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Opened 12 months ago
Last modified 12 months ago
#16555 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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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===== Log before crash start =====
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/deposit/q2_focus_dhx15/focus_head/run_class001.mrc
Opened run_class001.mrc as #1, grid size 480,480,480, pixel 0.932, shown at
level 0.00588, step 2, values float32
> volume #1 level 0.003655
> open
> /Users/lijuanyin/project/prp43/deposit/q2_focus_dhx15/local_c1_job195_new_2/relion_locres_filtered.mrc
Opened relion_locres_filtered.mrc as #2, grid size 480,480,480, pixel 0.932,
shown at level 0.00613, step 2, values float32
> volume #2 level 0.004065
> 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/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
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> color #1/F /V /W /Z /CN sky blue
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> color #1/J /M /N /S /CY /Cb /Cc pink
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> color #1/CR /CT /CX /CZ lime
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> color #1/Cd teal
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> 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
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> 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
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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
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> color #1/I /Y /CV light green
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> color #1/CR /CT /CX /CZ lime
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> color #1/2 /h /i /CS cornflower blue
> color #1/CP /CQ /CE /CF /CG /CI /CJ forest green
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> 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
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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
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> 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
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> 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
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> 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
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R | No description available
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T | No description available
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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
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> 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
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> cartoon style protein xsection oval width 3.2 thickness 1
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> 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
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i | No description available
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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
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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
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> hide #1/CM target r
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> 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
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> 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
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f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
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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
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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
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> show #1-2/2-8 #3/B /D /F target a
> nucleotides #1-2/2-8 #3/B /D /F ladder
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> 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
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> color #1/7 red
> color #1/8 magenta
> color #1/M dark red
> color #1/Cc orange
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> 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
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> 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
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> 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
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> color #1/J /M /N /S /CY /Cb /Cc /R pink
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> color #1/CR /CT /CX /CZ lime
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> color #1/Cb dodger blue
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> 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
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