Opened 11 months ago

Closed 11 months ago

#16477 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by: yaohe@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-15.1.1-arm64-arm-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: Segmentation fault

Thread 0x00000003100bf000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030f0b3000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030e0a7000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030d09b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030c08f000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030b083000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030a077000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030906b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030805f000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000307053000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000306047000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030503b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030402f000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000001f838f840 (most recent call first):
  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.pdb_lib._load_libs, 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, openmm._openmm, openmm.app.internal.compiled, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, psutil._psutil_osx, psutil._psutil_posix, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PIL._imagingmath (total: 59)


{"app_name":"ChimeraX","timestamp":"2024-12-16 10:22:12.00 -0800","app_version":"1.8.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.8.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.1.1 (24B91)","roots_installed":0,"name":"ChimeraX","incident_id":"119840D5-C878-4557-AB99-22E8C88A988F"}
{
  "uptime" : 72000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,3",
  "coalitionID" : 2630,
  "osVersion" : {
    "train" : "macOS 15.1.1",
    "build" : "24B91",
    "releaseType" : "User"
  },
  "captureTime" : "2024-12-16 10:21:54.8705 -0800",
  "codeSigningMonitor" : 1,
  "incident" : "119840D5-C878-4557-AB99-22E8C88A988F",
  "pid" : 2895,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-12-13 12:27:55.5198 -0800",
  "procStartAbsTime" : 197065507547,
  "procExitAbsTime" : 1740804141111,
  "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":"94145AA7-F194-5C87-AA1C-6A08E733EACE","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "A4BBACB1-6F97-89C6-DB33-7689FCB70FA5",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "bootSessionUUID" : "6D51ED96-ADD5-4D51-B778-2BE55F722617",
  "wakeTime" : 6,
  "sleepWakeUUID" : "4448A2AC-8ED4-41E0-804B-C57CF4C0BDEA",
  "sip" : "enabled",
  "vmRegionInfo" : "0x8f0000081c0 is not in any region.  Bytes after previous region: 9345848869313  Bytes before following region: 95726231060032\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV  ",
  "exception" : {"codes":"0x0000000000000001, 0x000088f0000081c0","rawCodes":[1,150564373561792],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000088f0000081c0 -> 0x000008f0000081c0 (possible pointer authentication failure)"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":2895},
  "vmregioninfo" : "0x8f0000081c0 is not in any region.  Bytes after previous region: 9345848869313  Bytes before following region: 95726231060032\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV  ",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6159515928},{"value":80},{"value":98},{"value":2305843014258063824},{"value":0},{"value":3263807400757536337},{"value":3263807393104485905},{"value":14757395258967641293},{"value":4294967286},{"value":6159515858},{"value":0},{"value":53},{"value":4294967280},{"value":328},{"value":8596150352},{"value":0},{"value":11},{"value":259},{"value":8459450656,"symbolLocation":224,"symbol":"_main_thread"},{"value":2},{"value":1},{"value":4325951024,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":8425754624,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTextView._tv_dragInfo"},{"value":8425754624,"symbolLocation":0,"symbol":"OBJC_IVAR_$_NSTextView._tv_dragInfo"},{"value":4},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6763818864},"cpsr":{"value":1073745920},"fp":{"value":6159516000},"sp":{"value":6159515968},"esr":{"value":1442840704,"description":" Address size 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fault"},"pc":{"value":6763552308},"far":{"value":0}},"frames":[{"imageOffset":3636,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":181},{"imageOffset":79312,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":181},{"imageOffset":39384,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":181},{"imageOffset":4476,"symbol":"mach_msg","symbolLocation":24,"imageIndex":181},{"imageOffset":66741424,"imageIndex":56},{"imageOffset":66197236,"imageIndex":56},{"imageOffset":66429892,"imageIndex":56},{"imageOffset":66433464,"imageIndex":56},{"imageOffset":66432016,"imageIndex":56},{"imageOffset":66431744,"imageIndex":56},{"imageOffset":66589352,"imageIndex":56},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":182},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":182}]},{"id":938789,"name":"ThreadPoolForegroundWorker","threadState":{"x":[{"value":268451845},{"value":17179869442},{"value":0},{"value":712633858654208},{"value":0},{"value":712633858654208},{"value":32},{"value":33000},{"value":18446744073709550527},{"value":32},{"value":0},{"value":0},{"value":0},{"value":165923},{"value":2319470905},{"value":2317371463},{"value":18446744073709551569},{"value":313},{"value":0},{"value":33000},{"value":32},{"value":712633858654208},{"value":0},{"value":712633858654208},{"value":14229056784},{"value":0},{"value":17179870466},{"value":17179869442},{"value":1282}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6763627984},"cpsr":{"value":4096},"fp":{"value":14229056128},"sp":{"value":14229056048},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6763552308},"far":{"value":0}},"frames":[{"imageOffset":3636,"symbol":"mach_msg2_trap","symbolLocation":8,"imageIndex":181},{"imageOffset":79312,"symbol":"mach_msg2_internal","symbolLocation":80,"imageIndex":181},{"imageOffset":39384,"symbol":"mach_msg_overwrite","symbolLocation":480,"imageIndex":181},{"imageOffset":4476,"symbol":"mach_msg","symbolLocation":24,"imageIndex":181},{"imageOffset":66741424,"imageIndex":56},{"imageOffset":66197236,"imageIndex":56},{"imageOffset":66429892,"imageIndex":56},{"imageOffset":66432404,"imageIndex":56},{"imageOffset":66432016,"imageIndex":56},{"imageOffset":66431744,"imageIndex":56},{"imageOffset":66589352,"imageIndex":56},{"imageOffset":29412,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":182},{"imageOffset":8444,"symbol":"thread_start","symbolLocation":8,"imageIndex":182}]}],
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[deleted to fit within ticket size limits]
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===== Log before crash start =====
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 "/Users/heyao/My Drive/RaiA_2024/PDB_deposition/raiA_3.0A/raiA_OD-
> coot-35_isolda_real_space_refined_delH_new_real_space_refined_051_isolda.pdb"

Chain information for raiA_OD-
coot-35_isolda_real_space_refined_delH_new_real_space_refined_051_isolda.pdb
#1  
---  
Chain | Description  
A | No description available  
  

> set bgColor white

> lighting soft

> graphics silhouettes true

> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA_3.0A/cryosparc_P44_J306_007_volume_map.mrc"

Opened cryosparc_P44_J306_007_volume_map.mrc as #2, grid size 256,256,256,
pixel 0.856, shown at level 0.0213, step 1, values float32  

> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA_3.0A/cryosparc_P44_J306_007_volume_map_sharp.mrc"

Opened cryosparc_P44_J306_007_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 0.856, shown at level 0.0348, step 1, values float32  

> ui mousemode right zoom

> hide #!2 models

> show atoms

> style stick

Changed 6580 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 6575 atom styles  

> select H

2195 atoms, 204 residues, 1 model selected  

> delete sel

> select clear

> show #!2 models

> volume #2 level 0.06175

> view

> select clear

> show #!3 models

> hide #!2 models

> hide #1 models

> volume #3 level 0.1598

> volume #3 level 0.2398

> show #1 models

> hide #!3 models

> cartoon style sel xsection oval width 1.6 thickness 1.6

> select clear

Drag select of 3161 atoms, 204 residues, 3480 bonds  

> cartoon style sel xsection oval width 1.6 thickness 1.6

> select clear

> select #1

4385 atoms, 4907 bonds, 209 residues, 1 model selected  

> select #1/1-14

Nothing selected  

> select #1/A:1-14

298 atoms, 332 bonds, 14 residues, 1 model selected  

> select #1/A:1-14,191-204

593 atoms, 661 bonds, 28 residues, 1 model selected  

> color sel orange red

> select clear

> color #1/A:1-14,191-204 orange red

> select /A:190

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:183

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /A:23

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color #1/A:15-23,183-190 purple

> select clear

> select add /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select clear

> select add /A:183

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add /A:184

44 atoms, 48 bonds, 2 residues, 1 model selected  

> color sel gray

> select clear

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color #1/A:15-23,185-190 purple

> select clear

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:186

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color #1/A:15-23,186-190 purple

> color sel light gray

> select clear

> select /A:24

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:25

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add /A:26

63 atoms, 67 bonds, 3 residues, 1 model selected  

> select add /A:27

86 atoms, 92 bonds, 4 residues, 1 model selected  

> select add /A:50

106 atoms, 113 bonds, 5 residues, 1 model selected  

> select add /A:49

128 atoms, 137 bonds, 6 residues, 1 model selected  

> select add /A:48

151 atoms, 162 bonds, 7 residues, 1 model selected  

> select add /A:47

171 atoms, 183 bonds, 8 residues, 1 model selected  

> select add /A:46

193 atoms, 207 bonds, 9 residues, 1 model selected  

> select add /A:45

215 atoms, 231 bonds, 10 residues, 1 model selected  

> color #1/A:24-27,45-50 royal blue

> color sel cornflower blue

> select clear

> color #1/A:24-27,45-50 cornflower blue

> select /A:28

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add /A:29

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add /A:30

65 atoms, 70 bonds, 3 residues, 1 model selected  

> select add /A:31

85 atoms, 91 bonds, 4 residues, 1 model selected  

> select add /A:32

105 atoms, 112 bonds, 5 residues, 1 model selected  

> color #1/A:28-32,40-44 yellow

> select clear

> color #1/A:33-39 green

> select /A:90

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

> color #1/A:33-39,85-90 green

> select clear

> select /A:84

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select clear

> select /A:33

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color sel gray

> select clear

> select /A:29

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

> select clear

> select /A:33

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select /A:35

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

> select clear

> select /A:34

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:35

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add /A:36

63 atoms, 67 bonds, 3 residues, 1 model selected  

> select add /A:37

86 atoms, 92 bonds, 4 residues, 1 model selected  

> select add /A:38

106 atoms, 113 bonds, 5 residues, 1 model selected  

> select add /A:39

128 atoms, 137 bonds, 6 residues, 1 model selected  

> select /A:85

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

> select add /A:34

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select clear

> select /A:85

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

> select add /A:90

40 atoms, 42 bonds, 2 residues, 1 model selected  

> color #1/A:34-39,85-90 green

> select clear

> select /A:51

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

> select add /A:52

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add /A:53

62 atoms, 66 bonds, 3 residues, 1 model selected  

> select add /A:54

82 atoms, 87 bonds, 4 residues, 1 model selected  

> color sel cyan

> select clear

> select add /A:51

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

> select add /A:52

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add /A:53

62 atoms, 66 bonds, 3 residues, 1 model selected  

> select add /A:54

82 atoms, 87 bonds, 4 residues, 1 model selected  

> select /A:177

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:176

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select add /A:175

66 atoms, 71 bonds, 3 residues, 1 model selected  

> select add /A:174

89 atoms, 96 bonds, 4 residues, 1 model selected  

> select /A:174

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color #1/A:51-54, 174-177 cyan

