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Opened 16 months ago
Closed 16 months ago
#15478 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.1-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Thread 0x00000002ff333000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000289067000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000028805b000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000028704f000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000286043000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000285037000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000028402b000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000028301f000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000282013000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000281007000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000017fba3000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000017eb97000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000017db8b000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000017a76f000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001f8617a80 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/_internal.py", line 255 in __init__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 333 in pointer
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 251 in set_cvec_pointer
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 133 in __init__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 1558 in __init__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2226 in process_changes
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2231 in changes
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 36 in check_for_changes
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 69 in draw_new_frame
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imagingmath, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.segment._segment, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 57)
{"app_name":"ChimeraX","timestamp":"2024-06-24 10:21:22.00 +0800","app_version":"1.7.1","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.7.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.1 (22C65)","roots_installed":0,"name":"ChimeraX","incident_id":"07735886-B343-4BC0-891C-E8C8075781DB"}
{
"uptime" : 320000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,1",
"coalitionID" : 2376,
"osVersion" : {
"train" : "macOS 13.1",
"build" : "22C65",
"releaseType" : "User"
},
"captureTime" : "2024-06-24 10:21:19.4634 +0800",
"incident" : "07735886-B343-4BC0-891C-E8C8075781DB",
"pid" : 1822,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-06-19 14:32:23.4278 +0800",
"procStartAbsTime" : 13829766428,
"procExitAbsTime" : 7683695049820,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"FA382B41-4902-558E-AA32-CD16C818C902","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "C9359081-19E8-2E09-A687-1105407B6F31",
"throttleTimeout" : 2147483647,
"wakeTime" : 1619,
"sleepWakeUUID" : "83197CFA-A3A6-4EFA-952E-A86D953F3432",
"sip" : "enabled",
"vmRegionInfo" : "0x105fd1040 is in 0x105fd0000-0x1060f0000; bytes after start: 4160 bytes before end: 1175487\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n __DATA_CONST 105fa0000-105fd0000 [ 192K] r--\/rwx SM=COW ...s\/3.11\/Python\n---> __DATA 105fd0000-1060f0000 [ 1152K] rw-\/rwx SM=COW ...s\/3.11\/Python\n __DATA 1060f0000-106134000 [ 272K] rw-\/rwx SM=PRV ...s\/3.11\/Python",
"exception" : {"codes":"0x0000000000000002, 0x0000000105fd1040","rawCodes":[2,4395438144],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000000105fd1040"},
"vmregioninfo" : "0x105fd1040 is in 0x105fd0000-0x1060f0000; bytes after start: 4160 bytes before end: 1175487\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n __DATA_CONST 105fa0000-105fd0000 [ 192K] r--\/rwx SM=COW ...s\/3.11\/Python\n---> __DATA 105fd0000-1060f0000 [ 1152K] rw-\/rwx SM=COW ...s\/3.11\/Python\n __DATA 1060f0000-106134000 [ 272K] rw-\/rwx SM=PRV ...s\/3.11\/Python",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
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"name" : "CoreFoundation",
"CFBundleVersion" : "1953.300"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 7090675712,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3358720,
"uuid" : "f1e0f4f6-dd7b-3d16-a622-5ee94a20fcaa",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6985445376,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 15773696,
"uuid" : "dbbd4dea-6c68-3200-a81b-79b6a62f4669",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2299.30.116"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4376330240,
"CFBundleShortVersionString" : "1.7.1",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 16384,
"uuid" : "17982d98-65bc-3327-8526-577ec996453c",
"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.7.1.0"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6928474112,
"size" : 568164,
"uuid" : "487cfdeb-9b07-39bf-bfb9-970b61aea2d1",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5795528704,
"size" : 144654336,
"uuid" : "21c8f378-4426-330a-89d1-26ab67c6fa56",
"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5207146496,
"size" : 16384,
"uuid" : "05bf27fd-ae65-3f9b-a9bc-60e1a55f235b",
"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_queue.cpython-311-darwin.so",
"name" : "_queue.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4384079872,
"size" : 32768,
"uuid" : "d4a30d1d-5ac5-31ab-8176-122870f0d37b",
"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/select.cpython-311-darwin.so",
"name" : "select.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4831838208,
"size" : 20922368,
"uuid" : "a47c5020-7d8a-3a70-8106-0225519e1c37",
"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4949278720,
"size" : 6127616,
"uuid" : "e75b517e-89e1-3643-b4d3-2e8e02322b44",
"path" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui",
"name" : "QtGui"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
}
],
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "62699e1ec1ff2978b47f6c3b",
"factorPackIds" : {
"SIRI_FIND_MY_CONFIGURATION_FILES" : "652805151bce5442b8d752e1"
},
"deploymentId" : 240000031
},
{
"rolloutId" : "645c2d2f9e69a025b0a37e29",
"factorPackIds" : {
},
"deploymentId" : 240000003
}
],
"experiments" : [
{
"treatmentId" : "c47ab4cc-c9c3-4b5d-a87c-e2433ce02597",
"experimentId" : "6639bc6ba73d460582162323",
"deploymentId" : 400000006
},
{
"treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000004
}
]
},
"reportNotes" : [
"dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/huanggq/Downloads/cryosparc_P124_J6644_008_volume_map.mrc
Opened cryosparc_P124_J6644_008_volume_map.mrc as #1, grid size 440,440,440,
pixel 0.835, shown at level 0.05, step 2, values float32
> volume #1 step 1
> lighting soft
> set bgColor white
> volume #1 level 0.0978
> ui mousemode right "map eraser"
> select add #2
1 model selected
> volume #1 level 0.03905
> volume #1 level 0.03
> volume #1 level 0.08192
> volume #1 level 0.03
> volume erase #1 center 182.43,119.71,271.65 radius 66.807 outside true
Opened cryosparc_P124_J6644_008_volume_map.mrc copy as #3, grid size
440,440,440, pixel 0.835, shown at step 1, values float32
> save
> /Users/huanggq/Downloads/cryosparc_P124_J6644_010_volume_map_LHCII_thre0p03.mrc
> models #3
> close #3
> volume erase #1 center 182.43,119.71,271.65 radius 66.683
Opened cryosparc_P124_J6644_008_volume_map.mrc copy as #3, grid size
440,440,440, pixel 0.835, shown at step 1, values float32
> save
> /Users/huanggq/Downloads/cryosparc_P124_J6644_010_volume_map_PSIIcore_thre0p03.mrc
> models #3
> close
> open /Users/huanggq/Downloads/cryosparc_P124_J6643_008_volume_map.mrc
Opened cryosparc_P124_J6643_008_volume_map.mrc as #1, grid size 360,360,360,
pixel 0.835, shown at level 0.0609, step 2, values float32
> volume #1 step 1
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/FV_Aa-PSI/FVPSI-
> model-0726/FvPSI_J94-230921-coot-2.pdb
Chain information for FvPSI_J94-230921-coot-2.pdb #2
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | 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
N | No description available
O | No description available
> hide atoms
> show cartoons
> select add #2
38187 atoms, 39722 bonds, 703 pseudobonds, 3637 residues, 2 models selected
> hide #3 models
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.75841,-0.54726,-0.35402,419.73,-0.21409,0.72218,-0.65774,184.22,0.61562,-0.42304,-0.66487,240.47
> view matrix models
> #2,-0.98593,-0.1632,-0.036224,343.62,-0.14321,0.93633,-0.3206,84.667,0.08624,-0.3109,-0.94652,351.97
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.98593,-0.1632,-0.036224,348.66,-0.14321,0.93633,-0.3206,76.408,0.08624,-0.3109,-0.94652,337.42
> view matrix models
> #2,-0.98593,-0.1632,-0.036224,347.94,-0.14321,0.93633,-0.3206,76.198,0.08624,-0.3109,-0.94652,336.47
> view matrix models
> #2,-0.98593,-0.1632,-0.036224,342.62,-0.14321,0.93633,-0.3206,64.596,0.08624,-0.3109,-0.94652,336.05
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.95747,-0.029144,-0.28706,357.98,0.064217,0.94841,-0.31047,28.45,0.2813,-0.3157,-0.9062,299.58
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.95747,-0.029144,-0.28706,359.43,0.064217,0.94841,-0.31047,39.323,0.2813,-0.3157,-0.9062,306.38
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule FvPSI_J94-230921-coot-2.pdb (#2) to map
cryosparc_P124_J6643_008_volume_map.mrc (#1) using 38187 atoms
average map value = 0.1616, steps = 256
shifted from previous position = 6.31
rotated from previous position = 21.5 degrees
atoms outside contour = 3016, contour level = 0.06089
Position of FvPSI_J94-230921-coot-2.pdb (#2) relative to
cryosparc_P124_J6643_008_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.99993709 -0.01100483 0.00217169 314.68125598
-0.01115933 0.99558635 -0.09318422 6.76256116
-0.00113663 -0.09320259 -0.99564652 325.23056437
Axis -0.00554720 0.99889593 -0.04664924
Axis point 157.49400239 0.00000000 162.64279280
Rotation angle (degrees) 179.90511876
Shift along axis -10.16226573
> select subtract #2
Nothing selected
> volume #1 level 0.08634
> save /Users/huanggq/Desktop/1/HGQ_MAC/project/FV/FVPSI-LHCII/PDB/FV-
> PSI-J6643.pdb relModel #1
> hide #!2 models
> hide #!1 models
> open /Users/huanggq/Downloads/cryosparc_P124_J6652_volume_map.mrc
Opened cryosparc_P124_J6652_volume_map.mrc as #4, grid size 440,440,440, pixel
0.835, shown at level 0.0111, step 2, values float32
> volume #4 step 1
> volume #4 level 0.03539
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> volume #4 level 0.035
> close
> open /Users/huanggq/Downloads/cryosparc_P124_J6641_008_volume_map.mrc
Opened cryosparc_P124_J6641_008_volume_map.mrc as #1, grid size 600,600,600,
pixel 0.85, shown at level 0.113, step 4, values float32
> volume #1 step 2
> volume #1 level 0.1877
> volume #1 step 1
> volume #1 level 0.2474
> volume #1 level 0.1638
> volume #1 level 0.322
> volume #1 level 0.1862
> show #!1 models
> hide #2 models
> volume #1 level 0.06983
> show #2 models
> hide #2 models
> volume #1 level 0.07
> ui tool show "Fit to Segments"
> ui tool show "Segment Map"
Segmenting cryosparc_P124_J6641_008_volume_map.mrc, density threshold 0.070000
Only showing 60 of 555 regions.
