

> select /B:1-40

1460 atoms, 1470 bonds, 200 residues, 5 models selected  

> select /B:1-30

1065 atoms, 1075 bonds, 150 residues, 5 models selected  

> hide sel & #!2 atoms

> select /B:55-168

4470 atoms, 4480 bonds, 570 residues, 5 models selected  

> hide sel & #!2 atoms

> select /A:140:180

170 atoms, 150 bonds, 20 residues, 10 models selected  

> select /A:368-400

2630 atoms, 2680 bonds, 330 residues, 10 models selected  

> hide sel & #!2 atoms

> select /A:400-500

8080 atoms, 8250 bonds, 1010 residues, 10 models selected  

> select /A:450-500

4130 atoms, 4200 bonds, 510 residues, 10 models selected  

> select /A:1-500

39730 atoms, 40400 bonds, 5000 residues, 10 models selected  

> select /A:1-4500

53420 atoms, 54420 bonds, 6750 residues, 10 models selected  

> select /A:1-450

35670 atoms, 36260 bonds, 4500 residues, 10 models selected  

> hide sel & #!2 atoms

> select /A:500-675

13770 atoms, 14090 bonds, 1760 residues, 10 models selected  

> hide sel & #!2 atoms

> select add #2.2

15063 atoms, 14090 bonds, 1928 residues, 16 models selected  

> hide #2.2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #2.1 models

> show #2.2 models

> select /A:365-675

24490 atoms, 25040 bonds, 3110 residues, 10 models selected  

> show sel & #!2 atoms

> select /A:600-675

5830 atoms, 5950 bonds, 760 residues, 10 models selected  

> select /A:600-630

2550 atoms, 2610 bonds, 310 residues, 10 models selected  

> hide sel & #!2 atoms

> select /A:630-640

830 atoms, 840 bonds, 110 residues, 10 models selected  

> hide sel & #!2 atoms

> select /A:640-650

820 atoms, 830 bonds, 110 residues, 10 models selected  

> show #2.1 models

> hide #2.1 models

> select /A:530-600

5770 atoms, 5910 bonds, 710 residues, 10 models selected  

> hide sel & #!2 atoms

> show sel & #!2 atoms

> show #2.1 models

> hide #2.1 models

> hide #!2 models

> hide #2.2 models

> show #!1 models

> show sel & #!1 surfaces

> select clear

> show #!3 models

> show #!4 models

> show #!5 models

> show #!6 models

> hide #!1 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!3 models

> show #!4 models

> show #!1 models

> show #!3 models

> hide #!3 models

> hide #!4 models

> show #!3 models

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!3 models

> hide #!1 models

> hide #!3 models

> show #!4 models

> show #!3 models

> show #!1 models

> hide #!1 models

> hide #!3 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!6 models

> show #!2 models

> show #!2,6 surfaces

> hide #!2 models

> show #!2 models

> hide #!6 models

> hide #!2 models

> show #!1 models

> ui tool show Contacts

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> contacts resSeparation 5 intraRes true ignoreHiddenModels true color #9d1700
> radius 0.105

1589 contacts  

> select add #11

1589 pseudobonds, 1 model selected  

> view clip false

> show #!1 cartoons

> hide #!1 surfaces

> hbonds #!1 reveal true

8904 hydrogen bonds found  

> hide #11 models

> show #11 models

> ui tool show Clashes

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> clashes overlapCutoff 1.0 ignoreHiddenModels true color #0a500b reveal true

No clashes  

> hide #!1 models

> show #7 models

> hide #7 models

> show #!1 models

> select add #12

10493 pseudobonds, 2 models selected  

> select clear

> show #!1 atoms

> hide #!1 cartoons

> hide #!1 surfaces

> show #!1 surfaces

> hide #!1 surfaces

> ui tool show "Show Sequence Viewer"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select /A:11-12

