Opened 10 months ago

Closed 10 months ago

#16555 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by: chimerax-bug-report@… 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-15.0-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000070001f8b2000 (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 0x000070001e8af000 (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 0x000070001d8ac000 (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 0x000070001c8a9000 (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 0x000070001b8a6000 (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 0x000070001a8a3000 (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 0x00007000198a0000 (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 0x000070001889d000 (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 0x000070001789a000 (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 0x0000700016897000 (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 0x0000700015894000 (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 0x0000700014891000 (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 0x000070001388e000 (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 0x000070001288b000 (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 0x0000700011888000 (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 0x0000700010885000 (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 0x000070000f882000 (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 0x000070000e87f000 (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 0x000070000d87c000 (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 0x00007ff84dee2680 (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, lxml._elementpath, lxml.etree, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 119)


{"app_name":"ChimeraX","timestamp":"2025-01-06 10:38:22.00 +0800","app_version":"1.8.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","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 15.0 (24A335)","roots_installed":0,"name":"ChimeraX","incident_id":"B7C335C4-FEE9-4F9C-B608-2A4EC9A9DF4F"}
{
  "uptime" : 1000000,
  "procRole" : "Background",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro16,1",
  "coalitionID" : 560,
  "osVersion" : {
    "train" : "macOS 15.0",
    "build" : "24A335",
    "releaseType" : "User"
  },
  "captureTime" : "2025-01-06 10:38:17.3221 +0800",
  "codeSigningMonitor" : 0,
  "incident" : "B7C335C4-FEE9-4F9C-B608-2A4EC9A9DF4F",
  "pid" : 94678,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-01-03 21:14:17.1226 +0800",
  "procStartAbsTime" : 1017775318471682,
  "procExitAbsTime" : 1087518888369563,
  "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":"AF0E444E-37B4-593A-957D-B5CF6828D46F","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "F7A40BD4-636A-5D03-BCEB-C22CD08BD04B",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "bootSessionUUID" : "7271DF61-C54B-4F26-A09D-192078EDC1F5",
  "wakeTime" : 49,
  "bridgeVersion" : {"build":"22P353","train":"9.0"},
  "sleepWakeUUID" : "824D7BBD-B0F4-4798-BD61-D73322623494",
  "sip" : "enabled",
  "vmRegionInfo" : "0 is not in any region.  Bytes before following region: 4474425344\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10ab25000-10ab29000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":94678},
  "vmregioninfo" : "0 is not in any region.  Bytes before following region: 4474425344\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      10ab25000-10ab29000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
  "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},
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/Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/multi/local_multi_c6_job26_body/relion_locres_filtered.mrc  

> open
> /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/multi/local_multi_c6_job26_head/relion_locres_filtered.mrc

No such file/path:
/Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/multi/local_multi_c6_job26_head/relion_locres_filtered.mrc  

> volume #2-10 step 1 level 0.0045

> volume #4 step 1 level 0.0075

No volumes specified  

> volume #5 step 1 level 0.003

No volumes specified  

> volume #4 step 1 level 0.0055

No volumes specified  

> surface dust #1-15 size 20

> set bgColor white

> windowsize 800 800

> color #1 #3-10 silver

> color #1 cyan

> color #2-10 silver

> color #1/a-g /j-p /u sienna

> color #1/K /L /P /R /T /q-t /CW wheat

> color #1/F /V /W /Z /CN sky blue

> color #1/B /Ca plum

> color #1/D /G /H /Q /X green

> color #1/I /Y /CV light green

> color #1/J /M /N /S /CY /Cb /Cc pink

> color #1/CD /CK /CL orange

> color #1/CR /CT /CX /CZ lime

> color #1/O /CA /CC /CU purple

> color #1/2 /h /i /CS cornflower blue

> color #1/CP /CQ /CE /CF /CG /CI /CJ forest green

> color #1/5 /A /C /E /CM hot pink

> color #1/6 /CB blue

> color #1/7 red

> color #1/8 magenta

> color #1/M dark red

> color #1/Cc orange

> color #1/U cyan

> color #1/Cb dodger blue

> color #1/CY dark red

> color #1/0 dark khaki

> color #1/Ch aquamarine

> color #1/Cf cyan

> color #1/Cd teal

> color #1/z tomato

> color #1/1 forest green

> color #1/Cg chocolate

> color #1/R dark violet

> color #1/F deep sky blue

> color #1/2 lime

> color #1/5 hot pink

> color #1/Y olive

> color #1/E tomato

> color #1/C deep pink

> color #1/V steel blue

> color #1/CV yellow green

> color #1/8 red

> hide #1 target a

> show #1/B /D /Cc /2 /6:1-90 target r

> hide #1/CM target r

> show #1/2 /6:1-90 target a

> nucleotides #1/2 /6:1-90 ladder

> cartoon style protein xsection oval width 2.4 thickness 0.6

> volume zone #2 nearAtoms #1/B /D /Cc /2 /6 range 6 newMap true

Opened run_class001.mrc zone as #3, grid size 480,480,480, pixel 0.932, shown
at step 1, values float32  

> volume #6 step 1 level 0.013

No volumes specified  

> surface dust #1-15 size 5

> color #6 silver

> transparency #6 50

> surface dust #1-15 size 5

> volume #3 level 0.004806

> volume #3 step 1 level 0.013

> surface dust #1-15 size 5

> color #3 silver

> transparency #3 50

> volume #3 level 0.0013

> volume #3 level 0.005

> close

> open
> /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/c6_job26_Q2-coot-56.pdb

Summary of feedback from opening
/Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/c6_job26_Q2-coot-56.pdb  
---  
warnings | Duplicate atom serial number found: 6524  
Duplicate atom serial number found: 6525  
Duplicate atom serial number found: 6526  
Duplicate atom serial number found: 6527  
Duplicate atom serial number found: 6528  
542 messages similar to the above omitted  
  
Chain information for c6_job26_Q2-coot-56.pdb #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
5 | No description available  
6 | No description available  
8 | No description available  
A | No description available  
B | No description available  
C | No description available  
CY | No description available  
Cb | No description available  
Cc | No description available  
Ck | No description available  
D | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
P | No description available  
R | No description available  
S | No description available  
T | No description available  
V | No description available  
W | No description available  
Y | No description available  
Z | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
z | No description available  
  

> open
> /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/focus_head/run_class001.mrc

Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at
level 0.00588, step 2, values float32  

> open
> /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/local_c6_job26_2/relion_locres_filtered.mrc

No such file/path:
/Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/local_c6_job26_2/relion_locres_filtered.mrc  

> open
> /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/multi/local_multi_c6_job26_body/relion_locres_filtered.mrc

No such file/path:
/Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/multi/local_multi_c6_job26_body/relion_locres_filtered.mrc  

> open
> /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/multi/local_multi_c6_job26_head/relion_locres_filtered.mrc

No such file/path:
/Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/multi/local_multi_c6_job26_head/relion_locres_filtered.mrc  

> volume #2-10 step 1 level 0.0045

> volume #4 step 1 level 0.0075

No volumes specified  

> volume #5 step 1 level 0.003

No volumes specified  

> volume #4 step 1 level 0.0055

No volumes specified  

> surface dust #1-15 size 20

> set bgColor white

> windowsize 800 800

> color #1 #3-10 silver

> color #1 cyan

> color #2-10 silver

> color #1/a-g /j-p /u sienna

> color #1/K /L /P /R /T /q-t /CW wheat

> color #1/F /V /W /Z /CN sky blue

> color #1/B /Ca plum

> color #1/D /G /H /Q /X green

> color #1/I /Y /CV light green

> color #1/J /M /N /S /CY /Cb /Cc pink

> color #1/CD /CK /CL orange

> color #1/CR /CT /CX /CZ lime

> color #1/O /CA /CC /CU purple

> color #1/2 /h /i /CS cornflower blue

> color #1/CP /CQ /CE /CF /CG /CI /CJ forest green

> color #1/5 /A /C /E /CM hot pink

> color #1/6 /CB blue

> color #1/7 red

> color #1/8 magenta

> color #1/M dark red

> color #1/Cc orange

> color #1/U cyan

> color #1/Cb dodger blue

> color #1/CY dark red

> color #1/0 dark khaki

> color #1/Ch aquamarine

> color #1/Cf cyan

> color #1/Cd teal

> color #1/z tomato

> color #1/1 forest green

> color #1/Cg chocolate

> color #1/R dark violet

> color #1/F deep sky blue

> color #1/2 lime

> color #1/5 hot pink

> color #1/Y olive

> color #1/E tomato

> color #1/C deep pink

> color #1/V steel blue

> color #1/CV yellow green

> color #1/8 red

> hide #1 target a

> show #1/B /D /Cc /2 /6:1-90 target r

> hide #1/CM target r

> show #1/2 /6:1-90 target a

> nucleotides #1/2 /6:1-90 ladder

> cartoon style protein xsection oval width 2.4 thickness 0.6

> volume zone #2 nearAtoms #1/B /D /Cc /2 /6 range 6 newMap true

Opened run_class001.mrc zone as #3, grid size 480,480,480, pixel 0.932, shown
at step 1, values float32  

> volume #3 step 1 level 0.013

> surface dust #1-15 size 5

> color #3 silver

> transparency #3 50

> volume #3 step 1 level 0.0045

> view matrix camera
> 0.4381,0.51596,0.73611,323.91,-0.87515,0.43191,0.21811,271.48,-0.20539,-0.73976,0.64076,242.62