Showing 60 of 555 region surfaces
19068 watershed regions, grouped to 555 regions
Showing cryosparc_P124_J6641_008_volume_map.seg - 555 regions, 60 surfaces
> hide #!3 models
> volume #1 level 0.2
> volume #1 level 0.07
> volume #1 level 0.1
> volume #1 level 0.07
> show #2 models
> select add #2
1 model selected
> view matrix models #2,1,0,0,252.23,0,1,0,319.91,0,0,1,346.93
> view matrix models #2,1,0,0,262.26,0,1,0,230.75,0,0,1,164.96
> view matrix models #2,1,0,0,263.23,0,1,0,221.05,0,0,1,99.43
> volume #1 level 0.2
> view matrix models #2,1,0,0,261.34,0,1,0,228.61,0,0,1,129.56
> view matrix models #2,1,0,0,259.17,0,1,0,219.7,0,0,1,126.77
> view matrix models #2,1,0,0,257.26,0,1,0,209.57,0,0,1,127.97
> view matrix models #2,1,0,0,251.65,0,1,0,216.88,0,0,1,129.5
> volume #1 level 0.4226
> volume #1 level 0.2747
> view matrix models #2,1,0,0,250.57,0,1,0,210.64,0,0,1,131.92
> view matrix models #2,1,0,0,251.54,0,1,0,214.42,0,0,1,132.15
> volume #1 level 0.07
> volume erase #1 center 251.54,214.42,132.15 radius 166.26
Opened cryosparc_P124_J6641_008_volume_map.mrc copy as #4, grid size
600,600,600, pixel 0.85, shown at step 1, values float32
> view matrix models #2,1,0,0,240.82,0,1,0,212.34,0,0,1,146.99
> view matrix models #2,1,0,0,164.69,0,1,0,290.04,0,0,1,165.72
> view matrix models #2,1,0,0,165.13,0,1,0,289.6,0,0,1,166.26
> view matrix models #2,1,0,0,138.45,0,1,0,312.74,0,0,1,261.39
> view matrix models #2,1,0,0,168.04,0,1,0,320.31,0,0,1,275.09
> view matrix models #2,1,0,0,145.36,0,1,0,307.87,0,0,1,274.73
> view matrix models #2,1,0,0,153.74,0,1,0,307,0,0,1,271.73
> view matrix models #2,1,0,0,154.27,0,1,0,306.81,0,0,1,272.13
> volume erase #4 center 154.27,306.81,272.13 radius 66.555
> view matrix models #2,1,0,0,155.3,0,1,0,240.18,0,0,1,280.33
> view matrix models #2,1,0,0,161.44,0,1,0,216.79,0,0,1,286.17
> view matrix models #2,1,0,0,162.19,0,1,0,222.9,0,0,1,286.49
> volume erase #4 center 162.19,222.9,286.49 radius 66.555
> hide #2 models
> save /Users/huanggq/Downloads/cryosparc_P124_J6641_008_volume_map_LHCII-
> half1_thre0p07.mrc models #4
> close
> open /Users/huanggq/Downloads/cryosparc_P125_J9545_003_volume_map.mrc
Opened cryosparc_P125_J9545_003_volume_map.mrc as #1, grid size 128,128,128,
pixel 1.67, shown at level 0.0915, step 1, values float32
> volume #1 level 0.1699
> volume #1 level 0.07939
> close
> open /Users/huanggq/Downloads/cryosparc_P124_J6663_006_volume_map.mrc
Opened cryosparc_P124_J6663_006_volume_map.mrc as #1, grid size 600,600,600,
pixel 0.85, shown at level 0.108, step 4, values float32
> volume #1 step 1
> volume #1 level 0.1986
> volume #1 level 0.2637
> open /Users/huanggq/Downloads/cryosparc_P125_J9548_005_volume_map.mrc
Opened cryosparc_P125_J9548_005_volume_map.mrc as #2, grid size 128,128,128,
pixel 1.67, shown at level 0.0878, step 1, values float32
> volume #2 level 0.2919
> volume #2 level 0.3116
> volume #2 level 0.2249
> close
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/FV/FVPSI-LHCII/PDB/FV-
> PSI-J6643-coot-8.pdb
Chain information for FV-PSI-J6643-coot-8.pdb #1
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | 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
N | No description available
O | No description available
> hide atoms
> show cartoons
> lighting soft
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/FV_Aa-PSI/FVPSI-
> model-0726/FvPSI_J94-230921-coot-2.pdb
Chain information for FvPSI_J94-230921-coot-2.pdb #2
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | 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
N | No description available
O | No description available
> hide atoms
> show cartoons
> color #2 #87dcebff
> lighting soft
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FV-PSI-J6643-coot-8.pdb, chain A (#1) with
FvPSI_J94-230921-coot-2.pdb, chain A (#2), sequence alignment score = 3882.5
RMSD between 742 pruned atom pairs is 0.258 angstroms; (across all 742 pairs:
0.258)
> close #2
> hide #!1 models
> open /Users/huanggq/Downloads/cryosparc_P124_J6644_010_volume_map_sharp.mrc
Opened cryosparc_P124_J6644_010_volume_map_sharp.mrc as #2, grid size
440,440,440, pixel 0.835, shown at level 0.0848, step 2, values float32
> volume #2 step 1
> volume #2 level 0.2071
> show #!1 models
> hide #3 models
> select add #1
38114 atoms, 39648 bonds, 703 pseudobonds, 3634 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-3.1537,0,1,0,43.28,0,0,1,26.676
> view matrix models #1,1,0,0,33.484,0,1,0,38.2,0,0,1,26.063
> view matrix models #1,1,0,0,33.616,0,1,0,37.431,0,0,1,27.57
> fitmap #1 inMap #2
Fit molecule FV-PSI-J6643-coot-8.pdb (#1) to map
cryosparc_P124_J6644_010_volume_map_sharp.mrc (#2) using 38114 atoms
average map value = 0.3464, steps = 64
shifted from previous position = 0.676
rotated from previous position = 2.13 degrees
atoms outside contour = 7220, contour level = 0.20713
Position of FV-PSI-J6643-coot-8.pdb (#1) relative to
cryosparc_P124_J6644_010_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99979454 -0.01924099 -0.00637702 37.68538079
0.01943071 0.99932554 0.03115943 29.40586975
0.00577318 -0.03127694 0.99949408 31.80506170
Axis -0.83873884 -0.16321979 0.51949635
Axis point 0.00000000 1360.27389009 -810.11635649
Rotation angle (degrees) 2.13306371
Shift along axis -19.88519883
> select subtract #1
Nothing selected
> fitmap #1 inMap #2
Fit molecule FV-PSI-J6643-coot-8.pdb (#1) to map
cryosparc_P124_J6644_010_volume_map_sharp.mrc (#2) using 38114 atoms
average map value = 0.3464, steps = 40
shifted from previous position = 0.0119
rotated from previous position = 0.00782 degrees
atoms outside contour = 7226, contour level = 0.20713
Position of FV-PSI-J6643-coot-8.pdb (#1) relative to
cryosparc_P124_J6644_010_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99979494 -0.01918756 -0.00647420 37.69039373
0.01938081 0.99932402 0.03123932 29.39721232
0.00587041 -0.03135839 0.99949097 31.79201698
Axis -0.83962284 -0.16557823 0.51731744
Axis point 0.00000000 1357.93914331 -805.28833568
Rotation angle (degrees) 2.13632573
Shift along axis -20.06668908
> transparency #2.1 50
> transparency #2.1 0
> volume #2 level 0.1897
> save /Users/huanggq/Desktop/1/HGQ_MAC/project/FV/FVPSI-LHCII/PDB/FV-PSI-
> LHCII-J6644.pdb relModel #2
> open /Users/huanggq/Downloads/cryosparc_P124_J6654_007_volume_map.mrc
Opened cryosparc_P124_J6654_007_volume_map.mrc as #4, grid size 440,440,440,
pixel 0.835, shown at level 0.011, step 2, values float32
> volume #4 step 1
> volume #4 level 0.09857
> volume #4 level 0.1544
> volume #4 level 0.09256
> volume #4 level 0.1398
> close
> open
> /Users/huanggq/Downloads/cryosparc_P124_J6668_00175_volume_series/J6668_class_00_00175_volume.mrc
Opened J6668_class_00_00175_volume.mrc as #1, grid size 128,128,128, pixel
2.87, shown at level 0.0369, step 1, values float32
> open
> /Users/huanggq/Downloads/cryosparc_P124_J6668_00175_volume_series/J6668_class_01_00175_volume.mrc
Opened J6668_class_01_00175_volume.mrc as #2, grid size 128,128,128, pixel
2.87, shown at level 0.0678, step 1, values float32
> open
> /Users/huanggq/Downloads/cryosparc_P124_J6668_00175_volume_series/J6668_class_02_00175_volume.mrc
Opened J6668_class_02_00175_volume.mrc as #3, grid size 128,128,128, pixel
2.87, shown at level 0.0385, step 1, values float32
> volume #1 level 0.06857
> hide #!2 models
> hide #!3 models
> volume #1 level 0.354
> volume #3 level 0.3303
> hide #!1 models
> show #!1 models
> volume #3 level 0.3339
> hide #!1 models
> hide #!3 models
> volume #2 level 0.3645
> volume #2 level 0.339
> hide #!2 models
> open /Users/huanggq/Downloads/cryosparc_P124_J6669_004_volume_map.mrc
Opened cryosparc_P124_J6669_004_volume_map.mrc as #4, grid size 600,600,600,
pixel 0.85, shown at level 0.111, step 4, values float32
> volume #4 step 1
> volume #4 level 0.2018
> close #4
> close
> open /Users/huanggq/Downloads/cryosparc_P124_J6654_007_volume_map.mrc
Opened cryosparc_P124_J6654_007_volume_map.mrc as #1, grid size 440,440,440,
pixel 0.835, shown at level 0.011, step 2, values float32
> volume #1 step 1
> volume #1 level 0.05609
> volume #1 level 0.09203
> volume #1 level 0.07291
> volume #1 level 0.1226
> volume #1 level 0.07291
> hide #!1 models
> show #!1 models
> volume #1 level 0.05838
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> volume #1 level 0.06
> hide #!1 models
> close #1
> open /Users/huanggq/Downloads/cryosparc_P124_J6656_map.mrc
Opened cryosparc_P124_J6656_map.mrc as #1, grid size 600,600,600, pixel 0.85,
shown at level 0.113, step 4, values float32
> volume #1 step 2
> volume #1 step 1
> volume #1 level 0.1
> ui tool show "Segment Map"
Segmenting cryosparc_P124_J6656_map.mrc, density threshold 0.100000
Only showing 60 of 540 regions.