120 atoms, 120 bonds, 20 residues, 10 models selected  

> select /A:10-11

140 atoms, 140 bonds, 20 residues, 10 models selected  

> ui tool show "Color Actions"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> color sel tomato

> select /A:12

50 atoms, 40 bonds, 10 residues, 10 models selected  

> color sel goldenrod

> select /A:10-11

140 atoms, 140 bonds, 20 residues, 10 models selected  

> hide #13 models

> select subtract #13

140 atoms, 140 bonds, 20 residues, 16 models selected  

> select add #11

140 atoms, 140 bonds, 1589 pseudobonds, 20 residues, 17 models selected  

> select subtract #11

140 atoms, 140 bonds, 20 residues, 16 models selected  

> show #13 models

> select subtract #13

140 atoms, 140 bonds, 20 residues, 16 models selected  

> select add #12

140 atoms, 140 bonds, 8904 pseudobonds, 20 residues, 17 models selected  

> hide #11 models

> hide #13 models

> select subtract #13

140 atoms, 140 bonds, 8904 pseudobonds, 20 residues, 17 models selected  

> hbonds sel & #!1 reveal true

0 hydrogen bonds found  

> select all

59885 atoms, 60920 bonds, 1611 pseudobonds, 7590 residues, 16 models selected  

> show #11 models

> hide #12 models

> select subtract #12

59885 atoms, 60920 bonds, 1611 pseudobonds, 7590 residues, 23 models selected  

> close #12

> show #13 models

> hide #11 models

> select subtract #11

59885 atoms, 60920 bonds, 22 pseudobonds, 7590 residues, 22 models selected  

> close #13

> show #11 models

> select add #11

59885 atoms, 60920 bonds, 1611 pseudobonds, 7590 residues, 23 models selected  

> select /A:1-40

2840 atoms, 2880 bonds, 400 residues, 10 models selected  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> close #11

> ui tool show Contacts

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> contacts sel resSeparation 5 intraRes true ignoreHiddenModels true color
> #9d1700 radius 0.105