> select clear

> select /A:55

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:79

46 atoms, 50 bonds, 2 residues, 1 model selected  

> color #1/A:55-79 orange

> select clear

> view

> color #1/A:55-79 goldenrod rod

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

> color #1/A:55-79 goldenrod

> select /A:80

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

> select add /A:81

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select clear

> select /A:82

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

> select add /A:83

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add /A:84

66 atoms, 71 bonds, 3 residues, 1 model selected  

> select clear

> select /A:84

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:80

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

> select /A:81

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select /A:84

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:83

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:82

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add /A:181

63 atoms, 67 bonds, 3 residues, 1 model selected  

> select add /A:182

85 atoms, 91 bonds, 4 residues, 1 model selected  

> select add /A:170

108 atoms, 116 bonds, 5 residues, 1 model selected  

> select add /A:121

130 atoms, 140 bonds, 6 residues, 1 model selected  

> select subtract /A:170

107 atoms, 115 bonds, 5 residues, 1 model selected  

> select subtract /A:121

85 atoms, 91 bonds, 4 residues, 1 model selected  

> select add /A:81

107 atoms, 115 bonds, 5 residues, 1 model selected  

> select add /A:180

127 atoms, 136 bonds, 6 residues, 1 model selected  

> select add /A:179

150 atoms, 161 bonds, 7 residues, 1 model selected  

> select add /A:178

173 atoms, 186 bonds, 8 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel salmon

> color sel dark salmon

> color sel salmon

> color sel light salmon

> select clear

> select add /A:178

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:179

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select add /A:180

66 atoms, 71 bonds, 3 residues, 1 model selected  

> select add /A:181

86 atoms, 92 bonds, 4 residues, 1 model selected  

> select add /A:182

108 atoms, 116 bonds, 5 residues, 1 model selected  

> select clear

> select /A:81

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add /A:82

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add /A:83

65 atoms, 70 bonds, 3 residues, 1 model selected  

> select clear

> select add /A:178

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:179

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select /A:180

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

> select add /A:181

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add /A:182

62 atoms, 66 bonds, 3 residues, 1 model selected  

> color #1/A:81-83, 178-182 salmon

> select clear

> select add /A:184

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color #1/A:81-83, 178-184 salmon

> select clear

> select add /A:183

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select /A:183@C3'

1 atom, 1 residue, 1 model selected  

> select clear

> select /A:173

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

> select add /A:172

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select clear

> select /A:91

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

> select clear

> select /A:99

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /A:100

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /A:101

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:100

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select add /A:99

67 atoms, 73 bonds, 3 residues, 1 model selected  

> select subtract /A:99

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select /A:103

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

> select add /A:168

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select clear

> color #1/A:119-163 hotpink

> select clear

> select /A:163

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select /A:118

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:106

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select /A:101

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:118

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:108

43 atoms, 46 bonds, 2 residues, 1 model selected  

> color #1/A:108-118 blue

> color #1/A:108-118 royalblue

> color #1/A:108-118 lblue

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

> color #1/A:108-118 blue

> select clear

> color #1/A:108-118 darkblue

> select /A:107

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

> color #1/A:101-107,164-170 limegreen

> select clear

> color #1/A:101-107,164-170 lime

> select clear

> select add /A:171

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add /A:172

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select add /A:173

65 atoms, 70 bonds, 3 residues, 1 model selected  

> select add /A:100

87 atoms, 94 bonds, 4 residues, 1 model selected  

> select add /A:91

107 atoms, 115 bonds, 5 residues, 1 model selected  

> color #1/A:91-100, 171-173 lightgray

> color #1/A:91-100, 171-173 gray

> color #1/A:91-100, 171-173 darkgray

> select clear

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:183

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:165

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

> select clear

> select /A:84

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:33

45 atoms, 49 bonds, 2 residues, 1 model selected  

> color #1/A:33, 84, 91-100, 171-173 darkgray

> select clear

> select add /A:29

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

> select clear

> select add /A:29

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

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:183

45 atoms, 49 bonds, 2 residues, 1 model selected  

> color #1/A:33, 84, 91-100, 171-173, 183,185 darkgray

> select clear

> color byhetero

> select clear

> undo

> select clear

> view

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!2 models

> volume #2 level 0.06614

> hide #!2 models

> view

> show #!2 models

> volume #2 level 0.07928

> volume #2 color #b2b2b283

> view

> show #!3 models

> hide #!3 models

> hide #!2 models

> save "/Users/heyao/Google Drive/My Drive/RaiA_2024/Figures/fig1.cxs"

> show #!2 models

> hide #!2 models

> select Mg

5 atoms, 5 residues, 1 model selected  

> hide sel target a

> select clear

Drag select of 3156 atoms, 204 residues, 3480 bonds  

> show #!2 models

> ui tool show "Color Zone"

> color zone #2 near #1 distance 5.14

> select clear

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> select clear

> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA_3.0A/cryosparc_P44_J306_007_volume_map.mrc"

Opened cryosparc_P44_J306_007_volume_map.mrc as #4, grid size 256,256,256,
pixel 0.856, shown at level 0.0213, step 1, values float32  

> volume #4 level 0.04781

> volume #4 color #b2b2b27a

> select clear

> view

> hide #!2 models

> show #!2 models

> hide #1 models

> hide #!4 models

> volume #2 level 0.06335

> select clear

> view

> view name p1

> ui tool show "Side View"

> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true

> surface dust size 3

Missing or invalid "surfaces" argument: invalid surfaces specifier  

> surface dust

Missing or invalid "surfaces" argument: empty atom specifier  

> surface dust #2 size 3

> select clear

> view p1

> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn x 90

> save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn x 90

> color single #2

> show #1 models

> hide #!2 models

> select clear

Drag select of 3156 atoms, 204 residues, 3480 bonds  

> show #!2 models

> hide #!2 models

> show #!4 models

> hide #!4 models

> show #!2 models

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

> color zone #2 near sel distance 5.14

> select clear

> hide #1 models

> select clear

> view p1

> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn x 90

> save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn x 90

> turn y 90

> save /Users/heyao/Desktop/3.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn x 90

> save /Users/heyao/Desktop/4.png width 2000 height 2000 supersample 3
> transparentBackground true

> view name p2

> view p1

> turn y 90

> turn y 190

> view p1

> view

> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA+P2_3.0A/cryosparc_P44_J208_006_volume_map.mrc"

Opened cryosparc_P44_J208_006_volume_map.mrc as #5, grid size 256,256,256,
pixel 0.856, shown at level 0.0194, step 1, values float32  

> volume #5 color #b2b2b2

> volume #5 level 0.04769

> ui mousemode right "rotate selected models"

> select add #5

2 models selected  

> view matrix models
> #5,0.98908,-0.10981,-0.098248,23.585,0.018638,0.75465,-0.65586,89.971,0.14617,0.64687,0.74846,-68.003

> fitmap #5 inMap #2

Fit map cryosparc_P44_J208_006_volume_map.mrc in map
cryosparc_P44_J306_007_volume_map.mrc using 57510 points  
correlation = 0.6961, correlation about mean = 0.1762, overlap = 166.5  
steps = 160, shift = 7.08, angle = 13.6 degrees  
  
Position of cryosparc_P44_J208_006_volume_map.mrc (#5) relative to
cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99520792 0.09266609 -0.03121206 -1.90478254  
-0.08638041 0.68359534 -0.72473156 121.64881794  
-0.04582162 0.72395470 0.68832403 -45.65379273  
Axis 0.99239916 0.01000804 -0.12265292  
Axis point 0.00000000 113.18746461 118.36999355  
Rotation angle (degrees) 46.87724941  
Shift along axis 4.92673271  
  

> select clear

> select add #5

2 models selected  

> view matrix models
> #5,-0.28863,-0.93163,0.22081,242.43,0.58353,-0.35401,-0.73086,165.17,0.75907,-0.082096,0.64582,-41.296

> view matrix models
> #5,-0.86039,-0.42794,0.27676,244.86,0.12692,-0.70587,-0.69688,256.01,0.49358,-0.56446,0.66164,44.269

> fitmap #5 inMap #2

Fit map cryosparc_P44_J208_006_volume_map.mrc in map
cryosparc_P44_J306_007_volume_map.mrc using 57510 points  
correlation = 0.9304, correlation about mean = 0.7264, overlap = 384.4  
steps = 420, shift = 27.3, angle = 61.9 degrees  
  
Position of cryosparc_P44_J208_006_volume_map.mrc (#5) relative to
cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.82309682 0.56737562 0.02442404 134.59045503  
-0.45808180 -0.63789380 -0.61907396 298.40293952  
-0.33566753 -0.52074601 0.78495280 110.25649577  
Axis 0.09010312 0.32997103 -0.93968109  
Axis point 119.35289183 147.39940598 0.00000000  
Rotation angle (degrees) 146.93150884  
Shift along axis 6.98539970  
  

> select clear

> view p1

> select clear

> hide #!2 models

> open "/Users/heyao/My Drive/RaiA_2024/PDB_deposition/raiA+P2_3.0A/KN-
> coot-13_isolde_real_space_refined_065_isolde.pdb"

Chain information for KN-coot-13_isolde_real_space_refined_065_isolde.pdb #6  
---  
Chain | Description  
A | No description available  
  

> select add #6

5353 atoms, 5988 bonds, 1 pseudobond, 249 residues, 2 models selected  

> view matrix models
> #6,-0.90858,0.1578,-0.38676,255.46,0.17715,-0.69294,-0.6989,251.02,-0.37829,-0.70352,0.60164,171.11

> view matrix models
> #6,-0.51182,0.84433,-0.15861,100.53,-0.62781,-0.49363,-0.60182,317.23,-0.58643,-0.20844,0.78272,119.21

> fitmap #6 inMap #5

Fit molecule KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) to map
cryosparc_P44_J208_006_volume_map.mrc (#5) using 5353 atoms  
average map value = 0.01605, steps = 132  
shifted from previous position = 4.23  
rotated from previous position = 9.84 degrees  
atoms outside contour = 4651, contour level = 0.047687  
  
Position of KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) relative
to cryosparc_P44_J208_006_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
0.86772792 -0.39727738 0.29869543 2.06277270  
0.42913695 0.90201861 -0.04694588 -47.94991180  
-0.25077830 0.16891749 0.95319313 19.39883446  
Axis 0.21254395 0.54102425 0.81370623  
Axis point 94.65981773 -21.12486692 0.00000000  
Rotation angle (degrees) 30.51798290  
Shift along axis -9.71868299  
  

> view matrix models
> #6,-0.62963,0.75199,0.19515,92.984,-0.76605,-0.55911,-0.3171,317.86,-0.12935,-0.34915,0.9281,70.549

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.62963,0.75199,0.19515,68.108,-0.76605,-0.55911,-0.3171,313.96,-0.12935,-0.34915,0.9281,63.027

> view matrix models
> #6,-0.62963,0.75199,0.19515,68.366,-0.76605,-0.55911,-0.3171,300.24,-0.12935,-0.34915,0.9281,53.164

> fitmap #6 inMap #5

Fit molecule KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) to map
cryosparc_P44_J208_006_volume_map.mrc (#5) using 5353 atoms  
average map value = 0.07683, steps = 172  
shifted from previous position = 10.1  
rotated from previous position = 25.4 degrees  
atoms outside contour = 1263, contour level = 0.047687  
  
Position of KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) relative
to cryosparc_P44_J208_006_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99999995 0.00001997 0.00032109 -0.03981368  
-0.00001996 1.00000000 -0.00003851 0.01104931  
-0.00032109 0.00003851 0.99999995 0.04171659  
Axis 0.11885500 0.99099744 -0.06162443  
Axis point 130.60221565 0.00000000 125.36760562  
Rotation angle (degrees) 0.01856408  
Shift along axis 0.00364702  
  