> show #1/B /D /Cc /2 /6:1-100 target r

> show #1/2 /6:1-100 target a

> nucleotides #1/2 /6:1-100 ladder

> nucleotides stubs

> graphics silhouettes true

> volume #3 level 0.005

> view matrix camera
> 0.4381,0.51596,0.73611,323.91,-0.87515,0.43191,0.21811,271.48,-0.20539,-0.73976,0.64076,242.62

> save
> /Users/lijuanyin/project/prp43/figure_new/figure4/q2_focus_dhx15_u6_view1.jpg

> close

> open /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/run_class001.mrc

Opened run_class001.mrc as #1, grid size 480,480,480, pixel 0.932, shown at
level 0.00668, step 2, values float32  

> open
> /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/focus_head/run_class001.mrc

Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at
level 0.00588, step 2, values float32  

> volume #2 level 0.005

> volume #2 level 0.01

> volume #2 level 0.008

> volume #2 level 0.009

> volume #2 level 0.006

> volume #2 level 0.005

> close

> open
> /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/c6_job26_Q2-coot-56.pdb

Summary of feedback from opening
/Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/c6_job26_Q2-coot-56.pdb  
---  
warnings | Duplicate atom serial number found: 6524  
Duplicate atom serial number found: 6525  
Duplicate atom serial number found: 6526  
Duplicate atom serial number found: 6527  
Duplicate atom serial number found: 6528  
542 messages similar to the above omitted  
  
Chain information for c6_job26_Q2-coot-56.pdb #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
5 | No description available  
6 | No description available  
8 | No description available  
A | No description available  
B | No description available  
C | No description available  
CY | No description available  
Cb | No description available  
Cc | No description available  
Ck | No description available  
D | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
P | No description available  
R | No description available  
S | No description available  
T | No description available  
V | No description available  
W | No description available  
Y | No description available  
Z | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
z | No description available  
  

> open /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/run_class001.mrc

Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at
level 0.00668, step 2, values float32  

> volume #2-10 step 1 level 0.005

> volume #4 step 1 level 0.0075

No volumes specified  

> volume #5 step 1 level 0.003

No volumes specified  

> volume #4 step 1 level 0.0055

No volumes specified  

> surface dust #1-15 size 20

> set bgColor white

> windowsize 800 800

> color #1 #3-10 silver

> color #1 cyan

> color #2-10 silver

> color #1/a-g /j-p /u sienna

> color #1/K /L /P /R /T /q-t /CW wheat

> color #1/F /V /W /Z /CN sky blue

> color #1/B /Ca plum

> color #1/D /G /H /Q /X green

> color #1/I /Y /CV light green

> color #1/J /M /N /S /CY /Cb /Cc pink

> color #1/CD /CK /CL orange

> color #1/CR /CT /CX /CZ lime

> color #1/O /CA /CC /CU purple

> color #1/2 /h /i /CS cornflower blue

> color #1/CP /CQ /CE /CF /CG /CI /CJ forest green

> color #1/5 /A /C /E /CM hot pink

> color #1/6 /CB blue

> color #1/7 red

> color #1/8 magenta

> color #1/M dark red

> color #1/Cc orange

> color #1/U cyan

> color #1/Cb dodger blue

> color #1/CY dark red

> color #1/0 green yellow

> color #1/Ch aquamarine

> color #1/Cf cyan

> color #1/Cd teal

> color #1/z tomato

> color #1/1 forest green

> color #1/Cg chocolate

> color #1/R dark violet

> color #1/F deep sky blue

> color #1/2 lime

> color #1/5 hot pink

> color #1/Y olive

> color #1/E tomato

> color #1/C deep pink

> color #1/V steel blue

> color #1/CV magenta

> color #1/8:0-300 red

> color zone #2-10 near #1 distance 6

> close

> open
> /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/c6_job26_Q2-coot-56.pdb

Summary of feedback from opening
/Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/c6_job26_Q2-coot-56.pdb  
---  
warnings | Duplicate atom serial number found: 6524  
Duplicate atom serial number found: 6525  
Duplicate atom serial number found: 6526  
Duplicate atom serial number found: 6527  
Duplicate atom serial number found: 6528  
542 messages similar to the above omitted  
  
Chain information for c6_job26_Q2-coot-56.pdb #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
5 | No description available  
6 | No description available  
8 | No description available  
A | No description available  
B | No description available  
C | No description available  
CY | No description available  
Cb | No description available  
Cc | No description available  
Ck | No description available  
D | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
P | No description available  
R | No description available  
S | No description available  
T | No description available  
V | No description available  
W | No description available  
Y | No description available  
Z | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
z | No description available  
  

> open
> /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/focus_head/run_class001.mrc

Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at
level 0.00588, step 2, values float32  

> volume #2-10 step 1 level 0.005

> volume #4 step 1 level 0.0075

No volumes specified  

> volume #5 step 1 level 0.003

No volumes specified  

> volume #4 step 1 level 0.0055

No volumes specified  

> surface dust #1-15 size 20

> set bgColor white

> windowsize 800 800

> color #1 #3-10 silver

> color #1 cyan

> color #2-10 silver

> color #1/a-g /j-p /u sienna

> color #1/K /L /P /R /T /q-t /CW wheat

> color #1/F /V /W /Z /CN sky blue

> color #1/B /Ca plum

> color #1/D /G /H /Q /X green

> color #1/I /Y /CV light green

> color #1/J /M /N /S /CY /Cb /Cc pink

> color #1/CD /CK /CL orange

> color #1/CR /CT /CX /CZ lime

> color #1/O /CA /CC /CU purple

> color #1/2 /h /i /CS cornflower blue

> color #1/CP /CQ /CE /CF /CG /CI /CJ forest green

> color #1/5 /A /C /E /CM hot pink

> color #1/6 /CB blue

> color #1/7 red

> color #1/8 magenta

> color #1/M dark red

> color #1/Cc orange

> color #1/U cyan

> color #1/Cb dodger blue

> color #1/CY dark red

> color #1/0 green yellow

> color #1/Ch aquamarine

> color #1/Cf cyan

> color #1/Cd teal

> color #1/z tomato

> color #1/1 forest green

> color #1/Cg chocolate

> color #1/R dark violet

> color #1/F deep sky blue

> color #1/2 lime

> color #1/5 hot pink

> color #1/Y olive

> color #1/E tomato

> color #1/C deep pink

> color #1/V steel blue

> color #1/CV magenta

> color #1/8:0-300 red

> color #1 #3-10 silver

> color #1/Cc orange

> color #1/z tomato

> color #1/1 forest green

> color zone #2-10 near #1 distance 6

> hide #!1 models

> close #2

> open
> /Users/lijuanyin/project/prp43/deposit/for_reviewer_2/state_BstarQ2_focusing_on_DHX15/run_class001_dc3.mrc

Opened run_class001_dc3.mrc as #2, grid size 160,160,160, pixel 2.8, shown at
level 0.045, step 1, values float32  

> volume #2 level 0.005

> volume #2 level 0.05

> volume #2 level 0.04295

> volume #2 level 0.04

> open
> /Users/lijuanyin/project/prp43/deposit/for_reviewer_2/state_BstarQ2_focusing_on_DHX15/run_class001_focusing_refine.mrc

Opened run_class001_focusing_refine.mrc as #3, grid size 480,480,480, pixel
0.932, shown at level 0.00588, step 2, values float32  

> volume #3 step 1

> volume #3 step 2

> close #3

> close #2

> open
> /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/focus_head/run_class001.mrc

Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at
level 0.00588, step 2, values float32  

> color zone #2-10 near #1 distance 6

> view matrix camera
> 0.52209,0.083337,-0.84881,-259.14,0.81484,0.24518,0.52528,513.87,0.25189,-0.96589,0.060097,250.86

> volume #2 level 0.005

> surface dust #1-15 size 20

> save
> /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_1.jpg

> close

> open /Users/lijuanyin/project/prp43/deposit/q2/c6_job26_Q2-coot-44.pdb

Summary of feedback from opening
/Users/lijuanyin/project/prp43/deposit/q2/c6_job26_Q2-coot-44.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
95 messages similar to the above omitted  
  
Chain information for c6_job26_Q2-coot-44.pdb #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
5 | No description available  
6 | No description available  
8 | No description available  
A | No description available  
B | No description available  
C | No description available  
CY | No description available  
Cb | No description available  
Cc | No description available  
D | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
P | No description available  
R | No description available  
S | No description available  
T | No description available  
V | No description available  
W | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
z | No description available  
  

> open /Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-35.pdb

Chain information for c34_job27_ILS-coot-35.pdb #2  
---  
Chain | Description  
0 | No description available  
2 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
A | No description available  
B | No description available  
C | No description available  
CY | No description available  
Cb | No description available  
Cc | No description available  
D | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
P | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
W | No description available  
Y | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
  

> open /Users/lijuanyin/project/prp43/deposit/published/5y88-ILS.cif-
> coot-0.pdb

Chain information for 5y88-ILS.cif-coot-0.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
a | No description available  
b i | No description available  
c j | No description available  
d k | No description available  
e l | No description available  
f m | No description available  
g | No description available  
h | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
x | No description available  
  