25 contacts  

> show sel & #!1 surfaces

> hide sel & #!1 surfaces

> select /A

53420 atoms, 54420 bonds, 47 pseudobonds, 6750 residues, 16 models selected  

> show sel & #!1 surfaces

> select /A:442

90 atoms, 80 bonds, 10 residues, 10 models selected  

> select /A:467

140 atoms, 150 bonds, 10 residues, 10 models selected  

> color (#!1 & sel) lime

> hide sel & #!1 surfaces

> select all

59885 atoms, 60920 bonds, 47 pseudobonds, 7590 residues, 16 models selected  

> select all

59885 atoms, 60920 bonds, 47 pseudobonds, 7590 residues, 16 models selected  

> hide sel & #!1 surfaces

> hbonds sel & #!1 reveal true

8904 hydrogen bonds found  

> select add #12

59885 atoms, 60920 bonds, 8951 pseudobonds, 7590 residues, 24 models selected  

> select subtract #11

59885 atoms, 60920 bonds, 8926 pseudobonds, 7590 residues, 23 models selected  

> select subtract #10

53250 atoms, 54178 bonds, 8011 pseudobonds, 6747 residues, 22 models selected  

> select subtract #9

46615 atoms, 47436 bonds, 7036 pseudobonds, 5904 residues, 21 models selected  

> select subtract #8

39980 atoms, 40694 bonds, 6134 pseudobonds, 5061 residues, 20 models selected  

> select subtract #7

33345 atoms, 33952 bonds, 5247 pseudobonds, 4218 residues, 19 models selected  

> select subtract #6

28003 atoms, 28510 bonds, 4386 pseudobonds, 3543 residues, 17 models selected  

> select subtract #5

22661 atoms, 23068 bonds, 3425 pseudobonds, 2868 residues, 14 models selected  

> select subtract #4

17319 atoms, 17626 bonds, 2443 pseudobonds, 2193 residues, 11 models selected  

> select subtract #3

11977 atoms, 12184 bonds, 1481 pseudobonds, 1518 residues, 8 models selected  

> select subtract #2

5342 atoms, 5442 bonds, 559 pseudobonds, 675 residues, 5 models selected  

> select /A:593

90 atoms, 80 bonds, 10 residues, 10 models selected  

> show sel & #!1 cartoons

> select all

59885 atoms, 60920 bonds, 8951 pseudobonds, 7590 residues, 17 models selected  

> hide sel & #!1 atoms

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> show sel & #!1 atoms

> select /A:3-20

1330 atoms, 1360 bonds, 6 pseudobonds, 180 residues, 11 models selected  

> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"

> select /A:467

140 atoms, 150 bonds, 10 residues, 10 models selected  

> select /A:467-470

350 atoms, 360 bonds, 11 pseudobonds, 40 residues, 11 models selected  

> select /A:460-470

970 atoms, 990 bonds, 16 pseudobonds, 110 residues, 15 models selected  

> select /A:460-480

1770 atoms, 1810 bonds, 151 pseudobonds, 210 residues, 15 models selected  

> select add #11

1770 atoms, 1810 bonds, 176 pseudobonds, 210 residues, 22 models selected  

> view clip false

> ui tool show Contacts

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> contacts sel saveFile /Users/lau/Desktop/COP1_contacts resSeparation 4 color
> #9d1700 radius 0.105 name contacts_2 reveal true

99163 contacts  

> hide #12 models

> hide #11 models

Cell requested for row 3 is out of bounds for table with 18 rows! Resizing
table model.  

> show #11 models

> hide #13 models

> show #13 models

> hide #13 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #7 models

> hide #7 models

> show #8 models

> hide #8 models

> show #9 models

> hide #9 models

> show #10 models

> hide #10 models

> show #!6 models

> hide #!6 models

> show #!5 models

> hide #!5 models

> show #12 models

> hide #12 models

> show #13 models

> hide #13 models

> show #13 models

> select /A

53420 atoms, 54420 bonds, 106213 pseudobonds, 6750 residues, 18 models
selected  

> select clear

> show #!1 cartoons

> hide #!1 atoms

> hide #11 models

> hide #13 models

> show #11 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> show #13 models

> show #!1 atoms

> hide #!1 cartoons

> ui tool show Contacts

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> contacts sel saveFile /Users/lau/Desktop/contactsCOP1_closed resSeparation 4
> interModel false color #e03200 radius 0.105 reveal true

No atoms match given atom specifier  

> contacts sel resSeparation 5 interModel false select true makePseudobonds
> false

No atoms match given atom specifier  

> show #12 models

> hide #12 models

> show #12 models

> style #!1 ball

Changed 5342 atom styles  

> select /A:1-7

550 atoms, 540 bonds, 5 pseudobonds, 70 residues, 11 models selected  

> select /A:1-7

550 atoms, 540 bonds, 5 pseudobonds, 70 residues, 11 models selected  

> hide sel & #!1 atoms

> select /A:15-200

14640 atoms, 14840 bonds, 1283 pseudobonds, 1860 residues, 13 models selected  

> hide sel & #!1 atoms

> select /A:201-300

7890 atoms, 8020 bonds, 682 pseudobonds, 1000 residues, 11 models selected  

> hide sel & #!1 atoms

> select /A:300-340

3380 atoms, 3410 bonds, 341 pseudobonds, 410 residues, 11 models selected  

> hide sel & #!1 atoms

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> select /A:341-360

1650 atoms, 1670 bonds, 241 pseudobonds, 200 residues, 11 models selected  

> hide sel & #!1 atoms

> select /A:340-350

870 atoms, 880 bonds, 199 pseudobonds, 110 residues, 11 models selected  

> hide sel & #!1 atoms

> select /A:340-380

3340 atoms, 3400 bonds, 347 pseudobonds, 410 residues, 11 models selected  

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:400-420

1600 atoms, 1620 bonds, 159 pseudobonds, 210 residues, 12 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> show sel & #!1 cartoons