> ui mousemode right zoom

> select clear

> view p1

> select clear

> view p1

> hide #!5 models

> hide #!6 models

> show #!6 models

> show #!5 models

> hide #!6 models

> show #!6 models

> hide #!5 models

> select clear

Drag select of 249 residues, 1 pseudobonds, 498 shapes  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 5353 atom styles  

> cartoon style sel xsection oval width 1.6 thickness 1.6

> select clear

> show #1 models

> hide #!6 models

> show #!6 models

> select #6/A:240

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:14

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:240

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:1

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

> select #6/A:253

22 atoms, 24 bonds, 1 residue, 1 model selected  

> P1a and P1b color #6/A:1-14,240-253 orange red

Unknown command: P1a and P1b color #6/A:1-14,240-253 orange red  

> color #6/A:1-14,240-253 orange red

> select clear

> select #6/A:15

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

> select clear

> select #6/A:239

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:238

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select #6/A:235

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #6/A:239

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select clear

> select #6/A:15

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

> select add #6/A:20

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select #6/A:19

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

> color #6/A:15-19,235-239 purple

> select #6/A:92

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select clear

> hide #1 models

> select #6/A:60

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #6/A:59

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add #6/A:20

65 atoms, 70 bonds, 3 residues, 1 model selected  

> ui tool show "Color Actions"

> color #6/A:20-60 darkgoldenrod

> select clear

> view

> select clear

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> color #6/A:20-60 pylegoldenrod

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

> color #6/A:20-60 palegoldenrod

> select clear

> view

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> color #6/A:20-60 tan

> select clear

> show #!2 models

> hide #!2 models

> show #1 models

> hide #!6 models

> show #!6 models

> select #1/A:23

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select #6/A:60

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color sel purple

> select clear

> select #6/A:20

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color sel purple

> select clear

> hide #1 models

> select #6/A:20

23 atoms, 25 bonds, 1 residue, 1 model selected  

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> show #1 models

> hide #!6 models

> show #!6 models

> select #6/A:60

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select #6/A:59

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

> color #6/A:15-20,60,235-239 purple

> select clear

> hide #1 models

> show #!2 models

> show #1 models

> hide #!2 models

> color #6/A:21-59 tan

> hide #1 models

> show #1 models

> select #6/A:61

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:64

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select add #1/A:50

66 atoms, 71 bonds, 3 residues, 2 models selected  

> select subtract #1/A:50

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select add #6/A:87

66 atoms, 71 bonds, 3 residues, 1 model selected  

> select add #6/A:82

88 atoms, 95 bonds, 4 residues, 1 model selected  

> color #6/A:61-64,82-87 cornflower blue

> select #6/A:65

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #1/A:33

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #6/A:65

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #6/A:69

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select #6/A:81

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color #6/A:65-69,77-81 yellow

> select clear

> select #6/A:70

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select #6/A:71

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:76

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select clear

> select #6/A:71

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:76

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select clear

> select #6/A:123

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

> select #6/A:118

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

> color #1/A:71-76,118-123 green

> undo

> color #6/A:71-76,118-123 green

> select clear

> hide #1 models

> show #1 models

> select #6/A:88

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

> select add #6/A:91

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add #6/A:92

63 atoms, 67 bonds, 3 residues, 1 model selected  

> select subtract #6/A:92

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select #6/A:226

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:223

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select subtract #6/A:223

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:223

46 atoms, 50 bonds, 2 residues, 1 model selected  

> color #6/A:88-91,223-226 cyan

> select clear

> select #1/A:55

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:92

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:112

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

> select clear

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> select #6/A:92

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:112

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

> hide #1 models

> show #1 models

> hide #!6 models

> select #1/A:80

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

> color #1/A:33,80,84,91-100,171-173,183,185 darkgray

> select clear

> show #!2 models

> hide #1 models

> show #1 models

> hide #!2 models

> select clear

Drag select of 3156 atoms, 204 residues, 3480 bonds  

> show #!2 models

> color #2 near 1 distance 5

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

> colorzone #2 near 1 distance 5

Unknown command: colorzone #2 near 1 distance 5  

> color zone #2 near 1 distance 5

Invalid "near" argument: invalid atoms specifier  

> color zone #2 near #1 distance 5

> select clear

> hide #!2 models

> hide #1 models

> view p1

> show #1 models

> show #!2 models

> hide #1 models

> show #!6 models

> hide #!2 models

> color #6/A:92-112 goldenrod

> select clear

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> show #1 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #1 models

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> select #6/A:70

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #1 models

> select #1/A:81

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #6/A:114

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #6/A:115

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add #6/A:116

65 atoms, 70 bonds, 3 residues, 1 model selected  

> select #6/A:227

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:233

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color #6/A:114-116,227-233 salmon

> hide #1 models

> show #1 models

> hide #!6 models

> show #!6 models

> select #1/A:183

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #6/A:232

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #1/A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> hide #1 models

> show #1 models

> hide #1 models

> select #6/A:234

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color #6/A:70,232,234 darkgray

> select clear

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> show #1 models

> select #1/A:170

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select clear

> select #6/A:219

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #1/A:170

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:170

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:219

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:213

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select #6/A:140

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

> select #6/A:134

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select clear

> color #6/A:134-140,213-219 lime

> select #6/A:141

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

> select #6/A:174

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color #6/A:141-174 darkblue

> select clear

> select #6/A:212

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #6/A:175

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color #6/A:175-212 hotpink

> hide #1 models

> view p1

> select clear

> show #1 models

> hide #1 models

> select #6/A:124

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

> select add #6/A:133

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select #6/A:222

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

> select add #6/A:220

42 atoms, 45 bonds, 2 residues, 1 model selected  

> color #6/A:70,113,117,124-133,220-222,232,234 darkgray

> select clear

> view p1

> show #!5 models

> volume #5 level 0.05695

> ui tool show "Color Zone"

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

> color zone #5 near #6 distance 5.14

> color zone #5 near #6 distance 5.1

> color zone #5 near #6 distance 5

> hide #!5 models

> show #!5 models

> hide #!6 models

> volume #5 level 0.05886

> volume #5 level 0.05504

> show #!2 models

> hide #!2 models

> show #1 models

> show #!6 models

> hide #!6 models

> hide #!5 models

> show #!2 models

> hide #1 models

> save /Users/heyao/Desktop/fig1.cxs

> show #!6 models

> hide #!2 models

> show #!2 models

> hide #!6 models

> show #1 models

> hide #!2 models

> show #!2 models

> hide #1 models

> view p1

> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p2

> save /Users/heyao/Desktop/3.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> turn x 180

> turn z 180

> save /Users/heyao/Desktop/4.png width 2000 height 2000 supersample 3
> transparentBackground true

> show #1 models

> hide #1 models

> hide #!2 models

> show #!6 models

> hide #!6 models

> show #!5 models

> ui tool show "Hide Dust"

> surface dust #5 size 5.14

> surface dust #5 size 4.94

> surface dust #5 size 1.19

> surface dust #5 size 1.74

> surface dust #5 size 1

> surface dust #5 size 3

> save /Users/heyao/Desktop/14.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn z 180

> save /Users/heyao/Desktop/13.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p1

> save /Users/heyao/Desktop/11.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> save /Users/heyao/Desktop/12.png width 2000 height 2000 supersample 3
> transparentBackground true

> view

> select clear

> volume #5 level 0.07883

> view p1

> volume #5 level 0.04591

> view p1

> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA+P2_3.0A/cryosparc_P44_J208_006_volume_map_sharp.mrc"

Opened cryosparc_P44_J208_006_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 0.856, shown at level 0.0321, step 1, values float32  

> volume #7 level 0.09953

> select add #7

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #7,-0.76381,0.63589,-0.11064,143.02,-0.52039,-0.70812,-0.47725,309.35,-0.38182,-0.30695,0.87178,93.617

> fitmap #7 inMap #5

Fit map cryosparc_P44_J208_006_volume_map_sharp.mrc in map
cryosparc_P44_J208_006_volume_map.mrc using 33096 points  
correlation = 0.9546, correlation about mean = 0.7783, overlap = 698.7  
steps = 164, shift = 18.4, angle = 13.5 degrees  
  
Position of cryosparc_P44_J208_006_volume_map_sharp.mrc (#7) relative to
cryosparc_P44_J208_006_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99999995 -0.00009731 0.00030468 -0.02233620  
0.00009737 0.99999998 -0.00018529 0.01126621  
-0.00030466 0.00018532 0.99999994 0.01925316  
Axis 0.50131231 0.82422219 0.26333202  
Axis point 60.44868633 0.00000000 78.51712028  
Rotation angle (degrees) 0.02117924  
Shift along axis 0.00315842  
  

> select clear

> hide #!5 models

> volume #7 level 0.1479

> volume #7 level 0.1142

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

> surface dust #7 size 5.14

> color zone #7 near #6 distance 5.14

> select clear

> volume #7 level 0.09513

> surface dust #7 size 5.17

> surface dust #7 size 2.59

> hide #!7 models

> show #1 models

> hide #1 models

> show #!2 models

> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA-P8_3.5A/cryosparc_P44_J119_007_volume_map.mrc"

Opened cryosparc_P44_J119_007_volume_map.mrc as #8, grid size 256,256,256,
pixel 0.856, shown at level 0.0109, step 1, values float32  

> volume #8 level 0.05676

> select add #8

2 models selected  

> view matrix models
> #8,-0.7258,0.66222,0.18623,91.252,0.62651,0.52455,0.57647,-87.693,0.28407,0.53508,-0.79561,134.51

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.7258,0.66222,0.18623,96.465,0.62651,0.52455,0.57647,-78.886,0.28407,0.53508,-0.79561,111.51

> view matrix models
> #8,-0.7258,0.66222,0.18623,95.693,0.62651,0.52455,0.57647,-77.05,0.28407,0.53508,-0.79561,109.84

> ui mousemode right "rotate selected models"

> view matrix models
> #8,-0.59361,-0.78521,0.17626,238.98,-0.41119,0.48422,0.77231,14.761,-0.69177,0.38597,-0.61031,208.04

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  
Must specify one map, got 0  

> fitmap #8 inMap #2

Fit map cryosparc_P44_J119_007_volume_map.mrc in map
cryosparc_P44_J306_007_volume_map.mrc using 32003 points  
correlation = 0.7141, correlation about mean = 0.06117, overlap = 96.41  
steps = 120, shift = 7.63, angle = 7.11 degrees  
  
Position of cryosparc_P44_J119_007_volume_map.mrc (#8) relative to
cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.67932839 -0.70734554 0.19538482 233.17463966  
-0.32924966 0.53174106 0.78028592 -1.20521285  
-0.65582589 0.46573999 -0.59412007 187.73366128  
Axis -0.31995815 0.86585704 0.38460157  
Axis point 145.04886475 0.00000000 58.92440994  
Rotation angle (degrees) 150.55799757  
Shift along axis -3.44700659  
  

> select clear

> select add #8

2 models selected  

> view matrix models
> #8,0.92597,-0.247,0.28559,-0.62486,-0.33951,-0.87565,0.34347,206.09,0.16524,-0.41501,-0.89469,231.71

> fitmap #8 inMap #2

Fit map cryosparc_P44_J119_007_volume_map.mrc in map
cryosparc_P44_J306_007_volume_map.mrc using 32003 points  
correlation = 0.918, correlation about mean = 0.5232, overlap = 217.2  
steps = 132, shift = 2.14, angle = 21.9 degrees  
  