> volume #2-10 step 1 level 0.0045

No volumes specified  

> surface dust #1-15 size 20

No surfaces specified  

> set bgColor white

> windowsize 800 800

> color #1 #3-10 silver

> color #1 cyan

> color #2-10 silver

> color #1/a-g /j-p /u sienna

> color #1/K /L /P /R /T /q-t /CW wheat

> color #1/F /V /W /Z /CN sky blue

> color #1/B /Ca plum

> color #1/D /G /H /Q /X green

> color #1/I /Y /CV light green

> color #1/J /M /N /S /CY /Cb /Cc pink

> color #1/CD /CK /CL orange

> color #1/CR /CT /CX /CZ lime

> color #1/O /CA /CC /CU purple

> color #1/2 /h /i /CS cornflower blue

> color #1/CP /CQ /CE /CF /CG /CI /CJ forest green

> color #1/5 /A /C /E /CM hot pink

> color #1/6 /CB blue

> color #1/7 red

> color #1/8 magenta

> color #1/M dark red

> color #1/Cc orange

> color #1/U lime

> color #1/Cb dodger blue

> color #1/CY dark red

> color #1/0 dark khaki

> color #1/Ch aquamarine

> color #1/Cf cyan

> color #1/Cd teal

> color #1/z tomato

> color #1/1 forest green

> color #1/Cg chocolate

> color #1-10 silver

> color #1-2/z tomato

> color #1-2/1 forest green

> color #1-2/5 /A:1898-3000 hot pink

> color #1-2/2 lime

> color #1-2/6 blue

> color #1-2/8 red

> color #2/U cyan

> color #2/X green

> color #2/x cyan

> color #1-2/Cb dodger blue

> color #1-2/CY dark red

> hide #1-2 target a

> show #1-2 target r

> hide #1/CM target r

> show #1-2/2-8 target a

> nucleotides #1-2/2-8 ladder

> ribbon style protein modeh tube rad 2 sides 24

> ribbon style nucleic xsect rect width 3.2 thick 1.6

> cartoon style protein xsection oval width 3.2 thickness 1

> cartoon style strand xsection rectangle width 3.2 thickness 1.6

> view matrix camera
> 0.10947,0.0052583,0.99397,808.15,-0.64091,0.76472,0.066542,251.91,-0.75977,-0.64433,0.087084,260.79

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

> hide #1-3 target a

> show #1-3 target r

> hide #!1 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> color #1/7 red

> color #1/8 magenta

> color #1/M dark red

> color #1/Cc orange

> color #1/U lime

> color #1/Cb dodger blue

> color #1/CY dark red

> color #1/0 dark khaki

> color #1/Ch aquamarine

> color #1/Cf cyan

> color #1/Cd teal

> color #1/z tomato

> color #1/1 forest green

> color #1/Cg chocolate

> color #1-10 silver

> color #1-2/z tomato

> color #1-2/1 forest green

> color #1-2/5 /A:1898-3000 #3/B /A:1840-2100 hot pink

> color #1-2/2 #3/F lime

> color #1-2/6 #3/D blue

> color #1-2/8 red

> color #2/U cyan

> color #2/X green

> color #2/x cyan

> color #1-2/Cb #3/U dodger blue

> color #1-2/CY 33/V dark red

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

> hide #1-3 target a

> show #1-3 target r

> hide #1/CM target r

> show #1-2/2-8 #3/B /D /F target a

> nucleotides #1-2/2-8 #3/B /D /F ladder

> color #1-2/CY #3/V dark red

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!1 models

> view matrix camera
> 0.10947,0.0052583,0.99397,808.15,-0.64091,0.76472,0.066542,251.91,-0.75977,-0.64433,0.087084,260.79

> hide #1.1 models

> hide #2.1 models

> hide #3.1 models

> hide #!3 models

> show #!3 models

> hide #!1 models

> save /Users/lijuanyin/project/prp43/figure_new/figure_s4/5y88_view1.jpg

> close

> open /Users/lijuanyin/project/prp43/deposit/q2/c6_job26_Q2-coot-43.pdb

Summary of feedback from opening
/Users/lijuanyin/project/prp43/deposit/q2/c6_job26_Q2-coot-43.pdb  
---  
warnings | Duplicate atom serial number found: 74678  
Duplicate atom serial number found: 74679  
Duplicate atom serial number found: 74680  
Duplicate atom serial number found: 74681  
Duplicate atom serial number found: 74682  
2401 messages similar to the above omitted  
  
Chain information for c6_job26_Q2-coot-43.pdb #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
5 | No description available  
6 | No description available  
8 | No description available  
A | No description available  
B | No description available  
C | No description available  
CY | No description available  
Cb | No description available  
Cc | No description available  
D | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
P | No description available  
R | No description available  
S | No description available  
T | No description available  
V | No description available  
W | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
z | No description available  
  

> open /Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-34.pdb

Summary of feedback from opening
/Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-34.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
15 messages similar to the above omitted  
  
Chain information for c34_job27_ILS-coot-34.pdb #2  
---  
Chain | Description  
0 | No description available  
2 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
A | No description available  
B | No description available  
C | No description available  
CY | No description available  
Cb | No description available  
Cc | No description available  
D | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
P | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
W | No description available  
Y | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
  

> open /Users/lijuanyin/project/prp43/deposit/published/5y88-ILS.cif-
> coot-0.pdb

Chain information for 5y88-ILS.cif-coot-0.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
a | No description available  
b i | No description available  
c j | No description available  
d k | No description available  
e l | No description available  
f m | No description available  
g | No description available  
h | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
x | No description available  
  

> volume #2-10 step 1 level 0.0045

No volumes specified  

> surface dust #1-15 size 20

No surfaces specified  

> set bgColor white

> windowsize 800 800

> color #1 #3-10 silver

> color #1 cyan

> color #2-10 silver

> color #1/a-g /j-p /u sienna

> color #1/K /L /P /R /T /q-t /CW wheat

> color #1/F /V /W /Z /CN sky blue

> color #1/B /Ca plum

> color #1/D /G /H /Q /X green

> color #1/I /Y /CV light green

> color #1/J /M /N /S /CY /Cb /Cc pink

> color #1/CD /CK /CL orange

> color #1/CR /CT /CX /CZ lime

> color #1/O /CA /CC /CU purple

> color #1/2 /h /i /CS cornflower blue

> color #1/CP /CQ /CE /CF /CG /CI /CJ forest green

> color #1/5 /A /C /E /CM hot pink

> color #1/6 /CB blue

> color #1/7 red

> color #1/8 magenta

> color #1/M dark red

> color #1/Cc orange

> color #1/U lime

> color #1/Cb dodger blue

> color #1/CY dark red

> color #1/0 dark khaki

> color #1/Ch aquamarine

> color #1/Cf cyan

> color #1/Cd teal

> color #1/z tomato

> color #1/1 forest green

> color #1/Cg chocolate

> color #1-10 silver

> color #1-2/R #3/Q dark violet

> color #1-2/Cb #3/U dodger blue

> color #1-2/CY #3/V dark red

> color #1-2/V deep sky blue

> color #1-2/Z light blue

> hide #1-2 target a

> show #1-2 target r

> hide #1/CM target r

> show #1-2/2-8 target a

> nucleotides #1-2/2-8 ladder

> ribbon style protein modeh tube rad 2 sides 24

> ribbon style nucleic xsect rect width 3.2 thick 1.6

> cartoon style protein xsection oval width 3.2 thickness 1

> cartoon style strand xsection rectangle width 3.2 thickness 1.6

> transparency #1-3 80 target r

> transparency #1-3 80 target a

> transparency #1-2/R /Cb /CY /V /Z #3/U /V /Q 0 target r

> view matrix camera
> 0.94275,-0.15187,-0.29692,58.621,0.3287,0.57375,0.75018,620.95,0.056428,-0.80483,0.59082,548.24

> close

> open /Users/lijuanyin/project/prp43/deposit/q2/c6_job26_Q2-coot-43.pdb

Summary of feedback from opening
/Users/lijuanyin/project/prp43/deposit/q2/c6_job26_Q2-coot-43.pdb  
---  
warnings | Duplicate atom serial number found: 74678  
Duplicate atom serial number found: 74679  
Duplicate atom serial number found: 74680  
Duplicate atom serial number found: 74681  
Duplicate atom serial number found: 74682  
2401 messages similar to the above omitted  
  
Chain information for c6_job26_Q2-coot-43.pdb #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
5 | No description available  
6 | No description available  
8 | No description available  
A | No description available  
B | No description available  
C | No description available  
CY | No description available  
Cb | No description available  
Cc | No description available  
D | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
P | No description available  
R | No description available  
S | No description available  
T | No description available  
V | No description available  
W | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
z | No description available  
  

> open /Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-34.pdb

Summary of feedback from opening
/Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-34.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
15 messages similar to the above omitted  
  
Chain information for c34_job27_ILS-coot-34.pdb #2  
---  
Chain | Description  
0 | No description available  
2 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
A | No description available  
B | No description available  
C | No description available  
CY | No description available  
Cb | No description available  
Cc | No description available  
D | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
P | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
W | No description available  
Y | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
  

> open /Users/lijuanyin/project/prp43/deposit/published/5y88-ILS.cif-
> coot-0.pdb

Chain information for 5y88-ILS.cif-coot-0.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
a | No description available  
b i | No description available  
c j | No description available  
d k | No description available  
e l | No description available  
f m | No description available  
g | No description available  
h | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
x | No description available  
  