Showing 60 of 540 region surfaces
14031 watershed regions, grouped to 540 regions
Showing cryosparc_P124_J6656_map.seg - 540 regions, 60 surfaces
> hide #3 models
Ungrouped to 767 regions, but did not show all surfaces, see Options
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
Smoothing and grouping, standard deviation 4 voxels
Only showing 60 of 540 regions.
Showing 60 of 540 region surfaces
Got 540 regions after smoothing 4 voxels.
Smoothing and grouping, standard deviation 5 voxels
Only showing 60 of 291 regions.
Showing 60 of 291 region surfaces
Got 291 regions after smoothing 5 voxels.
Smoothing and grouping, standard deviation 6 voxels
Only showing 60 of 162 regions.
Showing 60 of 162 region surfaces
Got 162 regions after smoothing 6 voxels.
Smoothing and grouping, standard deviation 7 voxels
Only showing 60 of 110 regions.
Showing 60 of 110 region surfaces
Got 110 regions after smoothing 7 voxels.
Smoothing and grouping, standard deviation 8 voxels
Only showing 60 of 79 regions.
Showing 60 of 79 region surfaces
Got 79 regions after smoothing 8 voxels.
Smoothing and grouping, standard deviation 9 voxels
Showing 58 region surfaces
Got 58 regions after smoothing 9 voxels.
Smoothing and grouping, standard deviation 10 voxels
Showing 51 region surfaces
Got 51 regions after smoothing 10 voxels.
Smoothing and grouping, standard deviation 11 voxels
Showing 38 region surfaces
Got 38 regions after smoothing 11 voxels.
Smoothing and grouping, standard deviation 12 voxels
Showing 27 region surfaces
Got 27 regions after smoothing 12 voxels.
Smoothing and grouping, standard deviation 13 voxels
Showing 25 region surfaces
Got 25 regions after smoothing 13 voxels.
Smoothing and grouping, standard deviation 14 voxels
Showing 23 region surfaces
Got 23 regions after smoothing 14 voxels.
Smoothing and grouping, standard deviation 15 voxels
Showing 21 region surfaces
Got 21 regions after smoothing 15 voxels.
Smoothing and grouping, standard deviation 16 voxels
Showing 20 region surfaces
Got 20 regions after smoothing 16 voxels.
Smoothing and grouping, standard deviation 17 voxels
Showing 17 region surfaces
Got 17 regions after smoothing 17 voxels.
Smoothing and grouping, standard deviation 18 voxels
Showing 9 region surfaces
Got 9 regions after smoothing 18 voxels.
Smoothing and grouping, standard deviation 19 voxels
Showing 3 region surfaces
Got 3 regions after smoothing 19 voxels.
Ungrouped to 9 regions
> select add #2.6
1 model selected
> select add #2.3
2 models selected
> select add #2.11
3 models selected
> select add #2.12
4 models selected
> select add #2.8
5 models selected
> select add #2.9
6 models selected
Grouped 6 regions
> select subtract #2.1
Nothing selected
> select add #2.7
1 model selected
> select add #2.4
2 models selected
> select add #2.10
3 models selected
Grouped 3 regions
> select add #2
3 models selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> select subtract #2
Nothing selected
> volume #1 level 0.2368
Segmenting cryosparc_P124_J6656_map.mrc, density threshold 0.236820
Only showing 60 of 466 regions.
Showing 60 of 466 region surfaces
5029 watershed regions, grouped to 466 regions
Showing cryosparc_P124_J6656_map.seg - 466 regions, 60 surfaces
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
Smoothing and grouping, standard deviation 5 voxels
Only showing 60 of 258 regions.
Showing 60 of 258 region surfaces
Got 258 regions after smoothing 5 voxels.
> hide #!2 models
> volume #1 level 0.01
> volume #1 level 0.02
> volume #1 level 0.03
> volume #1 level 0.05
> volume #1 level 0.1
> close #1
> close
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/FV_Aa-PSI/FVPSI-
> model-0726/FvPSI_J94-230921-coot-2.pdb format pdb
Chain information for FvPSI_J94-230921-coot-2.pdb #1
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | 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
N | No description available
O | No description available
> close
> open /Users/huanggq/Downloads/cryosparc_P124_J6672_map.mrc
Opened cryosparc_P124_J6672_map.mrc as #1, grid size 600,600,600, pixel 0.85,
shown at level 0.113, step 4, values float32
> lighting soft
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/FV/FVPSII/5xnl-J2699.pdb
5xnl-J2699.pdb title:
Structure of stacked C2S2M2-type psii-lhcii supercomplex from pisum sativum
[more info...]
Chain information for 5xnl-J2699.pdb #2
---
Chain | Description | UniProt
1 2 5 6 G N Y g n y | lhcii TYPE I CAB-8 | CB28_PEA 1-232
3 7 | chlorophyll A-B binding protein, chloroplastic | Q04918_PEA 1-243
4 8 | light harvesting chlorophyll A/B-binding protein LHCB6, CP24 |
A a | photosystem II protein D1 | PSBA_PEA 1-344
B b | photosystem II CP47 reaction center protein | Q9XQR6_PEA 1-507
C c | photosystem II CP43 reaction center protein | PSBC_PEA 1-473
D d | photosystem II D2 protein | PSBD_PEA 1-353
E e | PSII reaction center subunit V | PSBE_PEA 1-83
F f | cytochrome B559 subunit β, PSBF |
H h | photosystem II reaction center protein H | PSBH_PEA 1-73
I i | photosystem II reaction center protein I, PSBI |
J j | PSII-J | PSBJ_PEA 1-40
K k | PSII-K | D5MAJ8_PEA 1-61
L l | PSII-L | PSBL_PEA 1-38
M m | PSII-M | PSBM_PEA 1-34
O o | oxygen-evolving enhancer protein 1, chloroplastic | PSBO_PEA 1-248
P p | oxygen-evolving enhancer protein 2, chloroplastic | PSBP_PEA 1-186
Q q | oxygen-evolving enhancer protein 3 | Q7Y1T5_PEA 1-148
R r | light harvesting chlorophyll A/B-binding protein LHCB4, CP29 |
S s | light harvesting chlorophyll A/B-binding protein LHCB5, CP26 |
T t | PSII-T | PSBT_PEA 1-35
W w | photosystem II reaction center protein W |
X x | photosystem II reaction center protein X | Q8VYY1_PEA 1-86
Z z | PSII-Z | PSBZ_PEA 1-62
Non-standard residues in 5xnl-J2699.pdb #2
---
BCR — β-carotene
BCT — bicarbonate ion
CHL — chlorophyll B
CL — chloride ion
CLA — chlorophyll A
DGD — digalactosyl diacyl glycerol (DGDG)
FE2 — Fe (II) ion
HEM — protoporphyrin IX containing Fe (HEME)
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol, lutein)
NEX —
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol
((3S,5R,6R,3'S,5'R,6'S)-5',6'-epoxy-6,7-didehydro-
5,6,5',6'-tetrahydro-β,β-carotene-3,5,3'-triol, 9'-cis-
neoxanthin)
OEX — Ca-MN4-O5 cluster
PHO — pheophytin A
PL9 —
2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone
(plastoquinone 9)
SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol
(sulfoquinovosyldiacylglycerol)
XAT —
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-β,β-carotene-3,3'-diol
(violaxanthin)
> hide atoms
> volume #1 step 2
> show cartoons
> select add #2
98986 atoms, 101446 bonds, 1584 pseudobonds, 10930 residues, 3 models selected
> view matrix models #2,1,0,0,24.219,0,1,0,5.0508,0,0,1,-1.1643
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.2125,0.97074,-0.11182,99.025,0.097035,0.13483,0.98611,-59.218,0.97233,0.1987,-0.12285,11.168
> view matrix models
> #2,-0.024421,0.95297,-0.30209,108.48,0.064255,0.30305,0.95081,-84.421,0.99763,0.0038085,-0.068634,39.899
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.024421,0.95297,-0.30209,105.15,0.064255,0.30305,0.95081,-74.946,0.99763,0.0038085,-0.068634,15.843
> fitmap #2 inMap #1
Fit molecule 5xnl-J2699.pdb (#2) to map cryosparc_P124_J6672_map.mrc (#1)
using 98986 atoms
average map value = 0.1301, steps = 188
shifted from previous position = 13.9
rotated from previous position = 9.51 degrees
atoms outside contour = 48122, contour level = 0.11254
Position of 5xnl-J2699.pdb (#2) relative to cryosparc_P124_J6672_map.mrc (#1)
coordinates:
Matrix rotation and translation
-0.00453861 0.98703674 -0.16043034 51.69968668
-0.01032348 0.16037719 0.98700183 -43.28089030
0.99993643 0.00613581 0.00946177 -7.71921642
Axis -0.53968111 -0.63844400 -0.54875637
Axis point 46.92557931 0.00000000 41.77559374
Rotation angle (degrees) 114.66738298
Shift along axis 3.96704953
> select subtract #2
Nothing selected
> transparency 50
> transparency 0
> volume #1 step 1
> volume #1 level 0.1993
> fitmap #2 inMap #1
Fit molecule 5xnl-J2699.pdb (#2) to map cryosparc_P124_J6672_map.mrc (#1)
using 98986 atoms
average map value = 0.1301, steps = 48
shifted from previous position = 0.00385
rotated from previous position = 0.002 degrees
atoms outside contour = 78403, contour level = 0.19927
Position of 5xnl-J2699.pdb (#2) relative to cryosparc_P124_J6672_map.mrc (#1)
coordinates:
Matrix rotation and translation
-0.00451254 0.98703626 -0.16043407 51.69448007
-0.01030057 0.16038131 0.98700140 -43.28799167
0.99993678 0.00610644 0.00944331 -7.70326284
Axis -0.53969544 -0.63844436 -0.54874187
Axis point 46.91910843 0.00000000 41.78310238
Rotation angle (degrees) 114.66701329
Shift along axis 3.96480192
> hide #!2 models
> show #!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 #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> volume #1 level 0.1
Segmenting cryosparc_P124_J6672_map.mrc, density threshold 0.100000
Only showing 60 of 540 regions.