Position of cryosparc_P44_J119_007_volume_map.mrc (#8) relative to
cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.98172391 0.09005861 0.16765326 -29.84294848  
-0.01268335 -0.84802486 0.52980466 149.11768328  
0.18988760 -0.52224830 -0.83138403 232.76992784  
Axis -0.99504515 -0.02102952 -0.09717466  
Axis point 0.00000000 108.37326391 96.40524730  
Rotation angle (degrees) 148.08599472  
Shift along axis 3.93986945  
  

> select clear

> hide #!8 models

> show #!8 models

> hide #!2 models

> show #!2 models

> select clear

> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA-P8_3.5A/initial_model_AN-
> coot-11_isolde.pdb"

Chain information for initial_model_AN-coot-11_isolde.pdb #9  
---  
Chain | Description  
A | No description available  
  

> select add #9

3336 atoms, 3734 bonds, 2 pseudobonds, 155 residues, 2 models selected  

> hide #!2 models

> view matrix models
> #9,0.92235,0.35553,0.15123,-47.92,0.17678,-0.73639,0.65305,87.261,0.34354,-0.57561,-0.74206,237.51

> ui mousemode right "translate selected models"

> view matrix models
> #9,0.92235,0.35553,0.15123,-46.908,0.17678,-0.73639,0.65305,102.26,0.34354,-0.57561,-0.74206,218.07

> fitmap #9 inMap #8

Fit molecule initial_model_AN-coot-11_isolde.pdb (#9) to map
cryosparc_P44_J119_007_volume_map.mrc (#8) using 3336 atoms  
average map value = 0.06906, steps = 132  
shifted from previous position = 6.96  
rotated from previous position = 16.8 degrees  
atoms outside contour = 1046, contour level = 0.056762  
  
Position of initial_model_AN-coot-11_isolde.pdb (#9) relative to
cryosparc_P44_J119_007_volume_map.mrc (#8) coordinates:  
Matrix rotation and translation  
0.99999922 0.00120715 0.00033324 -0.17137916  
-0.00120711 0.99999926 -0.00015796 0.15354463  
-0.00033343 0.00015757 0.99999994 0.01154017  
Axis 0.12499238 0.26409247 -0.95636399  
Axis point 125.34278901 142.88874346 0.00000000  
Rotation angle (degrees) 0.07231914  
Shift along axis 0.00809228  
  

> select clear

> ui mousemode right zoom

> view p1

> select clear

> hide #!8 models

> select clear

Drag select of 155 residues, 2 pseudobonds, 310 shapes  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 3336 atom styles  

> cartoon style sel xsection oval width 1.6 thickness 1.6

> select clear

> show #!8 models

> hide #!8 models

> show #1 models

> select clear

> select #1/A:191

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:150

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:14

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:150

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:163

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color #9/A:1-14,150-163 orange red

> select clear

> select #1/A:190

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #1/A:15

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

> select add #9/A:23

42 atoms, 45 bonds, 2 residues, 2 models selected  

> select #1/A:190

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:149

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:145

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color #6/A:15-23,145-149 purple

> undo

> hide #1 models

> hide #!9 models

> show #!5 models

> hide #!5 models

> show #!6 models

> show #!9 models

> hide #!6 models

> undo

No undo action is available  

> undo

No undo action is available  

> undo

No undo action is available  

> undo

No undo action is available  

> select clear

> color #9/A:15-23,145-149 purple

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> select #1/A:24

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #1/A:27

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select add #1/A:50

66 atoms, 71 bonds, 3 residues, 1 model selected  

> select add #9/A:45

88 atoms, 95 bonds, 4 residues, 2 models selected  

> color #9/A:24-27,45-50 cornflower blue

> select clear

> hide #!9 models

> show #!9 models

> hide #1 models

> show #1 models

> select #9/A:28

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #9/A:32

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select #9/A:40

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #9/A:44

45 atoms, 49 bonds, 2 residues, 1 model selected  

> color #9/A:28-32,40-44 yellow

> select clear

> select #1/A:33

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #1/A:34

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:34

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #9/A:39

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select #9/A:92

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

> select #9/A:87

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

> color #9/A:34-39,87-92 green

> select clear

> hide #1 models

> show #1 models

> hide #1 models

> select #9/A:33

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color sel darg gray

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

> color sel darkgray

> select clear

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> show #1 models

> hide #!9 models

> show #!9 models

> select #1/A:51

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

> select #9/A:51

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

> select add #9/A:54

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select clear

> select #9/A:136

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #9/A:133

46 atoms, 50 bonds, 2 residues, 1 model selected  

> color #9/A:51-54,133-136 cyan

> select clear

> hide #1 models

> show #1 models

> select #9/A:55

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:81

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

> hide #1 models

> select clear

> select #9/A:81

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

> show #1 models

> color #9/A:55-81 goldenrod

> select clear

> hide #1 models

> show #1 models

> select #9/A:83

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #9/A:85

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select #1/A:81

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #9/A:83

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #9/A:85

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select #1/A:184

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #9/A:143

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #9/A:143

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #9/A:137

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color #9/A:83-85,137-143 salmon

> select clear

> select #1/A:183

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #1/A:185

45 atoms, 49 bonds, 2 residues, 1 model selected  

> hide #1 models

> show #1 models

> hide #1 models

> select add #9/A:142

67 atoms, 73 bonds, 3 residues, 2 models selected  

> select add #9/A:144

89 atoms, 97 bonds, 4 residues, 2 models selected  

> color #9/A:33, 82, 86, 142,144 darkgray

> select clear

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> select #9/A:93

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

> show #1 models

> select #9/A:121

23 atoms, 25 bonds, 1 residue, 1 model selected  

> hide #1 models

> select add #9/A:108

43 atoms, 46 bonds, 2 residues, 1 model selected  

> show #1 models

> hide #1 models

> color #9/A:108-121 darkblue

> select clear

> select add #9/A:107

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

> show #1 models

> select add #1/A:101

43 atoms, 46 bonds, 2 residues, 2 models selected  

> select add #9/A:102

65 atoms, 70 bonds, 3 residues, 2 models selected  

> select #1/A:102

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

> select #1/A:101

23 atoms, 25 bonds, 1 residue, 1 model selected  

> hide #!9 models

> show #!9 models

> hide #1 models

> select #9/A:107

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

> select #9/A:128

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

> select add #9/A:127

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add #9/A:126

66 atoms, 71 bonds, 3 residues, 1 model selected  

> show #1 models

> select add #9/A:129

88 atoms, 95 bonds, 4 residues, 1 model selected  

> select #9/A:103

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #9/A:107

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select clear

> color #9/A:103-107,126-129 lime

> select clear

> hide #1 models

> select #9/A:102

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #9/A:130

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #9/A:132

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select #9/A:93

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

> select add #9/A:102

42 atoms, 45 bonds, 2 residues, 1 model selected  

> color #9/A:33,82,86,93-102,130-132,142,144 darkgray

> select clear

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> save /Users/heyao/Desktop/fig1.cxs

> show #!8 models

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

> color zone #8 near #9 distance 5.14

> color zone #8 near #9 distance 4.96

> color zone #8 near #9 distance 3.98

> surface dust #8 size 5.14

> volume #8 level 0.06701

> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA-P8_3.5A/cryosparc_P44_J119_007_volume_map_sharp.mrc"

Opened cryosparc_P44_J119_007_volume_map_sharp.mrc as #10, grid size
256,256,256, pixel 0.856, shown at level 0.0198, step 1, values float32  

> volume #10 level 0.1802

> select add #10

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #10,-0.97132,-0.23766,0.0077356,235.93,-0.15228,0.64668,0.7474,-32.131,-0.18263,0.72479,-0.66433,134.13

> volume #10 level 0.08858

> view matrix models
> #10,0.93215,0.020628,0.36147,-38.767,-0.19435,-0.81384,0.54762,154.01,0.30548,-0.58072,-0.75462,233.48

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.93215,0.020628,0.36147,-35.457,-0.19435,-0.81384,0.54762,162.59,0.30548,-0.58072,-0.75462,224.58

Must specify one map, got 0  

> fitmap #10 inMap #8

Fit map cryosparc_P44_J119_007_volume_map_sharp.mrc in map
cryosparc_P44_J119_007_volume_map.mrc using 27855 points  
correlation = 0.931, correlation about mean = 0.5914, overlap = 393.1  
steps = 120, shift = 6.72, angle = 13 degrees  
  
Position of cryosparc_P44_J119_007_volume_map_sharp.mrc (#10) relative to
cryosparc_P44_J119_007_volume_map.mrc (#8) coordinates:  
Matrix rotation and translation  
0.99999985 0.00045450 0.00030702 -0.07641814  
-0.00045451 0.99999989 0.00002918 0.05384633  
-0.00030700 -0.00002931 0.99999995 0.03236712  
Axis -0.05324606 0.55895242 -0.82748840  
Axis point 109.35316698 167.30731259 0.00000000  
Rotation angle (degrees) 0.03147028  
Shift along axis 0.00738308  
  

> select clear

> save /Users/heyao/Desktop/fig1.cxs

> surface dust #10 size 5.14

> color zone #10 near #9 distance 5.14

> hide #!8 models

> hide #!9 models

> volume #10 level 0.08349

> view p1

> show #!2 models

> hide #!2 models

> show #!3 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> hide #!2 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!10 models

> show #!8 models

> hide #!10 models

> show #!10 models

> hide #!8 models

> volume #10 level 0.08172

> volume #10 level 0.07116

> show #!8 models

> volume #8 level 0.05258

> volume #8 level 0.04487

> select #8

2 models selected  

> show #!9 models

> hide #!8 models

> select clear

> show #!8 models

> color #8 #d6d6d6ff models

> color #8 silver models

> color zone #10 near #9 distance 5.14

> color zone #8 near #9 distance 5.14

> select clear

> hide #!8 models

> hide #!9 models

> show #1 models

> hide #1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> color #3 #b2b2b2ff models

> color zone #3 near #1 distance 5.14

> view

> view p1

> volume #3 level 0.1706

> volume #3 level 0.19

> volume #3 level 0.2

> volume #3 level 0.1481

> view

> view p1

> show #1 models

> hide #!2 models

Drag select of 3156 atoms, 204 residues, 3480 bonds  

> show #!2 models

> ui tool show "Color Zone"

> color zone #2 near sel distance 5

> hide #!2 models

> show #!2 models

> hide #1 models

> view p1

> volume #2 level 0.07

> volume #2 level 0.05

> volume #2 level 0.06

> view p1

> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p2

> turn z 180

> save /Users/heyao/Desktop/3.png width 2000 height 2000 supersample 3
> transparentBackground true

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!4 models

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> show #!3 models

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

> view p1

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!3 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!5 models

> volume #5 level 0.05207

> view p1

> save /Users/heyao/Desktop/11.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> save /Users/heyao/Desktop/12.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p2

> turn z 180

> save /Users/heyao/Desktop/13.png width 2000 height 2000 supersample 3
> transparentBackground true

> hide #!5 models

> show #!10 models

> show #!8 models

> hide #!10 models

> view p1

> volume #8 level 0.05187

> volume #8 level 0.04053

> view p1

> view

> view p1

> save /Users/heyao/Desktop/21.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> save /Users/heyao/Desktop/22.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p2

> turn z 180

> save /Users/heyao/Desktop/23.png width 2000 height 2000 supersample 3
> transparentBackground true