> volume #2-10 step 1 level 0.0045

No volumes specified  

> surface dust #1-15 size 20

No surfaces specified  

> set bgColor white

> windowsize 800 800

> color #1 #3-10 silver

> color #1 cyan

> color #2-10 silver

> color #1/a-g /j-p /u sienna

> color #1/K /L /P /R /T /q-t /CW wheat

> color #1/F /V /W /Z /CN sky blue

> color #1/B /Ca plum

> color #1/D /G /H /Q /X green

> color #1/I /Y /CV light green

> color #1/J /M /N /S /CY /Cb /Cc pink

> color #1/CD /CK /CL orange

> color #1/CR /CT /CX /CZ lime

> color #1/O /CA /CC /CU purple

> color #1/2 /h /i /CS cornflower blue

> color #1/CP /CQ /CE /CF /CG /CI /CJ forest green

> color #1/5 /A /C /E /CM hot pink

> color #1/6 /CB blue

> color #1/7 red

> color #1/8 magenta

> color #1/M dark red

> color #1/Cc orange

> color #1/U lime

> color #1/Cb dodger blue

> color #1/CY dark red

> color #1/0 dark khaki

> color #1/Ch aquamarine

> color #1/Cf cyan

> color #1/Cd teal

> color #1/z tomato

> color #1/1 forest green

> color #1/Cg chocolate

> color #1-10 silver

> color #1-2/R #3/Q dark violet

> color #1-2/Cb #3/U dodger blue

> color #1-2/CY #3/V dark red

> color #1-2/V deep sky blue

> color #1-2/Z light blue

> hide #1-3 target a

> show #1-3 target r

> hide #1/CM target r

> show #1-2/2-8 #3/B /F /D target a

> nucleotides #1-2/2-8 #3/B /F /D ladder

> ribbon style protein modeh tube rad 2 sides 24

> ribbon style nucleic xsect rect width 3.2 thick 1.6

> cartoon style protein xsection oval width 3.2 thickness 1

> cartoon style strand xsection rectangle width 3.2 thickness 1.6

> transparency #1-3 80 target r

> transparency #1-3 80 target a

> transparency #1-2/R /Cb /CY /V /Z #3/U /V /Q 0 target r

> view matrix camera
> 0.94275,-0.15187,-0.29692,58.621,0.3287,0.57375,0.75018,620.95,0.056428,-0.80483,0.59082,548.24

> hide #!2 models

> hide #!1 models

> show #!2 models

> hide #!3 models

> show #!1 models

> hide #!2 models

> transparency #1-3 80 target a

> hide #!1 atoms

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #1.1 models

> hide #2.1 models

> hide #3.1 models

> show #!3 models

> hide atoms

> hide #!2 models

> hide #!1 models

> save /Users/lijuanyin/project/prp43/figure_new/figure_s4/5y88_ntr_view2.jpg

> hide #!3 models

> show #!1 models

> save /Users/lijuanyin/project/prp43/figure_new/figure_s4/q2_ntr_view2.jpg

> show #!2 models

> hide #!1 models

> save /Users/lijuanyin/project/prp43/figure_new/figure_s4/ils_ntr_view2.jpg

> close

> open /Users/lijuanyin/project/prp43/deposit/q2/c6_job26_Q2-coot-44.pdb

Summary of feedback from opening
/Users/lijuanyin/project/prp43/deposit/q2/c6_job26_Q2-coot-44.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
95 messages similar to the above omitted  
  
Chain information for c6_job26_Q2-coot-44.pdb #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
5 | No description available  
6 | No description available  
8 | No description available  
A | No description available  
B | No description available  
C | No description available  
CY | No description available  
Cb | No description available  
Cc | No description available  
D | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
P | No description available  
R | No description available  
S | No description available  
T | No description available  
V | No description available  
W | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
z | No description available  
  

> open /Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-35.pdb

Chain information for c34_job27_ILS-coot-35.pdb #2  
---  
Chain | Description  
0 | No description available  
2 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
A | No description available  
B | No description available  
C | No description available  
CY | No description available  
Cb | No description available  
Cc | No description available  
D | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
P | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
W | No description available  
Y | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
  

> open /Users/lijuanyin/project/prp43/deposit/published/5y88-ILS.cif-
> coot-0.pdb

Chain information for 5y88-ILS.cif-coot-0.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
a | No description available  
b i | No description available  
c j | No description available  
d k | No description available  
e l | No description available  
f m | No description available  
g | No description available  
h | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
x | No description available  
  

> volume #2-10 step 1 level 0.0045

No volumes specified  

> surface dust #1-15 size 20

No surfaces specified  

> set bgColor white

> windowsize 800 800

> color #1 #3-10 silver

> color #1 cyan

> color #2-10 silver

> color #1/a-g /j-p /u sienna

> color #1/K /L /P /R /T /q-t /CW wheat

> color #1/F /V /W /Z /CN sky blue

> color #1/B /Ca plum

> color #1/D /G /H /Q /X green

> color #1/I /Y /CV light green

> color #1/J /M /N /S /CY /Cb /Cc pink

> color #1/CD /CK /CL orange

> color #1/CR /CT /CX /CZ lime

> color #1/O /CA /CC /CU purple

> color #1/2 /h /i /CS cornflower blue

> color #1/CP /CQ /CE /CF /CG /CI /CJ forest green

> color #1/5 /A /C /E /CM hot pink

> color #1/6 /CB blue

> color #1/7 red

> color #1/8 magenta

> color #1/M dark red

> color #1/Cc orange

> color #1/U lime

> color #1/Cb dodger blue

> color #1/CY dark red

> color #1/0 dark khaki

> color #1/Ch aquamarine

> color #1/Cf cyan

> color #1/Cd teal

> color #1/z tomato

> color #1/1 forest green

> color #1/Cg chocolate

> color #1-10 silver

> color #1-2/z tomato

> color #1-2/1 forest green

> color #1-2/5 /A:1898-3000 #3/B /A:1840-2100 hot pink

> color #1-2/2 #3/F lime

> color #1-2/6 #3/D blue

> color #1-2/8 red

> color #2/U cyan

> color #2/X green

> color #2/x cyan

> color #1-2/Cb #3/U dodger blue

> color #1-2/CY #3/V dark red

> hide #1-3 target a

> show #1-3 target r

> hide #1/CM target r

> show #1-2/2-8 #3/B /D /F target a

> nucleotides #1-2/2-8 #3/B /D /F ladder

> ribbon style protein modeh tube rad 2 sides 24

> ribbon style nucleic xsect rect width 3.2 thick 1.6

> cartoon style protein xsection oval width 3.2 thickness 1

> cartoon style strand xsection rectangle width 3.2 thickness 1.6

> view matrix camera
> 0.10947,0.0052583,0.99397,808.15,-0.64091,0.76472,0.066542,251.91,-0.75977,-0.64433,0.087084,260.79

> hide #!3 models

> hide #!2 models

> hide #1.1 models

> hide #2.1 models

> hide #3.1 models

> save /Users/lijuanyin/project/prp43/figure_new/figure_s4/q2_view1.jpg

> show #!2 models

> hide #!1 models

> hide #2.2 models

> save /Users/lijuanyin/project/prp43/figure_new/figure_s4/ils_view1.jpg

> show #!3 models

> hide #!2 models

> show #!1 models

> hide #!3 models

> close

> open
> /Users/lijuanyin/project/prp43/deposit/q1_tfip11/c34_job28_Q1-coot-48.pdb

Summary of feedback from opening
/Users/lijuanyin/project/prp43/deposit/q1_tfip11/c34_job28_Q1-coot-48.pdb  
---  
warnings | Duplicate atom serial number found: 4205  
Duplicate atom serial number found: 4206  
Duplicate atom serial number found: 4207  
Duplicate atom serial number found: 4208  
Duplicate atom serial number found: 4209  
993 messages similar to the above omitted  
  
Chain information for c34_job28_Q1-coot-48.pdb #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
5 | No description available  
6 | No description available  
8 | No description available  
A | No description available  
B | No description available  
C | No description available  
CV | No description available  
CY | No description available  
Cb | No description available  
Ck | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
P | No description available  
R | No description available  
S | No description available  
T | No description available  
V | No description available  
W | No description available  
Y | No description available  
Z | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
z | No description available  
  

> open /Users/lijuanyin/project/prp43/deposit/q1_tfip11/run_class001.mrc

Opened run_class001.mrc as #2, grid size 160,160,160, pixel 2.8, shown at
level 0.041, step 1, values float32  