> hide sel & #!1 atoms

> hide sel & #!1 cartoons

> select /A:600-675

5830 atoms, 5950 bonds, 1102 pseudobonds, 760 residues, 15 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:400-450

4020 atoms, 4110 bonds, 624 pseudobonds, 510 residues, 12 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:300-450

12150 atoms, 12370 bonds, 2053 pseudobonds, 1510 residues, 15 models selected  

> hide sel & #!1 cartoons

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:450-500

4130 atoms, 4200 bonds, 84864 pseudobonds, 510 residues, 12 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> select /A:450-470

1810 atoms, 1840 bonds, 39355 pseudobonds, 210 residues, 12 models selected  

> show sel & #!1 cartoons

> select /A:450-464

1300 atoms, 1310 bonds, 17649 pseudobonds, 150 residues, 12 models selected  

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:550-675

9810 atoms, 10010 bonds, 2098 pseudobonds, 1260 residues, 15 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> show sel & #!1 atoms

> hide sel & #!1 atoms

> show sel & #!1 atoms

> select /A:590-675

6610 atoms, 6740 bonds, 1304 pseudobonds, 860 residues, 15 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> hide #12 models

> select add #12

6610 atoms, 6740 bonds, 8908 pseudobonds, 860 residues, 21 models selected  

> select subtract #12

6610 atoms, 6740 bonds, 4 pseudobonds, 860 residues, 20 models selected  

> select add #2

12584 atoms, 12808 bonds, 248 pseudobonds, 1617 residues, 22 models selected  

> select subtract #2

5949 atoms, 6066 bonds, 4 pseudobonds, 774 residues, 20 models selected  

> select add #3

10630 atoms, 10834 bonds, 227 pseudobonds, 1363 residues, 19 models selected  

> select subtract #3

5288 atoms, 5392 bonds, 3 pseudobonds, 688 residues, 16 models selected  

> select add #4

9969 atoms, 10160 bonds, 226 pseudobonds, 1277 residues, 16 models selected  

> select subtract #4

4627 atoms, 4718 bonds, 2 pseudobonds, 602 residues, 13 models selected  

> select add #5

9308 atoms, 9486 bonds, 223 pseudobonds, 1191 residues, 13 models selected  

> select subtract #5

3966 atoms, 4044 bonds, 1 pseudobond, 516 residues, 10 models selected  

> select add #6

8647 atoms, 8812 bonds, 228 pseudobonds, 1105 residues, 10 models selected  

> select subtract #6

3305 atoms, 3370 bonds, 430 residues, 7 models selected  

> select add #7

9279 atoms, 9438 bonds, 262 pseudobonds, 1187 residues, 7 models selected  

> select subtract #7

2644 atoms, 2696 bonds, 344 residues, 5 models selected  

> select add #8

8618 atoms, 8764 bonds, 248 pseudobonds, 1101 residues, 6 models selected  

> select subtract #8

1983 atoms, 2022 bonds, 258 residues, 4 models selected  

> select add #9

7957 atoms, 8090 bonds, 241 pseudobonds, 1015 residues, 5 models selected  

> select subtract #9

1322 atoms, 1348 bonds, 172 residues, 3 models selected  

> select add #10

7296 atoms, 7416 bonds, 262 pseudobonds, 929 residues, 4 models selected  

> select subtract #10

661 atoms, 674 bonds, 86 residues, 2 models selected  

> select /A:593

90 atoms, 80 bonds, 10 residues, 10 models selected  

> show sel & #!1 cartoons

> show sel & #!1 atoms

> show #12 models

> hide #13 models

> show #13 models

> hide #11 models

> show #11 models

> hide #11 models

> hide #13 models

> hide #12 models

> show #12 models

> hide #12 models

> show #11 models

> show #13 models

> select /A:590-600

850 atoms, 850 bonds, 9 pseudobonds, 110 residues, 11 models selected  

> show sel & #!1 atoms

> select /A:465-500

2830 atoms, 2880 bonds, 61219 pseudobonds, 360 residues, 12 models selected  

> show sel & #!1 cartoons

> select /A:465-490

2010 atoms, 2040 bonds, 59279 pseudobonds, 260 residues, 12 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> show sel & #!1 atoms