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!10 models

> hide #!10 models

> show #!9 models

> hide #!9 models

> show #!8 models

> view p1

> hide #!8 models

> show #!8 models

> hide #!2 models

> volume #8 level 0.05

> view p1

> save /Users/heyao/Desktop/21.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> save /Users/heyao/Desktop/22.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p2

> turn z 180

> save /Users/heyao/Desktop/23.png width 2000 height 2000 supersample 3
> transparentBackground true

> save /Users/heyao/Desktop/fig1.cxs

> show #!2 models

> hide #!8 models

> view p2

> turn y 180

> save /Users/heyao/Desktop/4.png width 2000 height 2000 supersample 3
> transparentBackground true

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!5 models

> save /Users/heyao/Desktop/14.png width 2000 height 2000 supersample 3
> transparentBackground true

> volume #5 level 0.04797

> save /Users/heyao/Desktop/14.png width 2000 height 2000 supersample 3
> transparentBackground true

> hide #!5 models

> show #!10 models

> hide #!10 models

> show #!8 models

> view p1

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!8 models

> view p1

> turn y 90

> turn x 90

> hide #!2 models

> show #1 models

> select clear

> view p1

> save /Users/heyao/Desktop/31.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p2

> turn z 180

> save /Users/heyao/Desktop/32.png width 2000 height 2000 supersample 3
> transparentBackground true


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

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/heyao/Desktop/fig1.cxs

Opened cryosparc_P44_J306_007_volume_map.mrc as #2, grid size 256,256,256,
pixel 0.856, shown at level 0.06, step 1, values float32  
Opened cryosparc_P44_J306_007_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 0.856, shown at level 0.148, step 1, values float32  
Opened cryosparc_P44_J306_007_volume_map.mrc as #4, grid size 256,256,256,
pixel 0.856, shown at level 0.0478, step 1, values float32  
Opened cryosparc_P44_J208_006_volume_map.mrc as #5, grid size 256,256,256,
pixel 0.856, shown at level 0.0521, step 1, values float32  
Opened cryosparc_P44_J208_006_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 0.856, shown at level 0.0951, step 1, values float32  
Opened cryosparc_P44_J119_007_volume_map.mrc as #8, grid size 256,256,256,
pixel 0.856, shown at level 0.05, step 1, values float32  
Opened cryosparc_P44_J119_007_volume_map_sharp.mrc as #10, grid size
256,256,256, pixel 0.856, shown at level 0.0712, step 1, values float32  
Log from Sat Dec 14 18:45:20 2024You 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 "/Users/heyao/My Drive/RaiA_2024/PDB_deposition/raiA_3.0A/raiA_OD-
> coot-35_isolda_real_space_refined_delH_new_real_space_refined_051_isolda.pdb"

Chain information for raiA_OD-
coot-35_isolda_real_space_refined_delH_new_real_space_refined_051_isolda.pdb
#1  
---  
Chain | Description  
A | No description available  
  

> set bgColor white

> lighting soft

> graphics silhouettes true

> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA_3.0A/cryosparc_P44_J306_007_volume_map.mrc"

Opened cryosparc_P44_J306_007_volume_map.mrc as #2, grid size 256,256,256,
pixel 0.856, shown at level 0.0213, step 1, values float32  

> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA_3.0A/cryosparc_P44_J306_007_volume_map_sharp.mrc"

Opened cryosparc_P44_J306_007_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 0.856, shown at level 0.0348, step 1, values float32  

> ui mousemode right zoom

> hide #!2 models

> show atoms

> style stick

Changed 6580 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 6575 atom styles  

> select H

2195 atoms, 204 residues, 1 model selected  

> delete sel

> select clear

> show #!2 models

> volume #2 level 0.06175

> view

> select clear

> show #!3 models

> hide #!2 models

> hide #1 models

> volume #3 level 0.1598

> volume #3 level 0.2398

> show #1 models

> hide #!3 models

> cartoon style sel xsection oval width 1.6 thickness 1.6

> select clear

Drag select of 3161 atoms, 204 residues, 3480 bonds  

> cartoon style sel xsection oval width 1.6 thickness 1.6

> select clear

> select #1

4385 atoms, 4907 bonds, 209 residues, 1 model selected  

> select #1/1-14

Nothing selected  

> select #1/A:1-14

298 atoms, 332 bonds, 14 residues, 1 model selected  

> select #1/A:1-14,191-204

593 atoms, 661 bonds, 28 residues, 1 model selected  

> color sel orange red

> select clear

> color #1/A:1-14,191-204 orange red

> select /A:190

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:183

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /A:23

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color #1/A:15-23,183-190 purple

> select clear

> select add /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select clear

> select add /A:183

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add /A:184

44 atoms, 48 bonds, 2 residues, 1 model selected  

> color sel gray

> select clear

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color #1/A:15-23,185-190 purple

> select clear

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:186

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color #1/A:15-23,186-190 purple

> color sel light gray

> select clear

[Repeated 2 time(s)]

> select /A:24

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:25

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add /A:26

63 atoms, 67 bonds, 3 residues, 1 model selected  

> select add /A:27

86 atoms, 92 bonds, 4 residues, 1 model selected  

> select add /A:50

106 atoms, 113 bonds, 5 residues, 1 model selected  

> select add /A:49

128 atoms, 137 bonds, 6 residues, 1 model selected  

> select add /A:48

151 atoms, 162 bonds, 7 residues, 1 model selected  

> select add /A:47

171 atoms, 183 bonds, 8 residues, 1 model selected  

> select add /A:46

193 atoms, 207 bonds, 9 residues, 1 model selected  

> select add /A:45

215 atoms, 231 bonds, 10 residues, 1 model selected  

> color #1/A:24-27,45-50 royal blue

> color sel cornflower blue

> select clear

> color #1/A:24-27,45-50 cornflower blue

> select /A:28

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add /A:29

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add /A:30

65 atoms, 70 bonds, 3 residues, 1 model selected  

> select add /A:31

85 atoms, 91 bonds, 4 residues, 1 model selected  

> select add /A:32

105 atoms, 112 bonds, 5 residues, 1 model selected  

> color #1/A:28-32,40-44 yellow

> select clear

> color #1/A:33-39 green

> select /A:90

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

> color #1/A:33-39,85-90 green

> select clear

> select /A:84

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select clear

> select /A:33

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color sel gray

> select clear

> select /A:29

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

> select clear

> select /A:33

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select /A:35

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

> select clear

> select /A:34

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:35

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add /A:36

63 atoms, 67 bonds, 3 residues, 1 model selected  

> select add /A:37

86 atoms, 92 bonds, 4 residues, 1 model selected  

> select add /A:38

106 atoms, 113 bonds, 5 residues, 1 model selected  

> select add /A:39

128 atoms, 137 bonds, 6 residues, 1 model selected  

> select /A:85

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

> select add /A:34

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select clear

> select /A:85

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

> select add /A:90

40 atoms, 42 bonds, 2 residues, 1 model selected  

> color #1/A:34-39,85-90 green

> select clear

> select /A:51

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

> select add /A:52

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add /A:53

62 atoms, 66 bonds, 3 residues, 1 model selected  

> select add /A:54

82 atoms, 87 bonds, 4 residues, 1 model selected  

> color sel cyan

> select clear

> select add /A:51

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

> select add /A:52

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add /A:53

62 atoms, 66 bonds, 3 residues, 1 model selected  

> select add /A:54

82 atoms, 87 bonds, 4 residues, 1 model selected  

> select /A:177

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:176

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select add /A:175

66 atoms, 71 bonds, 3 residues, 1 model selected  

> select add /A:174

89 atoms, 96 bonds, 4 residues, 1 model selected  

> select /A:174

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color #1/A:51-54, 174-177 cyan

> select clear

> select /A:55

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:79

46 atoms, 50 bonds, 2 residues, 1 model selected  

> color #1/A:55-79 orange

> select clear

> view

[Repeated 1 time(s)]

> color #1/A:55-79 goldenrod rod

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

> color #1/A:55-79 goldenrod

> select /A:80

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

> select add /A:81

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select clear

> select /A:82

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

> select add /A:83

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add /A:84

66 atoms, 71 bonds, 3 residues, 1 model selected  

> select clear

> select /A:84

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:80

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

> select /A:81

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select /A:84

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:83

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:82

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add /A:181

63 atoms, 67 bonds, 3 residues, 1 model selected  

> select add /A:182

85 atoms, 91 bonds, 4 residues, 1 model selected  

> select add /A:170

108 atoms, 116 bonds, 5 residues, 1 model selected  

> select add /A:121

130 atoms, 140 bonds, 6 residues, 1 model selected  

> select subtract /A:170

107 atoms, 115 bonds, 5 residues, 1 model selected  

> select subtract /A:121

85 atoms, 91 bonds, 4 residues, 1 model selected  

> select add /A:81

107 atoms, 115 bonds, 5 residues, 1 model selected  

> select add /A:180

127 atoms, 136 bonds, 6 residues, 1 model selected  

> select add /A:179

150 atoms, 161 bonds, 7 residues, 1 model selected  

> select add /A:178

173 atoms, 186 bonds, 8 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel salmon

> color sel dark salmon

> color sel salmon

> color sel light salmon

> select clear

> select add /A:178

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:179

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select add /A:180

66 atoms, 71 bonds, 3 residues, 1 model selected  

> select add /A:181

86 atoms, 92 bonds, 4 residues, 1 model selected  

> select add /A:182

108 atoms, 116 bonds, 5 residues, 1 model selected  

> select clear

> select /A:81

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add /A:82

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add /A:83

65 atoms, 70 bonds, 3 residues, 1 model selected  

> select clear

> select add /A:178

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:179

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select /A:180

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

> select add /A:181

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add /A:182

62 atoms, 66 bonds, 3 residues, 1 model selected  

> color #1/A:81-83, 178-182 salmon

> select clear

> select add /A:184

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color #1/A:81-83, 178-184 salmon

> select clear

> select add /A:183

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select /A:183@C3'

1 atom, 1 residue, 1 model selected  

> select clear

> select /A:173

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

> select add /A:172

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select clear

> select /A:91

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

> select clear

> select /A:99

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /A:100

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select /A:101

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:100

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select add /A:99

67 atoms, 73 bonds, 3 residues, 1 model selected  

> select subtract /A:99

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select /A:103

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

> select add /A:168

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select clear

> color #1/A:119-163 hotpink

> select clear

> select /A:163

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select /A:118

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:106

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select /A:101

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:118

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:108

43 atoms, 46 bonds, 2 residues, 1 model selected  

> color #1/A:108-118 blue

> color #1/A:108-118 royalblue

> color #1/A:108-118 lblue

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

> color #1/A:108-118 blue

> select clear

> color #1/A:108-118 darkblue

> select /A:107

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

> color #1/A:101-107,164-170 limegreen

> select clear

> color #1/A:101-107,164-170 lime

> select clear

> select add /A:171

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add /A:172

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select add /A:173

65 atoms, 70 bonds, 3 residues, 1 model selected  

> select add /A:100

87 atoms, 94 bonds, 4 residues, 1 model selected  

> select add /A:91

107 atoms, 115 bonds, 5 residues, 1 model selected  

> color #1/A:91-100, 171-173 lightgray

> color #1/A:91-100, 171-173 gray

> color #1/A:91-100, 171-173 darkgray

> select clear

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:183

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:165

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

> select clear

> select /A:84

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:33

45 atoms, 49 bonds, 2 residues, 1 model selected  

> color #1/A:33, 84, 91-100, 171-173 darkgray

> select clear

> select add /A:29

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

> select clear

> select add /A:29

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

> select /A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add /A:183

45 atoms, 49 bonds, 2 residues, 1 model selected  

> color #1/A:33, 84, 91-100, 171-173, 183,185 darkgray

> select clear

> color byhetero

> select clear

[Repeated 1 time(s)]