> volume #2-10 step 1 level 0.005

> surface dust #1-15 size 20

> set bgColor white

> windowsize 800 800

> color #1 #3-10 silver

> color #1 cyan

> color #2-10 silver

> color #1/a-g /j-p /u sienna

> color #1/K /L /P /T /q-t /CW wheat

> color #1/F /V /W /Z /CN sky blue

> color #1/B /Ca plum

> color #1/D /G /H /Q /X green

> color #1/I /Y /CV light green

> color #1/J /M /N /S /CY /Cb /Cc /R pink

> color #1/CD /CK /CL orange

> color #1/CR /CT /CX /CZ lime

> color #1/O /CA /CC /CU purple

> color #1/2 /h /i /CS cornflower blue

> color #1/CP /CQ /CE /CF /CG /CI /CJ forest green

> color #1/5 /A /C /E /CM hot pink

> color #1/6 /CB blue

> color #1/7 red

> color #1/8 magenta

> color #1/M dark red

> color #1/Cc orange

> color #1/U lime

> color #1/Cb dodger blue

> color #1/CY dark red

> color #1/0 dark khaki

> color #1/Ch aquamarine

> color #1/Cf cyan

> color #1/Cd teal

> color #1/z tomato

> color #1/1 forest green

> color #1/Cg chocolate

> color #1/R dark violet

> volume #2 level 0.01125

> volume #2 level 0.02731

> volume zone #3 nearAtoms #1/Cb /Ck /CY range 6 newMap true

> volume zone #2 nearAtoms #1/Cb /Ck /CY range 6 newMap true

Opened run_class001.mrc zone as #3, grid size 160,160,160, pixel 2.8, shown at
step 1, values float32  

> close #3

> volume zone #2 nearAtoms #1/Cb /Ck range 6 newMap true

Opened run_class001.mrc zone as #3, grid size 160,160,160, pixel 2.8, shown at
step 1, values float32  

> volume #3 level 0.02527

> hide #!1 models

> show #!1 models

> surface dust #1-15 size 10

> color #3 silver

> hide #1 target a

> show #1/Cb target r

> transparency #3 50

> show #1/Cb /Ck target r

> color #1/CY /Ck dark red

> hide cartoons

> show #1/Cb target r

> volume #3 level 0.03158

> volume #3 level 0.03103

> volume #3 level 0.03

> view matrix

view matrix camera
0.51743,-0.042028,-0.8547,-2.7971,0.46455,-0.82501,0.3218,384.43,-0.71866,-0.56356,-0.40736,169.94  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0  
  

> graphics silhouettes false

> graphics silhouettes true

> save /Users/lijuanyin/project/prp43/figure/figure_s3/TFIP11_local_view1.jpg

> save
> /Users/lijuanyin/project/prp43/figure_new/figure_s3/TFIP11_local_view1.jpg

> close

> open /Users/lijuanyin/project/prp43/deposit/q1/c34_job28_Q1-coot-38.pdb

No such file/path:
/Users/lijuanyin/project/prp43/deposit/q1/c34_job28_Q1-coot-38.pdb  

> open /Users/lijuanyin/project/prp43/deposit/q1/run_class001.mrc

Opened run_class001.mrc as #1, grid size 480,480,480, pixel 0.932, shown at
level 0.00702, step 2, values float32  

> open
> /Users/lijuanyin/project/prp43/deposit/q1/multi/multi_ctf_c34_job28_dhx_high.mrc

Opened multi_ctf_c34_job28_dhx_high.mrc as #2, grid size 480,480,480, pixel
0.932, shown at level 0.00169, step 2, values float32  

> open
> /Users/lijuanyin/project/prp43/deposit/q1/multi/local_multi_ctf_c34_job28_dhx_2/relion_locres_filtered.mrc

Opened relion_locres_filtered.mrc as #3, grid size 480,480,480, pixel 0.932,
shown at level 0.00258, step 2, values float32  

> volume #2-10 step 1 level 0.005

> surface dust #1-15 size 20

> set bgColor white

> windowsize 800 800

> color #1 #3-10 silver

> color #1 cyan

> color #2-10 silver

> color #1/a-g /j-p /u sienna

> color #1/K /L /P /T /q-t /CW wheat

> color #1/F /V /W /Z /CN sky blue

> color #1/B /Ca plum

> color #1/D /G /H /Q /X green

> color #1/I /Y /CV light green

> color #1/J /M /N /S /CY /Cb /Cc /R pink

> color #1/CD /CK /CL orange

> color #1/CR /CT /CX /CZ lime

> color #1/O /CA /CC /CU purple

> color #1/2 /h /i /CS cornflower blue

> color #1/CP /CQ /CE /CF /CG /CI /CJ forest green

> color #1/5 /A /C /E /CM hot pink

> color #1/6 /CB blue

> color #1/7 red

> color #1/8 magenta

> color #1/M dark red

> color #1/Cc orange

> color #1/U lime

> color #1/Cb dodger blue

> color #1/CY dark red

> color #1/0 dark khaki

> color #1/Ch aquamarine

> color #1/Cf cyan

> color #1/Cd teal

> color #1/z tomato

> color #1/1 forest green

> color #1/Cg chocolate

> color #1/R dark violet

> volume zone #3 nearAtoms #1/CY:344-367 range 2 newMap true

no atoms specified for zone  

> hide #1 target r

> show #1/CY:344-367 target r

> show #1/CY:344-367 target a

> surface dust #1-15 size 10

> color #5 silver

> transparency #5 50

> color #1 byhetero

> close

> open /Users/lijuanyin/project/prp43/deposit/q1/c34_job28_Q1-coot-39.pdb

Summary of feedback from opening
/Users/lijuanyin/project/prp43/deposit/q1/c34_job28_Q1-coot-39.pdb  
---  
warnings | Duplicate atom serial number found: 4205  
Duplicate atom serial number found: 4206  
Duplicate atom serial number found: 4207  
Duplicate atom serial number found: 4208  
Duplicate atom serial number found: 4209  
556 messages similar to the above omitted  
  
Chain information for c34_job28_Q1-coot-39.pdb #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
5 | No description available  
6 | No description available  
8 | No description available  
A | No description available  
B | No description available  
C | No description available  
CY | No description available  
Cb | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
P | No description available  
R | No description available  
S | No description available  
T | No description available  
V | No description available  
W | No description available  
Y | No description available  
Z | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
z | No description available  
  

> open /Users/lijuanyin/project/prp43/deposit/q1/run_class001.mrc

Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at
level 0.00702, step 2, values float32  

> open
> /Users/lijuanyin/project/prp43/deposit/q1/multi/multi_ctf_c34_job28_dhx_high.mrc

Opened multi_ctf_c34_job28_dhx_high.mrc as #3, grid size 480,480,480, pixel
0.932, shown at level 0.00169, step 2, values float32  

> open
> /Users/lijuanyin/project/prp43/deposit/q1/multi/local_multi_ctf_c34_job28_dhx_2/relion_locres_filtered.mrc

Opened relion_locres_filtered.mrc as #4, grid size 480,480,480, pixel 0.932,
shown at level 0.00258, step 2, values float32  

> volume #2-10 step 1 level 0.005

> surface dust #1-15 size 20

> set bgColor white

> windowsize 800 800

> color #1 #3-10 silver

> color #1 cyan

> color #2-10 silver

> color #1/a-g /j-p /u sienna

> color #1/K /L /P /T /q-t /CW wheat

> color #1/F /V /W /Z /CN sky blue

> color #1/B /Ca plum

> color #1/D /G /H /Q /X green

> color #1/I /Y /CV light green

> color #1/J /M /N /S /CY /Cb /Cc /R pink

> color #1/CD /CK /CL orange

> color #1/CR /CT /CX /CZ lime

> color #1/O /CA /CC /CU purple

> color #1/2 /h /i /CS cornflower blue

> color #1/CP /CQ /CE /CF /CG /CI /CJ forest green

> color #1/5 /A /C /E /CM hot pink

> color #1/6 /CB blue

> color #1/7 red

> color #1/8 magenta

> color #1/M dark red

> color #1/Cc orange

> color #1/U lime

> color #1/Cb dodger blue

> color #1/CY dark red

> color #1/0 dark khaki

> color #1/Ch aquamarine

> color #1/Cf cyan

> color #1/Cd teal

> color #1/z tomato

> color #1/1 forest green

> color #1/Cg chocolate

> color #1/R dark violet

> volume zone #3 nearAtoms #1/CY:344-367 range 2 newMap true

Opened multi_ctf_c34_job28_dhx_high.mrc zone as #5, grid size 480,480,480,
pixel 0.932, shown at step 1, values float32  

> hide #1 target r

> show #1/CY:344-367 target r

> show #1/CY:344-367 target a

> surface dust #1-15 size 10

> color #5 silver

> transparency #5 50

> color #1 byhetero

> hide #1 target a

> show #1/CY:344-367 target r

> show #1/CY:344-367 target a

> style stick

Changed 86901 atom styles  

> close #5

> volume zone #4 nearAtoms #1/CY:344-367 range 2 newMap true

Opened relion_locres_filtered.mrc zone as #5, grid size 480,480,480, pixel
0.932, shown at step 1, values float32  

> hide #1 target a

> show #1/CY:344-367 target r

> show #1/CY:344-367 target a

> surface dust #1-15 size 10

> color #5 silver

> transparency #5 50

> color #1 byhetero

> surface dust #1-15 size 10

> view matrix

view matrix camera
0.11237,0.97632,-0.18486,185.03,0.47491,-0.21618,-0.85307,243.39,-0.87283,0.008072,-0.48795,215.23  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0  
  

> view matrix camera
> 0.11237,0.97632,-0.18486,185.03,0.47491,-0.21618,-0.85307,243.39,-0.87283,0.008072,-0.48795,215.23

> save
> /Users/lijuanyin/project/prp43/figure_new/figure_s3/gcfc2_detail_view1.jpg

> show cartoons

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_0.cif

Chain information for fold_human_ntr1_gcfc2_snw1_model_0.cif #6  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> close