> select /A:465-480

1310 atoms, 1340 bonds, 55637 pseudobonds, 160 residues, 12 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> select /A:465-475

950 atoms, 970 bonds, 37900 pseudobonds, 110 residues, 12 models selected  

> show sel & #!1 cartoons

> select A:14-464

Expected an objects specifier or a keyword  

> select /A:14-464

35950 atoms, 36540 bonds, 22504 pseudobonds, 4510 residues, 17 models selected  

> hide sel & #!1 atoms

> show sel & #!1 atoms

> hide sel & #!1 atoms

> show sel & #!1 atoms

> select /A:14

90 atoms, 80 bonds, 10 residues, 10 models selected  

> select all

59885 atoms, 60920 bonds, 108111 pseudobonds, 7590 residues, 19 models
selected  

> select /A:1-5

400 atoms, 390 bonds, 50 residues, 10 models selected  

> select /A:1-5

400 atoms, 390 bonds, 50 residues, 10 models selected  

> hide sel & #!1 atoms

> select /A:15-464

35860 atoms, 36450 bonds, 22502 pseudobonds, 4500 residues, 17 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:600-675

5830 atoms, 5950 bonds, 1102 pseudobonds, 760 residues, 15 models selected  

> hide sel & #!1 atoms

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> ui tool show "Show Sequence Viewer"

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> sequence chain #1/A #3/A #4/A #5/A #6/A #2/A #7/A #8/A #9/A #10/A

Alignment identifier is 1  

> select #1/A:491 #3/A:491 #4/A:491 #5/A:491 #6/A:491 #2/A:491 #7/A:491
> #8/A:491 #9/A:491 #10/A:491

140 atoms, 150 bonds, 10 residues, 10 models selected  

> select #1/A:491-507 #3/A:491-507 #4/A:491-507 #5/A:491-507 #6/A:491-507
> #2/A:491-507 #7/A:491-507 #8/A:491-507 #9/A:491-507 #10/A:491-507

1360 atoms, 1370 bonds, 52 pseudobonds, 170 residues, 11 models selected  
. [ID: 1] region 10 chains [491-507] RMSD: 0.512  
  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> show sel & #!1 cartoons

> select /A:540-550

900 atoms, 930 bonds, 6 pseudobonds, 110 residues, 11 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:540-550

900 atoms, 930 bonds, 6 pseudobonds, 110 residues, 11 models selected  

> select /A:540-550

900 atoms, 930 bonds, 6 pseudobonds, 110 residues, 11 models selected  

> select /A:540-550

900 atoms, 930 bonds, 6 pseudobonds, 110 residues, 11 models selected  

> select /A:469-490

1650 atoms, 1660 bonds, 42159 pseudobonds, 220 residues, 12 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:490-507

1430 atoms, 1440 bonds, 101 pseudobonds, 180 residues, 11 models selected  

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:441

120 atoms, 120 bonds, 2 pseudobonds, 10 residues, 11 models selected  

> hide sel & #!1 cartoons

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> select /A:468

60 atoms, 50 bonds, 1444 pseudobonds, 10 residues, 12 models selected  

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:465

110 atoms, 100 bonds, 2596 pseudobonds, 10 residues, 11 models selected  

> hide sel & #!1 cartoons

> show sel & #!1 cartoons

> hide sel & #!1 atoms

> hide sel & #!1 cartoons

> select /A:466

50 atoms, 40 bonds, 1115 pseudobonds, 10 residues, 11 models selected  

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:508

80 atoms, 70 bonds, 10 residues, 10 models selected  

> hide sel & #!1 atoms

> show sel & #!1 atoms

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:509

60 atoms, 50 bonds, 10 residues, 10 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:510-525