> undo

[Repeated 4 time(s)]

> select clear

> view

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!2 models

> volume #2 level 0.06614

> hide #!2 models

> view

[Repeated 1 time(s)]

> show #!2 models

> volume #2 level 0.07928

> volume #2 color #b2b2b283

> view

[Repeated 1 time(s)]

> show #!3 models

> hide #!3 models

> hide #!2 models

> save "/Users/heyao/Google Drive/My Drive/RaiA_2024/Figures/fig1.cxs"

> show #!2 models

> hide #!2 models

> select Mg

5 atoms, 5 residues, 1 model selected  

> hide sel target a

> select clear

Drag select of 3156 atoms, 204 residues, 3480 bonds  

> show #!2 models

> ui tool show "Color Zone"

> color zone #2 near #1 distance 5.14

> select clear

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> select clear

> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA_3.0A/cryosparc_P44_J306_007_volume_map.mrc"

Opened cryosparc_P44_J306_007_volume_map.mrc as #4, grid size 256,256,256,
pixel 0.856, shown at level 0.0213, step 1, values float32  

> volume #4 level 0.04781

> volume #4 color #b2b2b27a

> select clear

> view

> hide #!2 models

> show #!2 models

> hide #1 models

> hide #!4 models

> volume #2 level 0.06335

> select clear

> view

> view name p1

> ui tool show "Side View"

> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true

> surface dust size 3

Missing or invalid "surfaces" argument: invalid surfaces specifier  

> surface dust

Missing or invalid "surfaces" argument: empty atom specifier  

> surface dust #2 size 3

> select clear

> view p1

> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn x 90

> save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn x 90

[Repeated 2 time(s)]

> color single #2

> show #1 models

> hide #!2 models

> select clear

Drag select of 3156 atoms, 204 residues, 3480 bonds  

> show #!2 models

> hide #!2 models

> show #!4 models

> hide #!4 models

> show #!2 models

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

> color zone #2 near sel distance 5.14

> select clear

> hide #1 models

> select clear

> view p1

> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn x 90

> save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn x 90

[Repeated 2 time(s)]

> turn y 90

[Repeated 1 time(s)]

> save /Users/heyao/Desktop/3.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn x 90

> save /Users/heyao/Desktop/4.png width 2000 height 2000 supersample 3
> transparentBackground true

> view name p2

> view p1

> turn y 90

[Repeated 1 time(s)]

> turn y 190

[Repeated 1 time(s)]

> view p1

> view

> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA+P2_3.0A/cryosparc_P44_J208_006_volume_map.mrc"

Opened cryosparc_P44_J208_006_volume_map.mrc as #5, grid size 256,256,256,
pixel 0.856, shown at level 0.0194, step 1, values float32  

> volume #5 color #b2b2b2

> volume #5 level 0.04769

> ui mousemode right "rotate selected models"

> select add #5

2 models selected  

> view matrix models
> #5,0.98908,-0.10981,-0.098248,23.585,0.018638,0.75465,-0.65586,89.971,0.14617,0.64687,0.74846,-68.003

> fitmap #5 inMap #2

Fit map cryosparc_P44_J208_006_volume_map.mrc in map
cryosparc_P44_J306_007_volume_map.mrc using 57510 points  
correlation = 0.6961, correlation about mean = 0.1762, overlap = 166.5  
steps = 160, shift = 7.08, angle = 13.6 degrees  
  
Position of cryosparc_P44_J208_006_volume_map.mrc (#5) relative to
cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99520792 0.09266609 -0.03121206 -1.90478254  
-0.08638041 0.68359534 -0.72473156 121.64881794  
-0.04582162 0.72395470 0.68832403 -45.65379273  
Axis 0.99239916 0.01000804 -0.12265292  
Axis point 0.00000000 113.18746461 118.36999355  
Rotation angle (degrees) 46.87724941  
Shift along axis 4.92673271  
  

> select clear

> select add #5

2 models selected  

> view matrix models
> #5,-0.28863,-0.93163,0.22081,242.43,0.58353,-0.35401,-0.73086,165.17,0.75907,-0.082096,0.64582,-41.296

> view matrix models
> #5,-0.86039,-0.42794,0.27676,244.86,0.12692,-0.70587,-0.69688,256.01,0.49358,-0.56446,0.66164,44.269

> fitmap #5 inMap #2

Fit map cryosparc_P44_J208_006_volume_map.mrc in map
cryosparc_P44_J306_007_volume_map.mrc using 57510 points  
correlation = 0.9304, correlation about mean = 0.7264, overlap = 384.4  
steps = 420, shift = 27.3, angle = 61.9 degrees  
  
Position of cryosparc_P44_J208_006_volume_map.mrc (#5) relative to
cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.82309682 0.56737562 0.02442404 134.59045503  
-0.45808180 -0.63789380 -0.61907396 298.40293952  
-0.33566753 -0.52074601 0.78495280 110.25649577  
Axis 0.09010312 0.32997103 -0.93968109  
Axis point 119.35289183 147.39940598 0.00000000  
Rotation angle (degrees) 146.93150884  
Shift along axis 6.98539970  
  

> select clear

> view p1

> select clear

> hide #!2 models

> open "/Users/heyao/My Drive/RaiA_2024/PDB_deposition/raiA+P2_3.0A/KN-
> coot-13_isolde_real_space_refined_065_isolde.pdb"

Chain information for KN-coot-13_isolde_real_space_refined_065_isolde.pdb #6  
---  
Chain | Description  
A | No description available  
  

> select add #6

5353 atoms, 5988 bonds, 1 pseudobond, 249 residues, 2 models selected  

> view matrix models
> #6,-0.90858,0.1578,-0.38676,255.46,0.17715,-0.69294,-0.6989,251.02,-0.37829,-0.70352,0.60164,171.11

> view matrix models
> #6,-0.51182,0.84433,-0.15861,100.53,-0.62781,-0.49363,-0.60182,317.23,-0.58643,-0.20844,0.78272,119.21

> fitmap #6 inMap #5

Fit molecule KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) to map
cryosparc_P44_J208_006_volume_map.mrc (#5) using 5353 atoms  
average map value = 0.01605, steps = 132  
shifted from previous position = 4.23  
rotated from previous position = 9.84 degrees  
atoms outside contour = 4651, contour level = 0.047687  
  
Position of KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) relative
to cryosparc_P44_J208_006_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
0.86772792 -0.39727738 0.29869543 2.06277270  
0.42913695 0.90201861 -0.04694588 -47.94991180  
-0.25077830 0.16891749 0.95319313 19.39883446  
Axis 0.21254395 0.54102425 0.81370623  
Axis point 94.65981773 -21.12486692 0.00000000  
Rotation angle (degrees) 30.51798290  
Shift along axis -9.71868299  
  

> view matrix models
> #6,-0.62963,0.75199,0.19515,92.984,-0.76605,-0.55911,-0.3171,317.86,-0.12935,-0.34915,0.9281,70.549

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.62963,0.75199,0.19515,68.108,-0.76605,-0.55911,-0.3171,313.96,-0.12935,-0.34915,0.9281,63.027

> view matrix models
> #6,-0.62963,0.75199,0.19515,68.366,-0.76605,-0.55911,-0.3171,300.24,-0.12935,-0.34915,0.9281,53.164

> fitmap #6 inMap #5

Fit molecule KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) to map
cryosparc_P44_J208_006_volume_map.mrc (#5) using 5353 atoms  
average map value = 0.07683, steps = 172  
shifted from previous position = 10.1  
rotated from previous position = 25.4 degrees  
atoms outside contour = 1263, contour level = 0.047687  
  
Position of KN-coot-13_isolde_real_space_refined_065_isolde.pdb (#6) relative
to cryosparc_P44_J208_006_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99999995 0.00001997 0.00032109 -0.03981368  
-0.00001996 1.00000000 -0.00003851 0.01104931  
-0.00032109 0.00003851 0.99999995 0.04171659  
Axis 0.11885500 0.99099744 -0.06162443  
Axis point 130.60221565 0.00000000 125.36760562  
Rotation angle (degrees) 0.01856408  
Shift along axis 0.00364702  
  

> ui mousemode right zoom

> select clear

> view p1

> select clear

> view p1

> hide #!5 models

> hide #!6 models

> show #!6 models

> show #!5 models

> hide #!6 models

> show #!6 models

> hide #!5 models

> select clear

Drag select of 249 residues, 1 pseudobonds, 498 shapes  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 5353 atom styles  

> cartoon style sel xsection oval width 1.6 thickness 1.6

> select clear

> show #1 models

> hide #!6 models

> show #!6 models

> select #6/A:240

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:14

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:240

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:1

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

> select #6/A:253

22 atoms, 24 bonds, 1 residue, 1 model selected  

> P1a and P1b color #6/A:1-14,240-253 orange red

Unknown command: P1a and P1b color #6/A:1-14,240-253 orange red  

> color #6/A:1-14,240-253 orange red

> select clear

[Repeated 1 time(s)]

> select #6/A:15

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

> select clear

> select #6/A:239

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:238

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select #6/A:235

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #6/A:239

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select clear

> select #6/A:15

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

> select add #6/A:20

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select #6/A:19

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

> color #6/A:15-19,235-239 purple

> select #6/A:92

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select clear

> hide #1 models

> select #6/A:60

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #6/A:59

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add #6/A:20

65 atoms, 70 bonds, 3 residues, 1 model selected  

> ui tool show "Color Actions"

> color #6/A:20-60 darkgoldenrod

> select clear

> view

> select clear

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> color #6/A:20-60 pylegoldenrod

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

> color #6/A:20-60 palegoldenrod

> select clear

> view

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> color #6/A:20-60 tan

> select clear

[Repeated 1 time(s)]

> show #!2 models

> hide #!2 models

> show #1 models

> hide #!6 models

> show #!6 models

> select #1/A:23

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select #6/A:60

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color sel purple

> select clear

> select #6/A:20

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color sel purple

> select clear

[Repeated 1 time(s)]

> hide #1 models

> select #6/A:20

23 atoms, 25 bonds, 1 residue, 1 model selected  

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> show #1 models

> hide #!6 models

> show #!6 models

> select #6/A:60

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select #6/A:59

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

> color #6/A:15-20,60,235-239 purple

> select clear

> hide #1 models

> show #!2 models

> show #1 models

> hide #!2 models

> color #6/A:21-59 tan

> hide #1 models

> show #1 models

> select #6/A:61

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:64

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select add #1/A:50

66 atoms, 71 bonds, 3 residues, 2 models selected  

> select subtract #1/A:50

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select add #6/A:87

66 atoms, 71 bonds, 3 residues, 1 model selected  

> select add #6/A:82

88 atoms, 95 bonds, 4 residues, 1 model selected  

> color #6/A:61-64,82-87 cornflower blue

> select #6/A:65

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #1/A:33

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #6/A:65

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #6/A:69

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select #6/A:81

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color #6/A:65-69,77-81 yellow

> select clear

[Repeated 1 time(s)]