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_0.cif

Chain information for fold_human_ntr1_gcfc2_snw1_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> close

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_0.cif

Chain information for fold_human_ntr1_gcfc2_snw1_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_1.cif

Chain information for fold_human_ntr1_gcfc2_snw1_model_1.cif #2  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_2.cif

Chain information for fold_human_ntr1_gcfc2_snw1_model_2.cif #3  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_3.cif

Chain information for fold_human_ntr1_gcfc2_snw1_model_3.cif #4  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_4.cif

Chain information for fold_human_ntr1_gcfc2_snw1_model_4.cif #5  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> mmaker #2-6 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_human_ntr1_gcfc2_snw1_model_0.cif, chain A (#1) with
fold_human_ntr1_gcfc2_snw1_model_1.cif, chain A (#2), sequence alignment score
= 4374.2  
RMSD between 352 pruned atom pairs is 1.195 angstroms; (across all 837 pairs:
28.901)  
  
Matchmaker fold_human_ntr1_gcfc2_snw1_model_0.cif, chain A (#1) with
fold_human_ntr1_gcfc2_snw1_model_2.cif, chain A (#3), sequence alignment score
= 4365.2  
RMSD between 256 pruned atom pairs is 0.946 angstroms; (across all 837 pairs:
37.057)  
  
Matchmaker fold_human_ntr1_gcfc2_snw1_model_0.cif, chain A (#1) with
fold_human_ntr1_gcfc2_snw1_model_3.cif, chain A (#4), sequence alignment score
= 4380.8  
RMSD between 378 pruned atom pairs is 0.778 angstroms; (across all 837 pairs:
25.335)  
  
Matchmaker fold_human_ntr1_gcfc2_snw1_model_0.cif, chain A (#1) with
fold_human_ntr1_gcfc2_snw1_model_4.cif, chain A (#5), sequence alignment score
= 4350.2  
RMSD between 419 pruned atom pairs is 0.966 angstroms; (across all 837 pairs:
22.010)  
  

> hide #1 models

> hide #2 models

> hide #4 models

> hide #5 models

> close

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_yeast_ntr1_ntr2_prp45/fold_yeast_ntr1_ntr2_prp45_model_0.cif

Chain information for fold_yeast_ntr1_ntr2_prp45_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_yeast_ntr1_ntr2_prp45/fold_yeast_ntr1_ntr2_prp45_model_1.cif

Chain information for fold_yeast_ntr1_ntr2_prp45_model_1.cif #2  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_yeast_ntr1_ntr2_prp45/fold_yeast_ntr1_ntr2_prp45_model_2.cif

Chain information for fold_yeast_ntr1_ntr2_prp45_model_2.cif #3  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_yeast_ntr1_ntr2_prp45/fold_yeast_ntr1_ntr2_prp45_model_3.cif

Chain information for fold_yeast_ntr1_ntr2_prp45_model_3.cif #4  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_yeast_ntr1_ntr2_prp45/fold_yeast_ntr1_ntr2_prp45_model_4.cif

Chain information for fold_yeast_ntr1_ntr2_prp45_model_4.cif #5  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> mmaker #2-6 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_yeast_ntr1_ntr2_prp45_model_0.cif, chain A (#1) with
fold_yeast_ntr1_ntr2_prp45_model_1.cif, chain A (#2), sequence alignment score
= 3569.7  
RMSD between 325 pruned atom pairs is 0.726 angstroms; (across all 708 pairs:
17.705)  
  
Matchmaker fold_yeast_ntr1_ntr2_prp45_model_0.cif, chain A (#1) with
fold_yeast_ntr1_ntr2_prp45_model_2.cif, chain A (#3), sequence alignment score
= 3633.9  
RMSD between 393 pruned atom pairs is 0.821 angstroms; (across all 708 pairs:
23.511)  
  
Matchmaker fold_yeast_ntr1_ntr2_prp45_model_0.cif, chain A (#1) with
fold_yeast_ntr1_ntr2_prp45_model_3.cif, chain A (#4), sequence alignment score
= 3543.3  
RMSD between 320 pruned atom pairs is 0.989 angstroms; (across all 708 pairs:
28.396)  
  
Matchmaker fold_yeast_ntr1_ntr2_prp45_model_0.cif, chain A (#1) with
fold_yeast_ntr1_ntr2_prp45_model_4.cif, chain A (#5), sequence alignment score
= 3553.5  
RMSD between 346 pruned atom pairs is 0.881 angstroms; (across all 708 pairs:
39.832)  
  

> hide #1 models

> hide #2 models

> show #2 models

> hide #2 models

> hide #4 models

> hide #5 models

> show #2 models

> hide #3 models

> close

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_tfip11_gcfc2_snw1_3/fold_tfip11_gcfc2_snw1_3_model_0.cif

Chain information for fold_tfip11_gcfc2_snw1_3_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_tfip11_gcfc2_snw1_3/fold_tfip11_gcfc2_snw1_3_model_1.cif

Chain information for fold_tfip11_gcfc2_snw1_3_model_1.cif #2  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_tfip11_gcfc2_snw1_3/fold_tfip11_gcfc2_snw1_3_model_2.cif

Chain information for fold_tfip11_gcfc2_snw1_3_model_2.cif #3  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_tfip11_gcfc2_snw1_3/fold_tfip11_gcfc2_snw1_3_model_3.cif

Chain information for fold_tfip11_gcfc2_snw1_3_model_3.cif #4  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_tfip11_gcfc2_snw1_3/fold_tfip11_gcfc2_snw1_3_model_4.cif

Chain information for fold_tfip11_gcfc2_snw1_3_model_4.cif #5  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> mmaker #2-6 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with
fold_tfip11_gcfc2_snw1_3_model_1.cif, chain A (#2), sequence alignment score =
4939.4  
RMSD between 455 pruned atom pairs is 0.909 angstroms; (across all 975 pairs:
45.021)  
  
Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with
fold_tfip11_gcfc2_snw1_3_model_2.cif, chain A (#3), sequence alignment score =
4890.2  
RMSD between 402 pruned atom pairs is 0.781 angstroms; (across all 975 pairs:
41.499)  
  
Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with
fold_tfip11_gcfc2_snw1_3_model_3.cif, chain A (#4), sequence alignment score =
4577.6  
RMSD between 232 pruned atom pairs is 0.736 angstroms; (across all 975 pairs:
37.629)  
  
Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with
fold_tfip11_gcfc2_snw1_3_model_4.cif, chain A (#5), sequence alignment score =
4380.8  
RMSD between 364 pruned atom pairs is 0.992 angstroms; (across all 975 pairs:
37.404)  
  

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> close

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_2/fold_tfip11_gcfc2_snw1_3_model_0.cif

Chain information for fold_tfip11_gcfc2_snw1_3_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_2/fold_yeast_ntr1_ntr2_prp45_model_1.cif

Chain information for fold_yeast_ntr1_ntr2_prp45_model_1.cif #2  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_2/fold_human_ntr1_gcfc2_snw1_model_2.cif

Chain information for fold_human_ntr1_gcfc2_snw1_model_2.cif #3  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> surface dust #1-15 size 20

No surfaces specified  

> set bgColor white

> windowsize 800 800

> color #1-3/B dark red

> color #1-3/A dodger blue

> color #1-3/C dark violet

> mmaker #2-3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with
fold_yeast_ntr1_ntr2_prp45_model_1.cif, chain A (#2), sequence alignment score
= 570.3  
RMSD between 80 pruned atom pairs is 1.337 angstroms; (across all 639 pairs:
40.062)  
  
Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with
fold_human_ntr1_gcfc2_snw1_model_2.cif, chain A (#3), sequence alignment score
= 1102.1  
RMSD between 104 pruned atom pairs is 1.313 angstroms; (across all 779 pairs:
50.129)  
  

> mmaker #2-3/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with
fold_yeast_ntr1_ntr2_prp45_model_1.cif, chain A (#2), sequence alignment score
= 570.3  
RMSD between 80 pruned atom pairs is 1.337 angstroms; (across all 639 pairs:
40.062)  
  
Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with
fold_human_ntr1_gcfc2_snw1_model_2.cif, chain A (#3), sequence alignment score
= 1102.1  
RMSD between 104 pruned atom pairs is 1.313 angstroms; (across all 779 pairs:
50.129)  
  

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_0.cif

Chain information for fold_human_ntr1_gcfc2_snw1_model_0.cif #4  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_1.cif

Chain information for fold_human_ntr1_gcfc2_snw1_model_1.cif #5  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_2.cif

Chain information for fold_human_ntr1_gcfc2_snw1_model_2.cif #6  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_3.cif

Chain information for fold_human_ntr1_gcfc2_snw1_model_3.cif #7  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_human_ntr1_gcfc2_snw1/fold_human_ntr1_gcfc2_snw1_model_4.cif

Chain information for fold_human_ntr1_gcfc2_snw1_model_4.cif #8  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> mmaker #2-10/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with
fold_yeast_ntr1_ntr2_prp45_model_1.cif, chain A (#2), sequence alignment score
= 570.3  
RMSD between 80 pruned atom pairs is 1.337 angstroms; (across all 639 pairs:
40.062)  
  
Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with
fold_human_ntr1_gcfc2_snw1_model_2.cif, chain A (#3), sequence alignment score
= 1102.1  
RMSD between 104 pruned atom pairs is 1.313 angstroms; (across all 779 pairs:
50.129)  
  
Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with
fold_human_ntr1_gcfc2_snw1_model_0.cif, chain A (#4), sequence alignment score
= 1106.6  
RMSD between 105 pruned atom pairs is 1.289 angstroms; (across all 789 pairs:
44.972)  
  
Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with
fold_human_ntr1_gcfc2_snw1_model_1.cif, chain A (#5), sequence alignment score
= 1126.2  
RMSD between 87 pruned atom pairs is 1.087 angstroms; (across all 789 pairs:
40.149)  
  
Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with
fold_human_ntr1_gcfc2_snw1_model_2.cif, chain A (#6), sequence alignment score
= 1102.1  
RMSD between 104 pruned atom pairs is 1.313 angstroms; (across all 779 pairs:
50.129)  
  
Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with
fold_human_ntr1_gcfc2_snw1_model_3.cif, chain A (#7), sequence alignment score
= 1109.6  
RMSD between 98 pruned atom pairs is 1.385 angstroms; (across all 791 pairs:
41.636)  
  
Matchmaker fold_tfip11_gcfc2_snw1_3_model_0.cif, chain A (#1) with
fold_human_ntr1_gcfc2_snw1_model_4.cif, chain A (#8), sequence alignment score
= 1149.2  
RMSD between 96 pruned atom pairs is 1.200 angstroms; (across all 784 pairs:
43.119)  
  

> hide #2 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #8 models

> hide #7 models

> hide #4 models

> hide #5 models

> hide #6 models

> close #6-8

> close #4

> close #5

> show #2 models

> hide #3 models

> hide #2 models

> show #2 models

> hide #1 models

> hide #2 models

> show #3 models

> hide #1-3 target r

> show #1/A:418-860 /B /C #2/A:184-573 /B:236-321 /C:199-252 #3/A:319-725
> /B:254-340 /C:282-343 target r

> show #1 models

> show #2 models

> hide #2 models

> hide #3 models

> show #2 models

> hide #1 models

> show #1 models

> show #3 models

> hide #3 models

> hide #2 models

> ribbon style protein modeh tube rad 2 sides 24

> ribbon style nucleic xsect rect width 3.2 thick 1.6

> cartoon style protein xsection oval width 3.2 thickness 1

> cartoon style strand xsection rectangle width 3.2 thickness 1.6

> show #2 models

> hide #1 models

> show #3 models

> hide #2 models

> show #2 models

> hide #3 models

> show #1 models

> hide #2 models

> view matrix

view matrix camera
0.22966,-0.85104,0.47222,50.764,-0.52782,-0.51655,-0.67423,-142.75,0.81772,-0.094403,-0.56783,-85.002  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#2,-0.28808,0.21208,0.93383,-7.595,-0.93243,-0.28427,-0.22309,8.1887,0.21815,-0.93499,0.27964,10.063,#3,0.14178,0.89982,-0.41257,27.396,-0.32177,0.43604,0.84044,6.8166,0.93614,0.013594,0.35136,-30.218  
  

> save
> /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_2/ct.jpg

> show #2 models

> hide #1 models

> save
> /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_2/yeast.jpg

> show #3 models

> hide #2 models

> save
> /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_2/human.jpg

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_2024_12_13_14_46/fold_2024_12_13_14_46_model_0.cif

Chain information for fold_2024_12_13_14_46_model_0.cif #4  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
  

> hide #3 models

> show #4 cartoons

> hide #4 atoms

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_syf1_2_ccdc12/fold_syf1_2_ccdc12_model_0.cif

Chain information for fold_syf1_2_ccdc12_model_0.cif #5  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> hide #4 models

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_syf1_2_ccdc12/fold_syf1_2_ccdc12_model_1.cif

Chain information for fold_syf1_2_ccdc12_model_1.cif #6  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> hide #5 models

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_syf1_2_ccdc12/fold_syf1_2_ccdc12_model_2.cif

Chain information for fold_syf1_2_ccdc12_model_2.cif #7  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> hide #6 models

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_syf1_2_ccdc12/fold_syf1_2_ccdc12_model_3.cif

Chain information for fold_syf1_2_ccdc12_model_3.cif #8  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> hide #7 models

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/alphafold/fold_syf1_2_ccdc12/fold_syf1_2_ccdc12_model_4.cif

Chain information for fold_syf1_2_ccdc12_model_4.cif #9  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> hide #8 models

> close

> open /Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-41.pdb

Summary of feedback from opening
/Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-41.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
95 messages similar to the above omitted  
  
Chain information for c34_job27_ILS-coot-41.pdb #1  
---  
Chain | Description  
0 | No description available  
2 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
A | No description available  
B | No description available  
C | No description available  
CY | No description available  
Cb | No description available  
Cc | No description available  
Ci | No description available  
D | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
P | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
W | No description available  
Y | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
  

> open /Users/lijuanyin/project/prp43/deposit/ils/run_class001.mrc

Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at
level 0.00799, step 2, values float32  

> open
> /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_body_high.mrc

Opened multi_ctf_c34_job27_body_high.mrc as #3, grid size 480,480,480, pixel
0.932, shown at level 0.0045, step 2, values float32  

> open
> /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_bottom_high.mrc

Opened multi_ctf_c34_job27_bottom_high.mrc as #4, grid size 480,480,480, pixel
0.932, shown at level 0.000984, step 2, values float32  

> open
> /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_ntr_high.mrc

Opened multi_ctf_c34_job27_ntr_high.mrc as #5, grid size 480,480,480, pixel
0.932, shown at level 0.000544, step 2, values float32  

> open
> /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_prp43_high.mrc

Opened multi_ctf_c34_job27_prp43_high.mrc as #6, grid size 480,480,480, pixel
0.932, shown at level 0.00086, step 2, values float32  

> volume #3 step 1 level 0.01

> volume #4 step 1 level 0.01

> volume #5 step 1 level 0.01

> volume #6 step 1 level 0.01

> surface dust #1-15 size 20

> set bgColor white

> windowsize 800 800

> color #1 #3-10 silver

> color #1 cyan

> color #2-10 silver

> color #1/a-g /j-p /u sienna

> color #1/K /L /P /R /T /q-t /CW wheat

> color #1/F /V /W /Z /CN sky blue

> color #1/B /Ca plum

> color #1/D /G /H /Q /X green

> color #1/I /Y /CV light green

> color #1/J /M /N /S /CY /Cb /Cc pink

> color #1/CD /CK /CL orange

> color #1/CR /CT /CX /CZ lime

> color #1/O /CA /CC /CU purple

> color #1/2 /h /i /CS cornflower blue

> color #1/CP /CQ /CE /CF /CG /CI /CJ forest green

> color #1/5 /A /C /E /CM deep pink

> color #1/6 /CB blue

> color #1/A hot pink

> color #1/7 red

> color #1/8 magenta

> color #1/M dark red

> color #1/Cc orange

> color #1/U cyan

> color #1/Cb dodger blue

> color #1/CY dark red

> color #1/0 green yellow

> color #1/Ch aquamarine

> color #1/Cf cyan

> color #1/Cd teal

> color #1/z tomato

> color #1/1 forest green

> color #1/Cg chocolate

> color #1/R dark violet

> color #1/F deep sky blue

> color #1/2 lime

> color #1/5 hot pink

> color #1/Y olive

> color #1/E tomato

> color #1/Ci dark blue

> color zone #2-10 near #1 distance 6

> hide #!1 models

> show #!1 models

> show cartoons

> hide atoms

> view

> hide #!1 models

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!2 models

> hide #!1 models

> hide #1 target a

> ribbon style protein modeh tube rad 2 sides 24

> ribbon style nucleic xsect rect width 3.2 thick 1.6

> cartoon style protein xsection oval width 3.2 thickness 1

> cartoon style strand xsection rectangle width 3.2 thickness 1.6

> show #1/B /D /F /R target r

> volume zone #2 nearAtoms #1/Cj range 3 newMap true

no atoms specified for zone  

> close

> open /Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-53.pdb

Chain information for c34_job27_ILS-coot-53.pdb #1  
---  
Chain | Description  
0 | No description available  
2 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
A | No description available  
B | No description available  
C | No description available  
CY | No description available  
Cb | No description available  
Cc | No description available  
Ci | No description available  
Cj | No description available  
D | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
P | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
W | No description available  
Y | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
  

> open /Users/lijuanyin/project/prp43/deposit/ils/run_class001.mrc

Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at
level 0.00799, step 2, values float32  

> open
> /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_body_high.mrc

Opened multi_ctf_c34_job27_body_high.mrc as #3, grid size 480,480,480, pixel
0.932, shown at level 0.0045, step 2, values float32  

> open
> /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_bottom_high.mrc

Opened multi_ctf_c34_job27_bottom_high.mrc as #4, grid size 480,480,480, pixel
0.932, shown at level 0.000984, step 2, values float32  

> open
> /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_ntr_high.mrc

Opened multi_ctf_c34_job27_ntr_high.mrc as #5, grid size 480,480,480, pixel
0.932, shown at level 0.000544, step 2, values float32  

> open
> /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_prp43_high.mrc

Opened multi_ctf_c34_job27_prp43_high.mrc as #6, grid size 480,480,480, pixel
0.932, shown at level 0.00086, step 2, values float32  