1150 atoms, 1170 bonds, 178 pseudobonds, 160 residues, 11 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> show sel & #!1 cartoons

> select /A:539-550

960 atoms, 990 bonds, 9 pseudobonds, 120 residues, 11 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:510-525

1150 atoms, 1170 bonds, 178 pseudobonds, 160 residues, 11 models selected  

> hide sel & #!1 cartoons

> select up

1290 atoms, 1310 bonds, 178 pseudobonds, 180 residues, 17 models selected  

> select /A:470-490

1580 atoms, 1590 bonds, 38773 pseudobonds, 210 residues, 12 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> ui tool show Toolbar

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> select /A:8-14

490 atoms, 500 bonds, 70 residues, 10 models selected  

> select sel : select sel : show sel & #!1 cartoons

> hide sel & #!1 cartoons

> select /A:8-14

490 atoms, 500 bonds, 70 residues, 10 models selected  

> select sel : select /A:527-531

460 atoms, 480 bonds, 43 pseudobonds, 50 residues, 11 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:532-536

510 atoms, 520 bonds, 73 pseudobonds, 50 residues, 11 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 atoms

> hide sel & #!1 cartoons

> select /A:532-536

510 atoms, 520 bonds, 73 pseudobonds, 50 residues, 11 models selected  

> select /A:532-538

670 atoms, 680 bonds, 92 pseudobonds, 70 residues, 11 models selected  

> show sel & #!1 surfaces

> hide sel & #!1 surfaces

> show sel & #!1 cartoons

> select /A:532-539

730 atoms, 740 bonds, 128 pseudobonds, 80 residues, 11 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:578-590

1080 atoms, 1100 bonds, 9 pseudobonds, 130 residues, 11 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:569-575

620 atoms, 630 bonds, 47 pseudobonds, 70 residues, 11 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:577

70 atoms, 60 bonds, 10 residues, 10 models selected  

> hide sel & #!1 atoms

> select /A:578

90 atoms, 80 bonds, 10 residues, 10 models selected  

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:576

80 atoms, 70 bonds, 10 residues, 10 models selected  

> hide sel & #!1 atoms

> select /A:560-567

550 atoms, 540 bonds, 9 pseudobonds, 80 residues, 11 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:559-553

Nothing selected  

> select /A:553-559

590 atoms, 600 bonds, 9 pseudobonds, 70 residues, 11 models selected  

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:595-559

Nothing selected  

> select /A:595-599

370 atoms, 370 bonds, 1 pseudobond, 50 residues, 11 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:594-599