> select #6/A:70

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select #6/A:71

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:76

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select clear

> select #6/A:71

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:76

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select clear

> select #6/A:123

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

> select #6/A:118

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

> color #1/A:71-76,118-123 green

> undo

> color #6/A:71-76,118-123 green

> select clear

> hide #1 models

> show #1 models

> select #6/A:88

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

> select add #6/A:91

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add #6/A:92

63 atoms, 67 bonds, 3 residues, 1 model selected  

> select subtract #6/A:92

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select #6/A:226

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:223

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select subtract #6/A:223

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:223

46 atoms, 50 bonds, 2 residues, 1 model selected  

> color #6/A:88-91,223-226 cyan

> select clear

> select #1/A:55

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:92

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:112

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

> select clear

[Repeated 1 time(s)]

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> select #6/A:92

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:112

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

> hide #1 models

> show #1 models

> hide #!6 models

> select #1/A:80

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

> color #1/A:33,80,84,91-100,171-173,183,185 darkgray

> select clear

> show #!2 models

> hide #1 models

> show #1 models

> hide #!2 models

> select clear

Drag select of 3156 atoms, 204 residues, 3480 bonds  

> show #!2 models

> color #2 near 1 distance 5

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

> colorzone #2 near 1 distance 5

Unknown command: colorzone #2 near 1 distance 5  

> color zone #2 near 1 distance 5

Invalid "near" argument: invalid atoms specifier  

> color zone #2 near #1 distance 5

> select clear

> hide #!2 models

> hide #1 models

> view p1

> show #1 models

> show #!2 models

> hide #1 models

> show #!6 models

> hide #!2 models

> color #6/A:92-112 goldenrod

> select clear

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> show #1 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #1 models

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> select #6/A:70

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #1 models

> select #1/A:81

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #6/A:114

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #6/A:115

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add #6/A:116

65 atoms, 70 bonds, 3 residues, 1 model selected  

> select #6/A:227

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:233

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color #6/A:114-116,227-233 salmon

> hide #1 models

> show #1 models

> hide #!6 models

> show #!6 models

> select #1/A:183

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #6/A:232

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #1/A:185

23 atoms, 25 bonds, 1 residue, 1 model selected  

> hide #1 models

> show #1 models

> hide #1 models

> select #6/A:234

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color #6/A:70,232,234 darkgray

> select clear

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> show #1 models

> select #1/A:170

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select clear

> select #6/A:219

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #1/A:170

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select #1/A:170

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #6/A:219

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #6/A:213

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select #6/A:140

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

> select #6/A:134

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select clear

> color #6/A:134-140,213-219 lime

> select #6/A:141

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

> select #6/A:174

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color #6/A:141-174 darkblue

> select clear

> select #6/A:212

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #6/A:175

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color #6/A:175-212 hotpink

> hide #1 models

> view p1

> select clear

> show #1 models

> hide #1 models

> select #6/A:124

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

> select add #6/A:133

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select #6/A:222

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

> select add #6/A:220

42 atoms, 45 bonds, 2 residues, 1 model selected  

> color #6/A:70,113,117,124-133,220-222,232,234 darkgray

> select clear

> view p1

> show #!5 models

> volume #5 level 0.05695

> ui tool show "Color Zone"

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

> color zone #5 near #6 distance 5.14

> color zone #5 near #6 distance 5.1

> color zone #5 near #6 distance 5

[Repeated 2 time(s)]

> hide #!5 models

> show #!5 models

> hide #!6 models

> volume #5 level 0.05886

> volume #5 level 0.05504

> show #!2 models

> hide #!2 models

> show #1 models

> show #!6 models

> hide #!6 models

> hide #!5 models

> show #!2 models

> hide #1 models

> save /Users/heyao/Desktop/fig1.cxs

> show #!6 models

> hide #!2 models

> show #!2 models

> hide #!6 models

> show #1 models

> hide #!2 models

> show #!2 models

> hide #1 models

> view p1

> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p2

> save /Users/heyao/Desktop/3.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

[Repeated 1 time(s)]

> turn x 180

[Repeated 1 time(s)]

> turn z 180

> save /Users/heyao/Desktop/4.png width 2000 height 2000 supersample 3
> transparentBackground true

> show #1 models

> hide #1 models

> hide #!2 models

> show #!6 models

> hide #!6 models

> show #!5 models

> ui tool show "Hide Dust"

> surface dust #5 size 5.14

> surface dust #5 size 4.94

> surface dust #5 size 1.19

> surface dust #5 size 1.74

> surface dust #5 size 1

> surface dust #5 size 3

[Repeated 1 time(s)]

> save /Users/heyao/Desktop/14.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn z 180

> save /Users/heyao/Desktop/13.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p1

> save /Users/heyao/Desktop/11.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> save /Users/heyao/Desktop/12.png width 2000 height 2000 supersample 3
> transparentBackground true

> view

[Repeated 3 time(s)]

> select clear

> volume #5 level 0.07883

> view p1

> volume #5 level 0.04591

> view p1

> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA+P2_3.0A/cryosparc_P44_J208_006_volume_map_sharp.mrc"

Opened cryosparc_P44_J208_006_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 0.856, shown at level 0.0321, step 1, values float32  

> volume #7 level 0.09953

> select add #7

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #7,-0.76381,0.63589,-0.11064,143.02,-0.52039,-0.70812,-0.47725,309.35,-0.38182,-0.30695,0.87178,93.617

> fitmap #7 inMap #5

Fit map cryosparc_P44_J208_006_volume_map_sharp.mrc in map
cryosparc_P44_J208_006_volume_map.mrc using 33096 points  
correlation = 0.9546, correlation about mean = 0.7783, overlap = 698.7  
steps = 164, shift = 18.4, angle = 13.5 degrees  
  
Position of cryosparc_P44_J208_006_volume_map_sharp.mrc (#7) relative to
cryosparc_P44_J208_006_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99999995 -0.00009731 0.00030468 -0.02233620  
0.00009737 0.99999998 -0.00018529 0.01126621  
-0.00030466 0.00018532 0.99999994 0.01925316  
Axis 0.50131231 0.82422219 0.26333202  
Axis point 60.44868633 0.00000000 78.51712028  
Rotation angle (degrees) 0.02117924  
Shift along axis 0.00315842  
  

> select clear

> hide #!5 models

> volume #7 level 0.1479

> volume #7 level 0.1142

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

> surface dust #7 size 5.14

> color zone #7 near #6 distance 5.14

> select clear

> volume #7 level 0.09513

> surface dust #7 size 5.17

> surface dust #7 size 2.59

> hide #!7 models

> show #1 models

> hide #1 models

> show #!2 models

> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA-P8_3.5A/cryosparc_P44_J119_007_volume_map.mrc"

Opened cryosparc_P44_J119_007_volume_map.mrc as #8, grid size 256,256,256,
pixel 0.856, shown at level 0.0109, step 1, values float32  

> volume #8 level 0.05676

> select add #8

2 models selected  

> view matrix models
> #8,-0.7258,0.66222,0.18623,91.252,0.62651,0.52455,0.57647,-87.693,0.28407,0.53508,-0.79561,134.51

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.7258,0.66222,0.18623,96.465,0.62651,0.52455,0.57647,-78.886,0.28407,0.53508,-0.79561,111.51

> view matrix models
> #8,-0.7258,0.66222,0.18623,95.693,0.62651,0.52455,0.57647,-77.05,0.28407,0.53508,-0.79561,109.84

> ui mousemode right "rotate selected models"

> view matrix models
> #8,-0.59361,-0.78521,0.17626,238.98,-0.41119,0.48422,0.77231,14.761,-0.69177,0.38597,-0.61031,208.04

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  
Must specify one map, got 0  

> fitmap #8 inMap #2

Fit map cryosparc_P44_J119_007_volume_map.mrc in map
cryosparc_P44_J306_007_volume_map.mrc using 32003 points  
correlation = 0.7141, correlation about mean = 0.06117, overlap = 96.41  
steps = 120, shift = 7.63, angle = 7.11 degrees  
  
Position of cryosparc_P44_J119_007_volume_map.mrc (#8) relative to
cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.67932839 -0.70734554 0.19538482 233.17463966  
-0.32924966 0.53174106 0.78028592 -1.20521285  
-0.65582589 0.46573999 -0.59412007 187.73366128  
Axis -0.31995815 0.86585704 0.38460157  
Axis point 145.04886475 0.00000000 58.92440994  
Rotation angle (degrees) 150.55799757  
Shift along axis -3.44700659  
  

> select clear

> select add #8

2 models selected  

> view matrix models
> #8,0.92597,-0.247,0.28559,-0.62486,-0.33951,-0.87565,0.34347,206.09,0.16524,-0.41501,-0.89469,231.71

> fitmap #8 inMap #2

Fit map cryosparc_P44_J119_007_volume_map.mrc in map
cryosparc_P44_J306_007_volume_map.mrc using 32003 points  
correlation = 0.918, correlation about mean = 0.5232, overlap = 217.2  
steps = 132, shift = 2.14, angle = 21.9 degrees  
  
Position of cryosparc_P44_J119_007_volume_map.mrc (#8) relative to
cryosparc_P44_J306_007_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.98172391 0.09005861 0.16765326 -29.84294848  
-0.01268335 -0.84802486 0.52980466 149.11768328  
0.18988760 -0.52224830 -0.83138403 232.76992784  
Axis -0.99504515 -0.02102952 -0.09717466  
Axis point 0.00000000 108.37326391 96.40524730  
Rotation angle (degrees) 148.08599472  
Shift along axis 3.93986945  
  

> select clear

> hide #!8 models

> show #!8 models

> hide #!2 models

> show #!2 models

> select clear

> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA-P8_3.5A/initial_model_AN-
> coot-11_isolde.pdb"

Chain information for initial_model_AN-coot-11_isolde.pdb #9  
---  
Chain | Description  
A | No description available  
  

> select add #9

3336 atoms, 3734 bonds, 2 pseudobonds, 155 residues, 2 models selected  

> hide #!2 models

> view matrix models
> #9,0.92235,0.35553,0.15123,-47.92,0.17678,-0.73639,0.65305,87.261,0.34354,-0.57561,-0.74206,237.51

> ui mousemode right "translate selected models"

> view matrix models
> #9,0.92235,0.35553,0.15123,-46.908,0.17678,-0.73639,0.65305,102.26,0.34354,-0.57561,-0.74206,218.07

> fitmap #9 inMap #8

Fit molecule initial_model_AN-coot-11_isolde.pdb (#9) to map
cryosparc_P44_J119_007_volume_map.mrc (#8) using 3336 atoms  
average map value = 0.06906, steps = 132  
shifted from previous position = 6.96  
rotated from previous position = 16.8 degrees  
atoms outside contour = 1046, contour level = 0.056762  
  
Position of initial_model_AN-coot-11_isolde.pdb (#9) relative to
cryosparc_P44_J119_007_volume_map.mrc (#8) coordinates:  
Matrix rotation and translation  
0.99999922 0.00120715 0.00033324 -0.17137916  
-0.00120711 0.99999926 -0.00015796 0.15354463  
-0.00033343 0.00015757 0.99999994 0.01154017  
Axis 0.12499238 0.26409247 -0.95636399  
Axis point 125.34278901 142.88874346 0.00000000  
Rotation angle (degrees) 0.07231914  
Shift along axis 0.00809228  
  

> select clear

> ui mousemode right zoom

> view p1

> select clear

> hide #!8 models

> select clear

Drag select of 155 residues, 2 pseudobonds, 310 shapes  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 3336 atom styles  