Showing 60 of 540 region surfaces
14031 watershed regions, grouped to 540 regions
Showing cryosparc_P124_J6672_map.seg - 540 regions, 60 surfaces
Smoothing and grouping, standard deviation 5 voxels
Only showing 60 of 291 regions.
Showing 60 of 291 region surfaces
Got 291 regions after smoothing 5 voxels.
Smoothing and grouping, standard deviation 6 voxels
Only showing 60 of 162 regions.
Showing 60 of 162 region surfaces
Got 162 regions after smoothing 6 voxels.
Smoothing and grouping, standard deviation 7 voxels
Only showing 60 of 110 regions.
Showing 60 of 110 region surfaces
Got 110 regions after smoothing 7 voxels.
Segmenting cryosparc_P124_J6672_map.mrc, density threshold 0.100000
Only showing 60 of 540 regions.
Showing 60 of 540 region surfaces
14031 watershed regions, grouped to 540 regions
Showing cryosparc_P124_J6672_map.seg - 540 regions, 60 surfaces
Smoothing and grouping, standard deviation 5 voxels
Only showing 60 of 291 regions.
Showing 60 of 291 region surfaces
Got 291 regions after smoothing 5 voxels.
Smoothing and grouping, standard deviation 6 voxels
Only showing 60 of 162 regions.
Showing 60 of 162 region surfaces
Got 162 regions after smoothing 6 voxels.
Smoothing and grouping, standard deviation 7 voxels
Only showing 60 of 110 regions.
Showing 60 of 110 region surfaces
Got 110 regions after smoothing 7 voxels.
Smoothing and grouping, standard deviation 8 voxels
Only showing 60 of 79 regions.
Showing 60 of 79 region surfaces
Got 79 regions after smoothing 8 voxels.
Smoothing and grouping, standard deviation 9 voxels
Showing 58 region surfaces
Got 58 regions after smoothing 9 voxels.
Smoothing and grouping, standard deviation 10 voxels
Showing 51 region surfaces
Got 51 regions after smoothing 10 voxels.
Smoothing and grouping, standard deviation 11 voxels
Showing 38 region surfaces
Got 38 regions after smoothing 11 voxels.
Smoothing and grouping, standard deviation 12 voxels
Showing 27 region surfaces
Got 27 regions after smoothing 12 voxels.
Smoothing and grouping, standard deviation 13 voxels
Showing 25 region surfaces
Got 25 regions after smoothing 13 voxels.
Smoothing and grouping, standard deviation 14 voxels
Showing 23 region surfaces
Got 23 regions after smoothing 14 voxels.
Smoothing and grouping, standard deviation 15 voxels
Showing 21 region surfaces
Got 21 regions after smoothing 15 voxels.
Smoothing and grouping, standard deviation 16 voxels
Showing 20 region surfaces
Got 20 regions after smoothing 16 voxels.
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!1 models
Drag select of 1560 residues
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select up
12774 atoms, 13156 bonds, 1669 residues, 1 model selected
> select up
16075 atoms, 16551 bonds, 2085 residues, 1 model selected
> select up
16135 atoms, 16614 bonds, 2092 residues, 1 model selected
> select up
24643 atoms, 25540 bonds, 2374 residues, 1 model selected
> select up
98986 atoms, 101446 bonds, 10930 residues, 1 model selected
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select down
24643 atoms, 25540 bonds, 2374 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 2160 residues
> select up
18167 atoms, 18680 bonds, 2323 residues, 1 model selected
> select up
21788 atoms, 22427 bonds, 2791 residues, 1 model selected
> select up
27395 atoms, 27810 bonds, 3336 residues, 1 model selected
> select up
74343 atoms, 75906 bonds, 8556 residues, 1 model selected
> select down
27395 atoms, 27810 bonds, 3336 residues, 1 model selected
> select down
21788 atoms, 22427 bonds, 2791 residues, 1 model selected
> select down
18167 atoms, 18680 bonds, 2323 residues, 1 model selected
> select down
16875 atoms, 2160 residues, 1 model selected
> select down
16875 atoms, 2160 residues, 1 model selected
> select down
16875 atoms, 2160 residues, 1 model selected
> select clear
Drag select of 1362 residues
> select up
11996 atoms, 12321 bonds, 1537 residues, 1 model selected
> select up
18061 atoms, 18604 bonds, 2316 residues, 1 model selected
> select up
22461 atoms, 22788 bonds, 2766 residues, 1 model selected
> select up
74343 atoms, 75906 bonds, 8556 residues, 1 model selected
> select up
74343 atoms, 75906 bonds, 8556 residues, 4 models selected
> select down
74343 atoms, 75906 bonds, 8556 residues, 1 model selected
> select down
22461 atoms, 22788 bonds, 2766 residues, 1 model selected
> select down
18061 atoms, 18604 bonds, 2316 residues, 1 model selected
> select up
22461 atoms, 22788 bonds, 2766 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 119 residues
Drag select of 59 residues
Drag select of 80 residues
Drag select of 32 residues
> select up
567 atoms, 579 bonds, 70 residues, 1 model selected
> select up
630 atoms, 627 bonds, 85 residues, 1 model selected
> select up
51882 atoms, 53118 bonds, 5790 residues, 1 model selected
> select down
630 atoms, 627 bonds, 85 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 83 residues
> select up
788 atoms, 812 bonds, 97 residues, 1 model selected
> select down
677 atoms, 83 residues, 1 model selected
> select up
788 atoms, 812 bonds, 97 residues, 1 model selected
> select up
1129 atoms, 1157 bonds, 144 residues, 1 model selected
> select up
1189 atoms, 1203 bonds, 162 residues, 1 model selected
> select up
51252 atoms, 52491 bonds, 5705 residues, 1 model selected
> select down
1189 atoms, 1203 bonds, 162 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 26 residues
> select up
293 atoms, 299 bonds, 39 residues, 1 model selected
> select up
452 atoms, 461 bonds, 60 residues, 1 model selected
> select up
570 atoms, 565 bonds, 78 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!1 models
> transparency #1.1 50
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
Smoothing and grouping, standard deviation 17 voxels
Showing 17 region surfaces
Got 17 regions after smoothing 17 voxels.
Ungrouped to 6 regions
> select add #3.23
1 model selected
> select add #3.13
2 models selected
> select add #3.2
3 models selected
> select add #3.7
4 models selected
> select add #3.20
5 models selected
> select add #3.4
6 models selected
> select add #3.22
7 models selected
> select add #3.9
8 models selected
> select add #3.1
9 models selected
> select add #3.19
10 models selected
> select add #3.5
11 models selected
Grouped 11 regions
Grouped 9 regions
Opened cryosparc_P124_J6672_map_imasked as #4, grid size 600,600,600, pixel
0.85, shown at step 1, values float32
> hide #!3 models
> select add #3
3 models selected
> select subtract #3
Nothing selected
> transparency #4.1 0
> save /Users/huanggq/Downloads/cryosparc_P124_J6672_map_half1_thre0p1.mrc
> models #4
> close #1-4
> open /Users/huanggq/Downloads/cryosparc_P124_J6654_007_volume_map.mrc
Opened cryosparc_P124_J6654_007_volume_map.mrc as #1, grid size 440,440,440,
pixel 0.835, shown at level 0.011, step 2, values float32
> volume #1 step 1
> volume #1 level 0.02932
> volume #1 level 0.05456
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/FV/FVPSI-LHCII/PDB/FV-PSI-
> LHCII-J6644.pdb
Chain information for FV-PSI-LHCII-J6644.pdb #2
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | 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
N | No description available
O | No description available
> hide atoms
> show cartoons
> hide #!1 models
> show #!1 models
> hide #3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> ui tool show "Color Actions"
> color bychain
> show #!1 models
> ui tool show "Color Zone"
> color zone #1 near #2 distance 5.01
> hide #!1 models
> show #!1 models
> hide #!2 models
> volume #1 level 0.09815
> hide #!1 models
> show #!1 models
> volume #1 level 0.08897
> volume #1 level 0.09
> ui tool show "Segment Map"
Segmenting cryosparc_P124_J6654_007_volume_map.mrc, density threshold 0.090000
Only showing 60 of 77 regions.
Showing 60 of 77 region surfaces
1084 watershed regions, grouped to 77 regions
Showing cryosparc_P124_J6654_007_volume_map.seg - 77 regions, 60 surfaces
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> open /Users/huanggq/Downloads/8j6z.pdb
8j6z.pdb title:
Cryo-em structure of the arabidopsis thaliana photosystem I(ψ-lhcii- ST2)
[more info...]