450 atoms, 450 bonds, 1 pseudobond, 60 residues, 11 models selected  

> hide sel & #!1 cartoons

> hide sel & #!1 atoms

> select /A:552

70 atoms, 60 bonds, 10 residues, 10 models selected  

> hide sel & #!1 atoms

> select /A:592

90 atoms, 80 bonds, 10 residues, 10 models selected  

> hide sel & #!1 atoms

> select /A:591

80 atoms, 70 bonds, 10 residues, 10 models selected  

> hide sel & #!1 atoms

> select /A:593

90 atoms, 80 bonds, 10 residues, 10 models selected  

> hide sel & #!1 atoms

> show sel & #!1 atoms

> select /A

53420 atoms, 54420 bonds, 106213 pseudobonds, 6750 residues, 18 models
selected  

> show sel & #!1 surfaces

> transparency (#!1 & sel) 90

> show sel & #!1 cartoons

> select /A:465

110 atoms, 100 bonds, 2596 pseudobonds, 10 residues, 11 models selected  

> color (#!1 & sel) blue

> hide sel & #!1 atoms

> show sel & #!1 atoms

> hide sel & #!1 atoms

> select /A:464

90 atoms, 80 bonds, 2349 pseudobonds, 10 residues, 11 models selected  

> hide sel & #!1 atoms

> show sel & #!1 atoms

> hide sel & #!1 atoms

> show sel & #!1 atoms

> hide sel & #!1 atoms

> show sel & #!1 atoms

> hide sel & #!1 atoms

> select /A:458

90 atoms, 80 bonds, 10 residues, 10 models selected  

> show sel & #!1 atoms

> hide sel & #!1 atoms

> select /A:459

120 atoms, 120 bonds, 10 residues, 10 models selected  

> show sel & #!1 atoms

> hide sel & #!1 atoms

> select /A:528

100 atoms, 100 bonds, 10 residues, 10 models selected  

> hide sel & #!1 cartoons

> show sel & #!1 cartoons

> select /A:441

120 atoms, 120 bonds, 2 pseudobonds, 10 residues, 11 models selected  

> ui tool show "Color Actions"

> color sel royal blue

> select /A:441

120 atoms, 120 bonds, 2 pseudobonds, 10 residues, 11 models selected  

> hide sel & #!1 cartoons

> show sel & #!1 cartoons

> select /A:492

60 atoms, 50 bonds, 10 residues, 10 models selected  

> select /A:392

60 atoms, 50 bonds, 2 pseudobonds, 10 residues, 11 models selected  

> show sel & #!1 cartoons

> hide sel & #!1 cartoons

> show sel & #!1 cartoons

> select /A:370

60 atoms, 50 bonds, 2 pseudobonds, 10 residues, 11 models selected  

> select /A:467

140 atoms, 150 bonds, 5216 pseudobonds, 10 residues, 11 models selected  

> show sel & #!1 atoms

> hide sel & #!1 atoms

> show sel & #!1 atoms

> ui tool show "Color Actions"

> color sel royal blue

> select /A:467,593

230 atoms, 230 bonds, 5216 pseudobonds, 20 residues, 11 models selected  

> color sel medium spring green

> select /A:467,593,568

300 atoms, 290 bonds, 5221 pseudobonds, 30 residues, 12 models selected  

> color sel medium aquamarine

> color sel medium spring green

> select /A:467,593,568,551

350 atoms, 330 bonds, 5242 pseudobonds, 40 residues, 12 models selected  

> color sel medium spring green

> select /A:467,593,568,551,526

400 atoms, 370 bonds, 5242 pseudobonds, 50 residues, 12 models selected  

> color sel medium spring green

> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"

> select /A

53420 atoms, 54420 bonds, 106213 pseudobonds, 6750 residues, 18 models
selected  

> hide sel & #!1 surfaces

> select clear

> lighting simple

> lighting shadows true

> select A:3-8

Expected an objects specifier or a keyword  

> select /A:3-8

450 atoms, 450 bonds, 5 pseudobonds, 60 residues, 11 models selected  

> ~label (#!1 & sel) residues

> ui tool show "Side View"


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 INTEL-22.5.11
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
      OS Loader Version: 580.140.1~8

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 25 days, 14 hours, 27 minutes

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL P2425:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: BNPC304     
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7.55
        DELL P2425:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 59.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 1CRC304     
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    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: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    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: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    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-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    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
    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: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (2)

comment:1 by Eric Pettersen, 13 months ago

Component: UnassignedGraphics
Owner: set to Tom Goddard
Platform: all
Project: ChimeraX
Status: newassigned
Summary: ChimeraX bug report submissionGraphics hardware encountered an error and was reset

comment:2 by Tom Goddard, 13 months ago

Resolution: nonchimerax
Status: assignedclosed
Summary: Graphics hardware encountered an error and was resetGraphics crash, macOS 14.6.1, Intel Iris Plus Graphics 655

Crash in Apple's Intel graphics driver.

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