> volume #3 step 1 level 0.01

> volume #4 step 1 level 0.01

> volume #5 step 1 level 0.01

> volume #6 step 1 level 0.01

> surface dust #1-15 size 20

> set bgColor white

> windowsize 800 800

> color #1 #3-10 silver

> color #1 cyan

> color #2-10 silver

> color #1/a-g /j-p /u sienna

> color #1/K /L /P /R /T /q-t /CW wheat

> color #1/F /V /W /Z /CN sky blue

> color #1/B /Ca plum

> color #1/D /G /H /Q /X green

> color #1/I /Y /CV light green

> color #1/J /M /N /S /CY /Cb /Cc pink

> color #1/CD /CK /CL orange

> color #1/CR /CT /CX /CZ lime

> color #1/O /CA /CC /CU purple

> color #1/2 /h /i /CS cornflower blue

> color #1/CP /CQ /CE /CF /CG /CI /CJ forest green

> color #1/5 /A /C /E /CM deep pink

> color #1/6 /CB blue

> color #1/A hot pink

> color #1/7 red

> color #1/8 magenta

> color #1/M dark red

> color #1/Cc orange

> color #1/U cyan

> color #1/Cb dodger blue

> color #1/CY dark red

> color #1/0 green yellow

> color #1/Ch aquamarine

> color #1/Cf cyan

> color #1/Cd teal

> color #1/z tomato

> color #1/1 forest green

> color #1/Cg chocolate

> color #1/R dark violet

> color #1/F deep sky blue

> color #1/2 lime

> color #1/5 hot pink

> color #1/Y olive

> color #1/E tomato

> color #1/Ci dark blue

> color zone #2-10 near #1 distance 6

> hide #1 target a

> ribbon style protein modeh tube rad 2 sides 24

> ribbon style nucleic xsect rect width 3.2 thick 1.6

> cartoon style protein xsection oval width 3.2 thickness 1

> cartoon style strand xsection rectangle width 3.2 thickness 1.6

> show #1/B /D /F /R target r

> volume zone #2 nearAtoms #1/Cj range 3 newMap true

Opened run_class001.mrc zone as #7, grid size 480,480,480, pixel 0.932, shown
at step 1, values float32  

> show #1/B /D /F /R /I target r

> volume #7 level 0.005292

> volume #7 level 0.005

> volume #7 step 1

> volume #7 level 0.005606

> surface dust #1-15 size 20

> color #7 silver

> color #7 blue

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_2/fold_syf1_2_ccdc12_model_2.cif

No such file/path:
/Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_2/fold_syf1_2_ccdc12_model_2.cif  

> mmaker #8/A to #1/I

No molecules/chains to match specified  

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_4/fold_syf1_2_ccdc12_model_2.cif

Chain information for fold_syf1_2_ccdc12_model_2.cif #8  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> mmaker #8/A to #1/I

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker c34_job27_ILS-coot-53.pdb, chain I (#1) with
fold_syf1_2_ccdc12_model_2.cif, chain A (#8), sequence alignment score = 167.7  
RMSD between 6 pruned atom pairs is 1.389 angstroms; (across all 208 pairs:
22.859)  
  

> mmaker #8/C to #1/I

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker c34_job27_ILS-coot-53.pdb, chain I (#1) with
fold_syf1_2_ccdc12_model_2.cif, chain C (#8), sequence alignment score =
3787.8  
RMSD between 322 pruned atom pairs is 1.005 angstroms; (across all 738 pairs:
8.963)  
  

> color #8/C light green

> color #8/A deep sky blue

> color #8/B plum

> hide cartoons

> show #1/B /F /R /I target r

> show #8 target r

> color #8/C light green

> color #8/A deep sky blue

> color #8/B plum

> ribbon style protein modeh tube rad 2 sides 24

> ribbon style nucleic xsect rect width 3.2 thick 1.6

> cartoon style protein xsection oval width 3.2 thickness 1

> cartoon style strand xsection rectangle width 3.2 thickness 1.6

> ui tool show "Side View"

> view matrix

view matrix camera
0.87577,-0.47201,0.10115,188.83,-0.0021702,0.2057,0.97861,296.73,-0.48273,-0.85726,0.17912,178.61  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.81114,0.20413,0.54807,191.94,0.54382,0.081561,-0.83523,210.08,-0.2152,0.97554,-0.044853,157.4  
  

> lighting full

> view matrix

view matrix camera
0.87577,-0.47201,0.10115,188.83,-0.0021702,0.2057,0.97861,296.73,-0.48273,-0.85726,0.17912,178.61  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#7,1,0,0,0,0,1,0,0,0,0,1,0,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.81114,0.20413,0.54807,191.94,0.54382,0.081561,-0.83523,210.08,-0.2152,0.97554,-0.044853,157.4  
  

> hide #8 models

> save
> /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_4/unknown_ils.jpg

> show #8 models

> hide #!7 models

> hide #!1 models

> save
> /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_4/ccdc12_ils.jpg

> show #!1 models

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_5/cryosparc_P1_J375_004_volume_map.mrc

Opened cryosparc_P1_J375_004_volume_map.mrc as #9, grid size 480,480,480,
pixel 0.932, shown at level 0.121, step 2, values float32  

> close

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_5/cryosparc_P1_J375_004_volume_map.mrc

Opened cryosparc_P1_J375_004_volume_map.mrc as #1, grid size 480,480,480,
pixel 0.932, shown at level 0.121, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.1

> open /Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-53.pdb

Chain information for c34_job27_ILS-coot-53.pdb #2  
---  
Chain | Description  
0 | No description available  
2 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
A | No description available  
B | No description available  
C | No description available  
CY | No description available  
Cb | No description available  
Cc | No description available  
Ci | No description available  
Cj | No description available  
D | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
P | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
W | No description available  
Y | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
  

> hide #!1 models

> show #!1 models

> close

> open /Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-53.pdb

Chain information for c34_job27_ILS-coot-53.pdb #1  
---  
Chain | Description  
0 | No description available  
2 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
A | No description available  
B | No description available  
C | No description available  
CY | No description available  
Cb | No description available  
Cc | No description available  
Ci | No description available  
Cj | No description available  
D | No description available  
E | No description available  
F | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
P | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
W | No description available  
Y | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
  

> open
> /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_5/cryosparc_P1_J375_004_volume_map.mrc

Opened cryosparc_P1_J375_004_volume_map.mrc as #2, grid size 480,480,480,
pixel 0.932, shown at level 0.121, step 2, values float32  

> color #1 #3-10 silver

> color #1/I /Y /CV light green

> volume #2 level 0.1

> volume #2 step 1

> hide #!1 models

> color zone #2-10 near #1 distance 6

> color zone #2-10 near #1 distance 12

> surface dust #1-15 size 20

> save
> /Users/lijuanyin/project/prp43/figure_new/revision/review_figure/review_figure_5/cryoSPARC.jpg


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

Log:
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/lijuanyin/project/prp43/combine_142_169/job6/c6/job28/c34/dc3/job240/run_it200_class001.mrc

Opened run_it200_class001.mrc as #1, grid size 160,160,160, pixel 2.8, shown
at level 6.84e-07, step 1, values float32  

> open
> /Users/lijuanyin/project/prp43/combine_142_169/job6/c6/job28/c34/dc3/job240/run_it200_class002.mrc

Opened run_it200_class002.mrc as #2, grid size 160,160,160, pixel 2.8, shown
at level 1.3e-05, step 1, values float32  

> open
> /Users/lijuanyin/project/prp43/combine_142_169/job6/c6/job28/c34/dc3/job240/run_it200_class003.mrc

Opened run_it200_class003.mrc as #3, grid size 160,160,160, pixel 2.8, shown
at level 1.06e-05, step 1, values float32  

> open
> /Users/lijuanyin/project/prp43/combine_142_169/job6/c6/job28/c34/dc3/job240/run_it200_class004.mrc

Opened run_it200_class004.mrc as #4, grid size 160,160,160, pixel 2.8, shown
at level 7.99e-06, step 1, values float32  

> open
> /Users/lijuanyin/project/prp43/combine_142_169/job6/c6/job28/c34/dc3/job240/run_it200_class005.mrc

Opened run_it200_class005.mrc as #5, grid size 160,160,160, pixel 2.8, shown
at level 1.83e-06, step 1, values float32  

> open
> /Users/lijuanyin/project/prp43/combine_142_169/job6/c6/job28/c34/dc3/job240/run_it200_class006.mrc

Opened run_it200_class006.mrc as #6, grid size 160,160,160, pixel 2.8, shown
at level 1.47e-05, step 1, values float32  




OpenGL version: 4.1 ATI-6.1.13
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2,3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 64 GB
      System Firmware Version: 2069.0.0.0.0 (iBridge: 22.16.10353.0.0,0)
      OS Loader Version: 582~1023

Software:

    System Software Overview:

      System Version: macOS 15.0 (24A335)
      Kernel Version: Darwin 24.0.0
      Time since boot: 17天5小时17分钟

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-020
      Option ROM Version: 113-D32206U1-020
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        C34H89x:
          Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
          UI Looks like: 3440 x 1440 @ 50.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: H1AK500000  
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: Apple USB-C Digital AV Adapter
          Adapter Firmware Version: 2,35


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11

Change History (2)

comment:1 by Eric Pettersen, 10 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

comment:2 by Eric Pettersen, 10 months ago

Resolution: → duplicate
Status: assigned → closed
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