Chain information for 8j6z.pdb #4
---
Chain | Description | UniProt
1 | chlorophyll A-B binding protein 6, chloroplastic | CAB6_ARATH 1-241
2 | photosystem I chlorophyll A/B-binding protein 2, chloroplastic |
LHCA2_ARATH 1-257
3 | photosystem I chlorophyll A/B-binding protein 3-1, chloroplastic |
LHCA3_ARATH 1-273
4 | LHCI TYPE III CAB-4 | CA4_ARATH 1-251
A | photosystem I P700 chlorophyll A apoprotein A1 | PSAA_ARATH 1-750
B | photosystem I P700 chlorophyll A apoprotein A2 | PSAB_ARATH 1-734
C | photosystem I iron-sulfur center | PSAC_ARATH 1-81
D | photosystem I reaction center subunit II-2, chloroplastic | PSAD2_ARATH
1-204
E | ψ-E A | PSAE1_ARATH 1-143
F | photosystem I reaction center subunit III, chloroplastic | PSAF_ARATH
1-221
G | PSI-G | PSAG_ARATH 1-160
H | ψ-H1 | PSAH2_ARATH 1-145
I | PSI-I | PSAI_ARATH 1-37
J | PSI-J | PSAJ_ARATH 1-44
K | photosystem I reaction center subunit psak, chloroplastic | PSAK_ARATH
1-130
L | photosystem I reaction center subunit XI, chloroplastic | PSAL_ARATH 1-219
O | PSI-O | PSAO_ARATH 1-140
x y | chlorophyll A-B binding protein 2, chloroplastic | CB1A_ARATH -34-232
z | chlorophyll A-B binding protein 2.1, chloroplastic | CB21_ARATH -36-228
Non-standard residues in 8j6z.pdb #4
---
BCR — β-carotene
CHL — chlorophyll B
CL0 — chlorophyll A isomer
CLA — chlorophyll A
DGD — digalactosyl diacyl glycerol (DGDG)
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol; lutein)
NEX —
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol
((3S,5R,6R,3'S,5'R,6'S)-5',6'-epoxy-6,7-didehydro-
5,6,5',6'-tetrahydro-β,β-carotene-3,5,3'-triol; 9'-cis-
neoxanthin)
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)
SF4 — iron/sulfur cluster
XAT —
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-β,β-carotene-3,3'-diol
(violaxanthin)
> hide #!1 models
> hide #!4 atoms
> show #!4 cartoons
> ui tool show Matchmaker
> matchmaker #!4 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FV-PSI-LHCII-J6644.pdb, chain A (#2) with 8j6z.pdb, chain A (#4),
sequence alignment score = 3865.7
RMSD between 737 pruned atom pairs is 0.652 angstroms; (across all 737 pairs:
0.652)
> matchmaker #!4 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FV-PSI-LHCII-J6644.pdb, chain A (#2) with 8j6z.pdb, chain A (#4),
sequence alignment score = 3865.7
RMSD between 737 pruned atom pairs is 0.652 angstroms; (across all 737 pairs:
0.652)
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
Drag select of 2016 residues
> select up
17249 atoms, 17792 bonds, 2183 residues, 1 model selected
> select up
21710 atoms, 22407 bonds, 2751 residues, 1 model selected
> select up
30465 atoms, 31742 bonds, 2926 residues, 1 model selected
> select up
43924 atoms, 45757 bonds, 4227 residues, 1 model selected
> select down
30465 atoms, 31742 bonds, 2926 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 228 residues
> select up
2116 atoms, 2171 bonds, 281 residues, 1 model selected
> select up
2259 atoms, 2316 bonds, 302 residues, 1 model selected
> select up
3131 atoms, 3256 bonds, 322 residues, 1 model selected
> select up
13459 atoms, 14015 bonds, 1301 residues, 1 model selected
> select down
3131 atoms, 3256 bonds, 322 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 28 residues
> select up
574 atoms, 589 bonds, 78 residues, 1 model selected
> select up
1207 atoms, 1244 bonds, 160 residues, 1 model selected
> select up
1482 atoms, 1534 bonds, 166 residues, 1 model selected
> select up
10328 atoms, 10759 bonds, 979 residues, 1 model selected
> select down
1482 atoms, 1534 bonds, 166 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 49 residues
> select up
565 atoms, 585 bonds, 72 residues, 1 model selected
> select up
686 atoms, 710 bonds, 86 residues, 1 model selected
> select up
907 atoms, 945 bonds, 91 residues, 1 model selected
> select down
686 atoms, 710 bonds, 86 residues, 1 model selected
> select up
907 atoms, 945 bonds, 91 residues, 1 model selected
> select up
8846 atoms, 9225 bonds, 813 residues, 1 model selected
> select down
907 atoms, 945 bonds, 91 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> color #4 #a7ec92ff
> color #4 #31ec92ff
> style #!4 stick
Changed 7939 atom styles
> show #!4 atoms
> hide #!4 atoms
> select
> ::name="BCR"::name="CHL"::name="CLA"::name="DGD"::name="HTG"::name="LHG"::name="LMG"::name="LMT"::name="LUT"::name="NEX"::name="PQN"::name="SF4"::name="XAT"
14147 atoms, 15000 bonds, 872 pseudobonds, 279 residues, 4 models selected
> show sel & #!4 atoms
> select add #2
40962 atoms, 42682 bonds, 872 pseudobonds, 3691 residues, 4 models selected
> select subtract #2
2848 atoms, 3034 bonds, 169 pseudobonds, 57 residues, 2 models selected
> select add #4
7939 atoms, 8280 bonds, 179 pseudobonds, 722 residues, 2 models selected
> select subtract #4
Nothing selected
> show #!1 models
> fitmap #4 inMap #1
Fit molecule 8j6z.pdb (#4) to map cryosparc_P124_J6654_007_volume_map.mrc (#1)
using 7939 atoms
average map value = 0.1257, steps = 52
shifted from previous position = 2.46
rotated from previous position = 2.74 degrees
atoms outside contour = 2791, contour level = 0.09
Position of 8j6z.pdb (#4) relative to cryosparc_P124_J6654_007_volume_map.mrc
(#1) coordinates:
Matrix rotation and translation
-0.99978456 0.01440478 -0.01494454 368.77996412
-0.00958924 -0.95909134 -0.28293436 407.76419676
-0.01840879 -0.28273010 0.95902284 65.07248369
Axis 0.00842540 0.14289277 -0.98970231
Axis point 185.91690671 207.45034572 0.00000000
Rotation angle (degrees) 179.30545278
Shift along axis -3.02871094
> color zone #1 near #4 distance 5.01
> hide #!1 models
> show #!1 models
> color zone #1 near #4 distance 5.22
> color zone #1 near #4 distance 1.9
> hide #!4 models
> show #!2 models
> color zone #1 near #2 distance 1.9
> color #2 #7b4deeff
> color zone #1 near #2 distance 1.9
> hide #!1 models
> show #!1 models
> hide #!2 models
Segmenting cryosparc_P124_J6654_007_volume_map.mrc, density threshold 0.090000
Only showing 60 of 77 regions.
Showing 60 of 77 region surfaces
1084 watershed regions, grouped to 77 regions
Showing cryosparc_P124_J6654_007_volume_map.seg - 77 regions, 60 surfaces
Smoothing and grouping, standard deviation 5 voxels
Showing 35 region surfaces
Got 35 regions after smoothing 5 voxels.
Smoothing and grouping, standard deviation 6 voxels
Showing 26 region surfaces
Got 26 regions after smoothing 6 voxels.
> show #!2 models
> hide #!2 models
> show #!4 models
> transparency 50
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> transparency 0
> select add #3.5
1 model selected
> select subtract #3.5
Nothing selected
> select add #3.5
1 model selected
Ungrouped to 3 regions
Ungrouped to 7 regions
> select subtract #3.27
6 models selected
> select subtract #3.33
5 models selected
> select add #3.7
6 models selected
> select add #3.3
7 models selected
> select subtract #3.7
6 models selected
> select add #3.7
7 models selected
> select subtract #3.3
6 models selected
Grouped 6 regions
> select add #3.33
2 models selected
Grouped 2 regions
> select subtract #3.5
Nothing selected
> select add #3.27
1 model selected
Ungrouped to 5 regions
> select subtract #3.20
4 models selected
Grouped 4 regions
> select add #3.5
2 models selected
Grouped 2 regions
> select subtract #3.5
Nothing selected
> select add #3.17
1 model selected
Ungrouped to 2 regions
> select subtract #3.7
1 model selected
> select add #3.9
2 models selected
> select subtract #3.9
1 model selected
> select add #3.5
2 models selected
Grouped 2 regions
> select subtract #3.5
Nothing selected
> select add #3.6
1 model selected
Ungrouped to 3 regions
Ungrouped to 13 regions
> select subtract #3.26
12 models selected
Grouped 12 regions
> select subtract #3.6
Nothing selected
> select add #3.26
1 model selected
> select add #3.6
2 models selected
> select subtract #3.6
1 model selected
> select add #3.5
2 models selected
Grouped 2 regions
> select subtract #3.5
Nothing selected
> select add #3.8
1 model selected
Ungrouped to 3 regions
Ungrouped to 8 regions
Ungrouped to 24 regions
> select subtract #3.38
23 models selected
Grouped 23 regions
> select subtract #3.8
Nothing selected
> select add #3.3
1 model selected
Ungrouped to 2 regions
> select subtract #3.17
1 model selected
Grouped 1 regions
> select add #3.38
2 models selected
> select add #3.5
3 models selected
Grouped 3 regions
> select add #3
27 models selected
> transparency sel 50
> select subtract #3
Nothing selected
> hide #!3 models
> hide #!1 models
> show #!3 models
> show #!1 models
> transparency 0
> select add #3.3
1 model selected
Grouped 25 regions
Opened cryosparc_P124_J6654_007_volume_map_imasked as #5, grid size
440,440,440, pixel 0.835, shown at step 1, values float32
> hide #!3 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> ui mousemode right "map eraser"
> ui mousemode right "translate selected models"
> view matrix models #3.1,1,0,0,-4.0377,0,1,0,-5.836,0,0,1,9.519
> select add #6
2 models selected
> view matrix models
> #3.1,1,0,0,-12.465,0,1,0,-11.472,0,0,1,24.353,#6,1,0,0,175.67,0,1,0,149.92,0,0,1,248.47
> view matrix models
> #3.1,1,0,0,-10.763,0,1,0,-9.69,0,0,1,22.152,#6,1,0,0,177.38,0,1,0,151.7,0,0,1,246.27
> view matrix models
> #3.1,1,0,0,-9.585,0,1,0,-9.3898,0,0,1,22.169,#6,1,0,0,178.55,0,1,0,152,0,0,1,246.28
> volume erase #5 center 178.55,152,246.28 radius 7.1605
> view matrix models
> #3.1,1,0,0,-13.566,0,1,0,-12.274,0,0,1,21.1,#6,1,0,0,174.57,0,1,0,149.12,0,0,1,245.22
> view matrix models
> #3.1,1,0,0,-13.808,0,1,0,-12.25,0,0,1,20.474,#6,1,0,0,174.33,0,1,0,149.14,0,0,1,244.59
> volume erase #5 center 174.33,149.14,244.59 radius 7.1605
> view matrix models
> #3.1,1,0,0,-17.482,0,1,0,-17.61,0,0,1,14.804,#6,1,0,0,170.66,0,1,0,143.78,0,0,1,238.92
> view matrix models
> #3.1,1,0,0,-17.799,0,1,0,-16.542,0,0,1,16.105,#6,1,0,0,170.34,0,1,0,144.85,0,0,1,240.22
> view matrix models
> #3.1,1,0,0,-18.778,0,1,0,-16.359,0,0,1,15.47,#6,1,0,0,169.36,0,1,0,145.04,0,0,1,239.59
> view matrix models
> #3.1,1,0,0,-18.796,0,1,0,-16.067,0,0,1,15.17,#6,1,0,0,169.34,0,1,0,145.33,0,0,1,239.29
> volume erase #5 center 169.34,145.33,239.29 radius 7.1605
> view matrix models
> #3.1,1,0,0,-9.2654,0,1,0,-14.414,0,0,1,20.193,#6,1,0,0,178.87,0,1,0,146.98,0,0,1,244.31
> volume erase #5 center 178.87,146.98,244.31 radius 7.1605
> view matrix models
> #3.1,1,0,0,-18.928,0,1,0,-26.814,0,0,1,7.9312,#6,1,0,0,169.21,0,1,0,134.58,0,0,1,232.05
> view matrix models
> #3.1,1,0,0,-19.044,0,1,0,-26.591,0,0,1,7.6567,#6,1,0,0,169.1,0,1,0,134.8,0,0,1,231.77
> volume erase #5 center 169.1,134.8,231.77 radius 7.1605
> save
> /Users/huanggq/Downloads/cryosparc_P124_J6654_007_volume_map_4subtract_thre0p09.mrc
> models #5
> select subtract #6
1 model selected
> hide #6 models
> hide #!5 models
> open /Users/huanggq/Downloads/cryosparc_P124_J6677_mask.mrc
Opened cryosparc_P124_J6677_mask.mrc as #7, grid size 440,440,440, pixel
0.835, shown at level 5e-05, step 2, values float32
> show #!1 models
> volume #7 step 1
> volume #7 level 0.4985
> volume #7 level 0.9772
> hide #!1 models
> transparency #7.1 50
> show #!1 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> close #7
> ui tool show "Volume Viewer"
> open /Users/huanggq/Downloads/cryosparc_P124_J6677_mask.mrc
Opened cryosparc_P124_J6677_mask.mrc as #6, grid size 440,440,440, pixel
0.835, shown at level 5e-05, step 2, values float32
> volume #6 step 1
> volume #6 level 0.4622
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> volume #6 level 1
> volume #5 level 0.1068
> close #5
> close #6
> show #!4 models
> close #3-4
> close #1
> show #!2 models
> open /Users/huanggq/Downloads/8j6z.pdb
8j6z.pdb title:
Cryo-em structure of the arabidopsis thaliana photosystem I(ψ-lhcii- ST2)
[more info...]