> cartoon style sel xsection oval width 1.6 thickness 1.6

> select clear

> show #!8 models

> hide #!8 models

> show #1 models

> select clear

> select #1/A:191

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:150

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:14

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:150

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:163

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color #9/A:1-14,150-163 orange red

> select clear

> select #1/A:190

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #1/A:15

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

> select add #9/A:23

42 atoms, 45 bonds, 2 residues, 2 models selected  

> select #1/A:190

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:149

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:145

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color #6/A:15-23,145-149 purple

[Repeated 1 time(s)]

> undo

[Repeated 2 time(s)]

> hide #1 models

> hide #!9 models

> show #!5 models

> hide #!5 models

> show #!6 models

> show #!9 models

> hide #!6 models

> undo

[Repeated 10 time(s)]No undo action is available  

> undo

No undo action is available  

> undo

No undo action is available  

> undo

No undo action is available  

> select clear

[Repeated 1 time(s)]

> color #9/A:15-23,145-149 purple

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> select #1/A:24

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #1/A:27

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select add #1/A:50

66 atoms, 71 bonds, 3 residues, 1 model selected  

> select add #9/A:45

88 atoms, 95 bonds, 4 residues, 2 models selected  

> color #9/A:24-27,45-50 cornflower blue

> select clear

> hide #!9 models

> show #!9 models

> hide #1 models

> show #1 models

> select #9/A:28

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #9/A:32

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select #9/A:40

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #9/A:44

45 atoms, 49 bonds, 2 residues, 1 model selected  

> color #9/A:28-32,40-44 yellow

> select clear

> select #1/A:33

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #1/A:34

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:34

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #9/A:39

46 atoms, 50 bonds, 2 residues, 1 model selected  

> select #9/A:92

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

> select #9/A:87

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

> color #9/A:34-39,87-92 green

> select clear

> hide #1 models

> show #1 models

> hide #1 models

> select #9/A:33

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color sel darg gray

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

> color sel darkgray

> select clear

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> show #1 models

> hide #!9 models

> show #!9 models

> select #1/A:51

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

> select #9/A:51

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

> select add #9/A:54

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select clear

> select #9/A:136

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #9/A:133

46 atoms, 50 bonds, 2 residues, 1 model selected  

> color #9/A:51-54,133-136 cyan

> select clear

> hide #1 models

> show #1 models

> select #9/A:55

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select #9/A:81

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

> hide #1 models

> select clear

> select #9/A:81

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

> show #1 models

> color #9/A:55-81 goldenrod

> select clear

> hide #1 models

> show #1 models

> select #9/A:83

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #9/A:85

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select #1/A:81

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #9/A:83

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #9/A:85

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select #1/A:184

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #9/A:143

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #9/A:143

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #9/A:137

23 atoms, 25 bonds, 1 residue, 1 model selected  

> color #9/A:83-85,137-143 salmon

> select clear

> select #1/A:183

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #1/A:185

45 atoms, 49 bonds, 2 residues, 1 model selected  

> hide #1 models

> show #1 models

> hide #1 models

> select add #9/A:142

67 atoms, 73 bonds, 3 residues, 2 models selected  

> select add #9/A:144

89 atoms, 97 bonds, 4 residues, 2 models selected  

> color #9/A:33, 82, 86, 142,144 darkgray

> select clear

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> select #9/A:93

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

> show #1 models

> select #9/A:121

23 atoms, 25 bonds, 1 residue, 1 model selected  

> hide #1 models

> select add #9/A:108

43 atoms, 46 bonds, 2 residues, 1 model selected  

> show #1 models

> hide #1 models

> color #9/A:108-121 darkblue

> select clear

> select add #9/A:107

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

> show #1 models

> select add #1/A:101

43 atoms, 46 bonds, 2 residues, 2 models selected  

> select add #9/A:102

65 atoms, 70 bonds, 3 residues, 2 models selected  

> select #1/A:102

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

> select #1/A:101

23 atoms, 25 bonds, 1 residue, 1 model selected  

> hide #!9 models

> show #!9 models

> hide #1 models

> select #9/A:107

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

> select #9/A:128

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

> select add #9/A:127

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add #9/A:126

66 atoms, 71 bonds, 3 residues, 1 model selected  

> show #1 models

> select add #9/A:129

88 atoms, 95 bonds, 4 residues, 1 model selected  

> select #9/A:103

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #9/A:107

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select clear

> color #9/A:103-107,126-129 lime

> select clear

> hide #1 models

> select #9/A:102

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #9/A:130

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #9/A:132

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select #9/A:93

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

> select add #9/A:102

42 atoms, 45 bonds, 2 residues, 1 model selected  

> color #9/A:33,82,86,93-102,130-132,142,144 darkgray

> select clear

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> save /Users/heyao/Desktop/fig1.cxs

> show #!8 models

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

> color zone #8 near #9 distance 5.14

> color zone #8 near #9 distance 4.96

> color zone #8 near #9 distance 3.98

> surface dust #8 size 5.14

> volume #8 level 0.06701

> open "/Users/heyao/My
> Drive/RaiA_2024/PDB_deposition/raiA-P8_3.5A/cryosparc_P44_J119_007_volume_map_sharp.mrc"

Opened cryosparc_P44_J119_007_volume_map_sharp.mrc as #10, grid size
256,256,256, pixel 0.856, shown at level 0.0198, step 1, values float32  

> volume #10 level 0.1802

> select add #10

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #10,-0.97132,-0.23766,0.0077356,235.93,-0.15228,0.64668,0.7474,-32.131,-0.18263,0.72479,-0.66433,134.13

> volume #10 level 0.08858

> view matrix models
> #10,0.93215,0.020628,0.36147,-38.767,-0.19435,-0.81384,0.54762,154.01,0.30548,-0.58072,-0.75462,233.48

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.93215,0.020628,0.36147,-35.457,-0.19435,-0.81384,0.54762,162.59,0.30548,-0.58072,-0.75462,224.58

Must specify one map, got 0  

> fitmap #10 inMap #8

Fit map cryosparc_P44_J119_007_volume_map_sharp.mrc in map
cryosparc_P44_J119_007_volume_map.mrc using 27855 points  
correlation = 0.931, correlation about mean = 0.5914, overlap = 393.1  
steps = 120, shift = 6.72, angle = 13 degrees  
  
Position of cryosparc_P44_J119_007_volume_map_sharp.mrc (#10) relative to
cryosparc_P44_J119_007_volume_map.mrc (#8) coordinates:  
Matrix rotation and translation  
0.99999985 0.00045450 0.00030702 -0.07641814  
-0.00045451 0.99999989 0.00002918 0.05384633  
-0.00030700 -0.00002931 0.99999995 0.03236712  
Axis -0.05324606 0.55895242 -0.82748840  
Axis point 109.35316698 167.30731259 0.00000000  
Rotation angle (degrees) 0.03147028  
Shift along axis 0.00738308  
  

> select clear

> save /Users/heyao/Desktop/fig1.cxs

> surface dust #10 size 5.14

> color zone #10 near #9 distance 5.14

> hide #!8 models

> hide #!9 models

> volume #10 level 0.08349

> view p1

> show #!2 models

> hide #!2 models

> show #!3 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> hide #!2 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!10 models

> show #!8 models

> hide #!10 models

> show #!10 models

> hide #!8 models

> volume #10 level 0.08172

> volume #10 level 0.07116

> show #!8 models

> volume #8 level 0.05258

> volume #8 level 0.04487

> select #8

2 models selected  

> show #!9 models

> hide #!8 models

> select clear

> show #!8 models

> color #8 #d6d6d6ff models

> color #8 silver models

> color zone #10 near #9 distance 5.14

[Repeated 1 time(s)]

> color zone #8 near #9 distance 5.14

> select clear

> hide #!8 models

> hide #!9 models

> show #1 models

> hide #1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> color #3 #b2b2b2ff models

> color zone #3 near #1 distance 5.14

> view

> view p1

> volume #3 level 0.1706

> volume #3 level 0.19

> volume #3 level 0.2

> volume #3 level 0.1481

> view

> view p1

> show #1 models

> hide #!2 models

Drag select of 3156 atoms, 204 residues, 3480 bonds  

> show #!2 models

> ui tool show "Color Zone"

> color zone #2 near sel distance 5

> hide #!2 models

> show #!2 models

> hide #1 models

> view p1

> volume #2 level 0.07

> volume #2 level 0.05

> volume #2 level 0.06

> view p1

> save /Users/heyao/Desktop/1.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> save /Users/heyao/Desktop/2.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p2

> turn z 180

> save /Users/heyao/Desktop/3.png width 2000 height 2000 supersample 3
> transparentBackground true

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!4 models

> show #!2 models

> hide #!2 models

> show #1 models

> hide #1 models

> show #!3 models

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

> view p1

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!3 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!5 models

> volume #5 level 0.05207

> view p1

> save /Users/heyao/Desktop/11.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> save /Users/heyao/Desktop/12.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p2

> turn z 180

> save /Users/heyao/Desktop/13.png width 2000 height 2000 supersample 3
> transparentBackground true

> hide #!5 models

> show #!10 models

> show #!8 models

> hide #!10 models

> view p1

> volume #8 level 0.05187

> volume #8 level 0.04053

> view p1

> view

> view p1

> save /Users/heyao/Desktop/21.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> save /Users/heyao/Desktop/22.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p2

> turn z 180

> save /Users/heyao/Desktop/23.png width 2000 height 2000 supersample 3
> transparentBackground true

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!10 models

> hide #!10 models

> show #!9 models

> hide #!9 models

> show #!8 models

> view p1

> hide #!8 models

> show #!8 models

> hide #!2 models

> volume #8 level 0.05

> view p1

> save /Users/heyao/Desktop/21.png width 2000 height 2000 supersample 3
> transparentBackground true

> turn y 180

> save /Users/heyao/Desktop/22.png width 2000 height 2000 supersample 3
> transparentBackground true

> view p2

[Repeated 1 time(s)]

> turn z 180

> save /Users/heyao/Desktop/23.png width 2000 height 2000 supersample 3
> transparentBackground true

> save /Users/heyao/Desktop/fig1.cxs

——— End of log from Sat Dec 14 18:45:20 2024 ———

opened ChimeraX session  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

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: MacBookPro18,3
      Model Number: MKGQ3LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.41.5
      OS Loader Version: 11881.41.5

Software:

    System Software Overview:

      System Version: macOS 15.1.1 (24B91)
      Kernel Version: Darwin 24.1.0
      Time since boot: 3 days, 25 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        ROG PG278QR:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


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-Clipper: 0.23.1
    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-ISOLDE: 1.8
    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-PICKLUSTER: 0.5
    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, 11 months ago

Component: Unassigned → Window Toolkit
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash on Mac waking from sleep

Reported by Yao He

comment:2 by Tom Goddard, 11 months ago

Resolution: → duplicate
Status: assigned → closed

This Mac ChimeraX crash is a bug in the Qt window toolkit and happens some times when disconnecting or connecting an external display or waking from sleep. We don't have a fix for. ChimeraX 1.9 was just released on has a newer Qt version 6.7 that may encounter the crash less often, but we have also seen it happen with Qt 6.7 several times. We are hoping that the next version of Qt 6.8 will fix it and we will be switching the ChimeraX daily builds to use Qt 6.8 which just came out in the next few weeks.

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