Chain information for 8j6z.pdb #1
---
Chain | Description | UniProt
1 | chlorophyll A-B binding protein 6, chloroplastic | CAB6_ARATH 1-241
2 | photosystem I chlorophyll A/B-binding protein 2, chloroplastic |
LHCA2_ARATH 1-257
3 | photosystem I chlorophyll A/B-binding protein 3-1, chloroplastic |
LHCA3_ARATH 1-273
4 | LHCI TYPE III CAB-4 | CA4_ARATH 1-251
A | photosystem I P700 chlorophyll A apoprotein A1 | PSAA_ARATH 1-750
B | photosystem I P700 chlorophyll A apoprotein A2 | PSAB_ARATH 1-734
C | photosystem I iron-sulfur center | PSAC_ARATH 1-81
D | photosystem I reaction center subunit II-2, chloroplastic | PSAD2_ARATH
1-204
E | ψ-E A | PSAE1_ARATH 1-143
F | photosystem I reaction center subunit III, chloroplastic | PSAF_ARATH
1-221
G | PSI-G | PSAG_ARATH 1-160
H | ψ-H1 | PSAH2_ARATH 1-145
I | PSI-I | PSAI_ARATH 1-37
J | PSI-J | PSAJ_ARATH 1-44
K | photosystem I reaction center subunit psak, chloroplastic | PSAK_ARATH
1-130
L | photosystem I reaction center subunit XI, chloroplastic | PSAL_ARATH 1-219
O | PSI-O | PSAO_ARATH 1-140
x y | chlorophyll A-B binding protein 2, chloroplastic | CB1A_ARATH -34-232
z | chlorophyll A-B binding protein 2.1, chloroplastic | CB21_ARATH -36-228
Non-standard residues in 8j6z.pdb #1
---
BCR — β-carotene
CHL — chlorophyll B
CL0 — chlorophyll A isomer
CLA — chlorophyll A
DGD — digalactosyl diacyl glycerol (DGDG)
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol; lutein)
NEX —
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol
((3S,5R,6R,3'S,5'R,6'S)-5',6'-epoxy-6,7-didehydro-
5,6,5',6'-tetrahydro-β,β-carotene-3,5,3'-triol; 9'-cis-
neoxanthin)
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)
SF4 — iron/sulfur cluster
XAT —
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-β,β-carotene-3,3'-diol
(violaxanthin)
> hide atoms
> show cartoons
> ui tool show Matchmaker
> matchmaker #!1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FV-PSI-LHCII-J6644.pdb, chain A (#2) with 8j6z.pdb, chain A (#1),
sequence alignment score = 3865.7
RMSD between 737 pruned atom pairs is 0.652 angstroms; (across all 737 pairs:
0.652)
> hide #!2 models
> hide #!1 models
> open /Users/huanggq/Downloads/cryosparc_P124_J6682_volume_map.mrc
Opened cryosparc_P124_J6682_volume_map.mrc as #3, grid size 440,440,440, pixel
0.835, shown at level 0.0125, step 2, values float32
> volume #3 level 0.04822
> volume #3 step 1
> open /Users/huanggq/Downloads/cryosparc_P124_J6682_volume_mask_fsc.mrc
Opened cryosparc_P124_J6682_volume_mask_fsc.mrc as #4, grid size 440,440,440,
pixel 0.835, shown at level 5e-05, step 2, values float32
> volume #4 level 0.05032
> hide #!3 models
> show #!3 models
> volume #4 step 1
> close #3
> close #4
> open /Users/huanggq/Downloads/cryosparc_P124_J6685_volume_map.mrc
Opened cryosparc_P124_J6685_volume_map.mrc as #3, grid size 256,256,256, pixel
0.835, shown at level 0.0325, step 1, values float32
> volume #3 level 0.04218
> volume #3 level 0.06146
> volume #3 level 0.05012
> open /Users/huanggq/Downloads/cryosparc_P124_J6685_volume_mask_fsc.mrc
Opened cryosparc_P124_J6685_volume_mask_fsc.mrc as #4, grid size 256,256,256,
pixel 0.835, shown at level 1, step 1, values float32
> volume #4 level 0.9749
> hide #!4 models
> close #3-4
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/FV/FVPSI-
> LHCII/map/cryosparc_P124_J6644_010_volume_map_sharp.mrc
Opened cryosparc_P124_J6644_010_volume_map_sharp.mrc as #3, grid size
440,440,440, pixel 0.835, shown at level 0.0848, step 2, values float32
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/FV/FVPSI-LHCII/PDB/FV-PSI-
> LHCII-J6644-coot-0.pdb
Chain information for FV-PSI-LHCII-J6644-coot-0.pdb #4
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | 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
N | No description available
O | No description available
> volume #3 level 0.1893
> volume #3 step 1
> hide #!4 atoms
> show #!4 cartoons
> close #3-4
> open /Users/huanggq/Downloads/cryosparc_P124_J6686_001_volume_map.mrc
Opened cryosparc_P124_J6686_001_volume_map.mrc as #3, grid size 440,440,440,
pixel 0.835, shown at level 0.00591, step 2, values float32
> volume #3 step 1
> volume #3 level 0.07957
> close #3
> open /Users/huanggq/Downloads/cryosparc_P124_J6681_004_volume_map.mrc
Opened cryosparc_P124_J6681_004_volume_map.mrc as #3, grid size 600,600,600,
pixel 0.85, shown at level 0.11, step 4, values float32
> volume #3 step 2
> volume #3 step 1
> volume #3 level 0.1729
> volume #3 level 0.2355
> volume #3 level 0.1473
> volume #3 level 0.1937
> close #3
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/FV/FVPSI-
> LHCII/phenix/RealSpaceRefine_1/FV-PSI-
> LHCII-J6644-coot-0_real_space_refined.pdb
Chain information for FV-PSI-LHCII-J6644-coot-0_real_space_refined.pdb #3
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | 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
N | No description available
O | No description available
> hide #!3 atoms
> show #!3 cartoons
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/FV/FVPSI-
> LHCII/map/cryosparc_P124_J6644_010_volume_map_sharp.mrc
Opened cryosparc_P124_J6644_010_volume_map_sharp.mrc as #4, grid size
440,440,440, pixel 0.835, shown at level 0.0848, step 2, values float32
> volume #4 step 1
> volume #4 level 0.1719
> hide #!4 models
> color #3 #af88f3ff
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> open /Users/huanggq/Downloads/cryosparc_P124_J6644_010_volume_map.mrc
Opened cryosparc_P124_J6644_010_volume_map.mrc as #5, grid size 440,440,440,
pixel 0.835, shown at level 0.0499, step 2, values float32
> volume #5 step 1
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> volume #5 level 0.04
> ui mousemode right "map eraser"
> select add #6
1 model selected
> volume #5 level 0.1281
> select subtract #6
Nothing selected
> close #6
> hide #!5 models
> show #!5 models
> show #!3 models
> hide #!5 models
> show #!5 models
> ui tool show "Color Actions"
> color bychain
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> volume erase #5 center 217.56,96.878,184.77 radius 108.75
Opened cryosparc_P124_J6644_010_volume_map.mrc copy as #7, grid size
440,440,440, pixel 0.835, shown at step 1, values float32
> volume #7 level 0.1
> volume #7 level 0.05
> volume #7 level 0.06
> volume #7 level 0.05
> hide #!7 models
> show #!7 models
> hide #6 models
> show #6 models
> hide #!3 models
> show #!3 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> volume erase #7 center 182.61,90.931,320.33 radius 108.75
> volume erase #7 center 136.38,114.89,193.98 radius 77.889
> volume erase #7 center 137.9,109.84,162.35 radius 77.889
> volume #7 level 0.1095
> hide #6 models
> hide #!3 models
> hide #!7 models
> show #!5 models
> show #!3 models
> hide #!5 models
> select add #3/1:222
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3/4:229
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #3/2:250
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add #3/3:219
32 atoms, 28 bonds, 4 residues, 1 model selected
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select up
479 atoms, 488 bonds, 61 residues, 1 model selected
> select up
6480 atoms, 6709 bonds, 825 residues, 1 model selected
> select up
10197 atoms, 10673 bonds, 900 residues, 1 model selected
> select up
38114 atoms, 39648 bonds, 3634 residues, 1 model selected
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select down
10197 atoms, 10673 bonds, 900 residues, 1 model selected
> color sel cyan
> show #!5 models
> volume #7 level 0.08809
> ui tool show "Color Zone"
> color zone #5 near sel distance 5.01
> hide #!7 models
> volume #5 level 0.09539
> volume #5 level 0.05
> volume #5 level 0.06
> volume #5 level 0.08
> volume splitbyzone #5
Opened cryosparc_P124_J6644_010_volume_map.mrc 0 as #8.1, grid size
440,440,440, pixel 0.835, shown at level 0.08, step 1, values float32
Opened cryosparc_P124_J6644_010_volume_map.mrc 1 as #8.2, grid size
440,440,440, pixel 0.835, shown at level 0.08, step 1, values float32
> hide #!8 models
> show #!8 models
> hide #!8.1 models
> volume #8.2 level 0.07
> volume #8.2 level 0.05
> save /Users/huanggq/Downloads/cryosparc_P124_J6644_010_volume_map_LHCI-
> belt_thre0p05.mrc models #8.2
> close
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/FV/FVPSI-LHCII/PDB/FV-PSI-
> LHCII-J6644-coot-2.pdb
Chain information for FV-PSI-LHCII-J6644-coot-2.pdb #1
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | 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
N | No description available
O | No description available
> hide atoms
> show cartoons
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/FV/FVPSI-LHCII/PDB/FV-
> PSI-J6643-coot-8.pdb
Chain information for FV-PSI-J6643-coot-8.pdb #2
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | 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
N | No description available
O | No description available
> hide #!2 models
> close #2
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/FV_Aa-PSI/FVPSI-
> model-0726/FvPSI_J94-230921-coot-2.pdb
Chain information for FvPSI_J94-230921-coot-2.pdb #2
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | 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
N | No description available
O | No description available
> hide atoms
> show cartoons
> lighting soft
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FV-PSI-LHCII-J6644-coot-2.pdb, chain A (#1) with
FvPSI_J94-230921-coot-2.pdb, chain A (#2), sequence alignment score = 3885.5
RMSD between 742 pruned atom pairs is 0.258 angstroms; (across all 742 pairs:
0.258)
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FV-PSI-LHCII-J6644-coot-2.pdb, chain A (#1) with
FvPSI_J94-230921-coot-2.pdb, chain A (#2), sequence alignment score = 3885.5
RMSD between 742 pruned atom pairs is 0.258 angstroms; (across all 742 pairs:
0.258)
> color #2 #87ce3aff
> select
> ::name="BCR"::name="CHL"::name="CLA"::name="DGD"::name="HTG"::name="LHG"::name="LMG"::name="LMT"::name="LUT"::name="PQN"::name="SF4"::name="XAT"
22573 atoms, 23900 bonds, 1398 pseudobonds, 445 residues, 4 models selected
> show sel atoms
> select add #2
49388 atoms, 51582 bonds, 1398 pseudobonds, 3857 residues, 4 models selected
> select add #1
76203 atoms, 79264 bonds, 1398 pseudobonds, 7269 residues, 4 models selected
> select subtract #1
38187 atoms, 39722 bonds, 703 pseudobonds, 3637 residues, 2 models selected
> select subtract #2
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> close #1-2
> open /Users/huanggq/Downloads/cryosparc_P124_J6644_010_volume_map.mrc
Opened cryosparc_P124_J6644_010_volume_map.mrc as #1, grid size 440,440,440,
pixel 0.835, shown at level 0.0499, step 2, values float32
> volume #1 step 1
> volume #1 level 0.2351
> select add #2
1 model selected
> volume #1 level 0.1189
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> volume #1 level 0.05
> volume erase #1 center 208.17,128.42,177.98 radius 82.481
Opened cryosparc_P124_J6644_010_volume_map.mrc copy as #3, grid size
440,440,440, pixel 0.835, shown at step 1, values float32
> volume #3 level 0.1386
> volume #3 level 0.05
> volume erase #3 center 179.4,113.14,286.45 radius 82.481
> volume erase #3 center 89.131,124.23,193.81 radius 82.481
> volume erase #3 center 106.94,109.46,155.59 radius 82.481
> select subtract #2
Nothing selected
> hide #2 models
> save /Users/huanggq/Downloads/cryosparc_P124_J6644_010_volume_map_LHCI-
> belt_thre0p05.mrc models #3
> hide #!3 models
> open /Users/huanggq/Downloads/cryosparc_P124_J6688_cluster_000.mrc
Opened cryosparc_P124_J6688_cluster_000.mrc as #4, grid size 440,440,440,
pixel 0.835, shown at level 0.00715, step 2, values float32
> volume #4 level 0.02739
> volume #4 step 1
> volume #4 level 0.05432
> open /Users/huanggq/Downloads/cryosparc_P124_J6688_cluster_002.mrc
Opened cryosparc_P124_J6688_cluster_002.mrc as #5, grid size 440,440,440,
pixel 0.835, shown at level 0.00679, step 2, values float32
> volume #5 step 1
> volume #5 level 0.05447
> volume #4 level 0.06838
> volume #5 level 0.06486
> volume #4 level 0.03302
> volume #4 level 0.03
> volume #5 level 0.03
> hide #!5 models
> close #2#1,3-5
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/FV_Aa-PSI/FVPSI-
> model-0726/FvPSI_J94-230921-coot-2.pdb
Chain information for FvPSI_J94-230921-coot-2.pdb #1
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | 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
N | No description available
O | No description available
> close #1
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/FV/FVPSI-LHCII/PDB/FV-PSI-
> LHCII-J6644-coot-7.pdb
Chain information for FV-PSI-LHCII-J6644-coot-7.pdb #1
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | 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
N | No description available
O | No description available
> hide atoms
> show cartoons
> lighting soft
> select
> ::name="BCR"::name="CHL"::name="CLA"::name="DGD"::name="HTG"::name="LHG"::name="LMG"::name="LUT"::name="PQN"::name="SF4"::name="XAT"
11166 atoms, 11824 bonds, 695 pseudobonds, 219 residues, 2 models selected
> show sel atoms
> select add #1
37972 atoms, 39497 bonds, 695 pseudobonds, 3630 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/FV_Aa-PSI/FVPSI-
> model-0726/FvPSI_J94-230921-coot-2.pdb
Chain information for FvPSI_J94-230921-coot-2.pdb #2
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | 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
N | No description available
O | No description available
> show #!1 models
> hide atoms
> show cartoons
> color #2 #87ce34ff
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FV-PSI-LHCII-J6644-coot-7.pdb, chain A (#1) with
FvPSI_J94-230921-coot-2.pdb, chain A (#2), sequence alignment score = 3852.5
RMSD between 742 pruned atom pairs is 0.282 angstroms; (across all 742 pairs:
0.282)
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/FV/FVPSI-LHCII/PDB/FV-
> PSI-J6643-coot-8.pdb
Chain information for FV-PSI-J6643-coot-8.pdb #3
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | 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
N | No description available
O | No description available
> hide atoms
> show cartoons
> color #3 #dd03ddff
> ui tool show Matchmaker
> matchmaker #!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 FV-PSI-LHCII-J6644-coot-7.pdb, chain B (#1) with FV-
PSI-J6643-coot-8.pdb, chain B (#3), sequence alignment score = 3896.6
RMSD between 733 pruned atom pairs is 0.204 angstroms; (across all 733 pairs:
0.204)
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> open /Users/huanggq/Downloads/cryosparc_P124_J6695_002_volume_map.mrc
Opened cryosparc_P124_J6695_002_volume_map.mrc as #4, grid size 440,440,440,
pixel 0.835, shown at level 0.0084, step 2, values float32
> open /Users/huanggq/Downloads/cryosparc_P124_J6696_001_volume_map.mrc
Opened cryosparc_P124_J6696_001_volume_map.mrc as #5, grid size 440,440,440,
pixel 0.835, shown at level 0.00617, step 2, values float32
> volume #4 step 1
> volume #4 level 0.04117
> volume #4 level 0.07651
> volume #5 step 1
> volume #5 level 0.06039
> close #5
> open /Users/huanggq/Downloads/cryosparc_P124_J6696_002_volume_map.mrc
Opened cryosparc_P124_J6696_002_volume_map.mrc as #5, grid size 440,440,440,
pixel 0.835, shown at level 0.00897, step 2, values float32
> volume #5 level 0.0317
> volume #5 step 1
> volume #5 level 0.07324
> open /Users/huanggq/Downloads/8j6z.pdb
8j6z.pdb title:
Cryo-em structure of the arabidopsis thaliana photosystem I(ψ-lhcii- ST2)
[more info...]
Chain information for 8j6z.pdb #6
---
Chain | Description | UniProt
1 | chlorophyll A-B binding protein 6, chloroplastic | CAB6_ARATH 1-241
2 | photosystem I chlorophyll A/B-binding protein 2, chloroplastic |
LHCA2_ARATH 1-257
3 | photosystem I chlorophyll A/B-binding protein 3-1, chloroplastic |
LHCA3_ARATH 1-273
4 | LHCI TYPE III CAB-4 | CA4_ARATH 1-251
A | photosystem I P700 chlorophyll A apoprotein A1 | PSAA_ARATH 1-750
B | photosystem I P700 chlorophyll A apoprotein A2 | PSAB_ARATH 1-734
C | photosystem I iron-sulfur center | PSAC_ARATH 1-81
D | photosystem I reaction center subunit II-2, chloroplastic | PSAD2_ARATH
1-204
E | ψ-E A | PSAE1_ARATH 1-143
F | photosystem I reaction center subunit III, chloroplastic | PSAF_ARATH
1-221
G | PSI-G | PSAG_ARATH 1-160
H | ψ-H1 | PSAH2_ARATH 1-145
I | PSI-I | PSAI_ARATH 1-37
J | PSI-J | PSAJ_ARATH 1-44
K | photosystem I reaction center subunit psak, chloroplastic | PSAK_ARATH
1-130
L | photosystem I reaction center subunit XI, chloroplastic | PSAL_ARATH 1-219
O | PSI-O | PSAO_ARATH 1-140
x y | chlorophyll A-B binding protein 2, chloroplastic | CB1A_ARATH -34-232
z | chlorophyll A-B binding protein 2.1, chloroplastic | CB21_ARATH -36-228
Non-standard residues in 8j6z.pdb #6
---
BCR — β-carotene
CHL — chlorophyll B
CL0 — chlorophyll A isomer
CLA — chlorophyll A
DGD — digalactosyl diacyl glycerol (DGDG)
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol; lutein)
NEX —
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol
((3S,5R,6R,3'S,5'R,6'S)-5',6'-epoxy-6,7-didehydro-
5,6,5',6'-tetrahydro-β,β-carotene-3,5,3'-triol; 9'-cis-
neoxanthin)
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)
SF4 — iron/sulfur cluster
XAT —
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-β,β-carotene-3,3'-diol
(violaxanthin)
> hide #!6 atoms
> show #!6 cartoons
> ui tool show Matchmaker
> matchmaker #!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 FV-PSI-LHCII-J6644-coot-7.pdb, chain A (#1) with 8j6z.pdb, chain A
(#6), sequence alignment score = 3839.3
RMSD between 736 pruned atom pairs is 0.660 angstroms; (across all 737 pairs:
0.664)
> hide #!4 models
Drag select of 2851 residues
> select up
23224 atoms, 23965 bonds, 2955 residues, 1 model selected
> select up
24583 atoms, 25368 bonds, 3129 residues, 1 model selected
> select up
34238 atoms, 35668 bonds, 3324 residues, 1 model selected
> select up
43924 atoms, 45757 bonds, 4227 residues, 1 model selected
> select down
34238 atoms, 35668 bonds, 3324 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 82 residues
> select clear
Drag select of 58 residues
> select up
879 atoms, 901 bonds, 119 residues, 1 model selected
> select up
1279 atoms, 1309 bonds, 170 residues, 1 model selected
> select up
1747 atoms, 1809 bonds, 181 residues, 1 model selected
> select up
9686 atoms, 10089 bonds, 903 residues, 1 model selected
> select down
1747 atoms, 1809 bonds, 181 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show "Fit in Map"
> fitmap #6 inMap #4
Fit molecule 8j6z.pdb (#6) to map cryosparc_P124_J6695_002_volume_map.mrc (#4)
using 7939 atoms
average map value = 0.09055, steps = 56
shifted from previous position = 2.55
rotated from previous position = 2.76 degrees
atoms outside contour = 3341, contour level = 0.076514
Position of 8j6z.pdb (#6) relative to cryosparc_P124_J6695_002_volume_map.mrc
(#4) coordinates:
Matrix rotation and translation
-0.99980311 0.01435483 -0.01369979 368.54177644
-0.00991352 -0.95941905 -0.28180988 407.71615498
-0.01718917 -0.28161858 0.95937245 64.35345056
Axis 0.00780218 0.14231536 -0.98979062
Axis point 185.78827761 207.34327292 0.00000000
Rotation angle (degrees) 179.29757428
Shift along axis -2.79673889
> volume #4 level 0.07844
> select
> ::name="BCR"::name="CHL"::name="CLA"::name="DGD"::name="HTG"::name="LHG"::name="LMG"::name="LMT"::name="LUT"::name="NEX"::name="PQN"::name="SF4"::name="XAT"
36685 atoms, 38864 bonds, 2270 pseudobonds, 723 residues, 8 models selected
> show sel & #!6 atoms
> select add #6
41776 atoms, 44110 bonds, 2280 pseudobonds, 1388 residues, 8 models selected
> select subtract #6
33837 atoms, 35830 bonds, 2101 pseudobonds, 666 residues, 6 models selected
> transparency #4.1 50
Drag select of 4 cryosparc_P124_J6695_002_volume_map.mrc , 59 atoms, 12
residues, 7 pseudobonds, 69 bonds
> select add #6
41776 atoms, 44110 bonds, 2280 pseudobonds, 1388 residues, 10 models selected
> select subtract #6
33837 atoms, 35830 bonds, 2101 pseudobonds, 666 residues, 8 models selected
> select subtract #4
33837 atoms, 35830 bonds, 2101 pseudobonds, 666 residues, 6 models selected
> hide #!6 models
> volume #5 level 0.07664
> transparency 0
> show #!6 models
> transparency 50
> hide #!6 models
> show #!5 models
> show #!4 models
> transparency 0
> close
> open /Users/huanggq/Downloads/cryosparc_P124_J6698_class_00_00040_volume.mrc
Opened cryosparc_P124_J6698_class_00_00040_volume.mrc as #1, grid size
180,180,180, pixel 2.83, shown at level 0.635, step 1, values float32
> volume #1 level 0.9702
> volume #1 level 0.5967
> volume #1 level 0.6996
> open /Users/huanggq/Downloads/cryosparc_P124_J6698_class_02_00040_volume.mrc
Opened cryosparc_P124_J6698_class_02_00040_volume.mrc as #3, grid size
180,180,180, pixel 2.83, shown at level 0.651, step 1, values float32
> hide #2 models
> volume #3 level 0.8287
> show #!3 models
> hide #!3 models
> close
> open /Users/huanggq/Downloads/cryosparc_P124_J6705_003_volume_map.mrc
Opened cryosparc_P124_J6705_003_volume_map.mrc as #1, grid size 600,600,600,
pixel 0.85, shown at level 0.118, step 4, values float32
> volume #1 step 1
> volume #1 level 0.171
> volume #1 level 0.2243
> close #1
> open /Users/huanggq/Downloads/cryosparc_P124_J6697_cluster_001.mrc
Opened cryosparc_P124_J6697_cluster_001.mrc as #1, grid size 600,600,600,
pixel 0.85, shown at level 0.118, step 4, values float32
> volume #1 step 1
> volume #1 level 0.1429
> volume #1 level 0.1201
> hide #!1 models
> open /Users/huanggq/Downloads/cryosparc_P124_J6696_006_volume_map.mrc
Opened cryosparc_P124_J6696_006_volume_map.mrc as #2, grid size 440,440,440,
pixel 0.835, shown at level 0.0136, step 2, values float32
> open /Users/huanggq/Downloads/cryosparc_P124_J6695_007_volume_map.mrc
Opened cryosparc_P124_J6695_007_volume_map.mrc as #4, grid size 440,440,440,
pixel 0.835, shown at level 0.0135, step 2, values float32
> hide #3 models
> volume #4 step 1
> volume #4 level 0.07599
> volume #4 level 0.09182
> volume #2 step 1
> volume #2 level 0.08263
> volume #2 level 0.1005
> volume #4 level 0.09622
> volume #2 level 0.1439
> close
> open /Users/huanggq/Downloads/cryosparc_P124_J6681_006_volume_map.mrc
Opened cryosparc_P124_J6681_006_volume_map.mrc as #1, grid size 600,600,600,
pixel 0.85, shown at level 0.11, step 4, values float32
> volume #1 step 2
> volume #1 step 1
> volume #1 level 0.368
> volume #1 level 0.3262
> close #1
> open /Users/huanggq/Desktop/J6681_006_volume_map_EMReady.mrc
Opened J6681_006_volume_map_EMReady.mrc as #1, grid size 1019,1019,1019, pixel
0.5, shown at step 1, values float32
> volume #1 region 0,0,0,1018,1018,1018 step 4
> volume #1 style surface region 0,0,0,1018,1018,1018 step 4
> hide #2 models
> volume #1 change image level -0.08693,0 level 5.363,0.8 level 18.16,1
> volume #1 level 1.503
> volume #1 step 2
> volume #1 level 6.019
> volume #1 step 1
> volume #1 style image region 0,0,509,1018,1018,509 step 1 showOutlineBox
> true
> hide #!1 models
> close #2#1
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/FV/FVPSI-LHCII/PDB/FV-PSI-
> LHCII-J6644-coot-7.pdb
Chain information for FV-PSI-LHCII-J6644-coot-7.pdb #1
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | 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
N | No description available
O | No description available
> hide atoms
> show cartoons
> hide cartoons
> select
> ::name="BCR"::name="CHL"::name="CLA"::name="DGD"::name="HTG"::name="LHG"::name="LMG"::name="LUT"::name="PQN"::name="SF4"::name="XAT"
11166 atoms, 11824 bonds, 695 pseudobonds, 219 residues, 2 models selected
> show sel atoms
> select add #1
37972 atoms, 39497 bonds, 695 pseudobonds, 3630 residues, 2 models selected
> select subtract #1
Nothing selected
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/FV_Aa-PSI/FVPSI-
> model-0726/FvPSI_J94-230921-coot-2.pdb
Chain information for FvPSI_J94-230921-coot-2.pdb #2
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | 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
N | No description available
O | No description available
> hide atoms
> select
> ::name="BCR"::name="CHL"::name="CLA"::name="DGD"::name="HTG"::name="LHG"::name="LMG"::name="LMT"::name="LUT"::name="PQN"::name="SF4"::name="XAT"
22538 atoms, 23864 bonds, 1398 pseudobonds, 444 residues, 4 models selected
> show sel atoms
> select add #2
49353 atoms, 51546 bonds, 1398 pseudobonds, 3856 residues, 4 models selected
> select subtract #2
11166 atoms, 11824 bonds, 695 pseudobonds, 219 residues, 2 models selected
> select add #1
37972 atoms, 39497 bonds, 695 pseudobonds, 3630 residues, 2 models selected
> select subtract #1
Nothing selected
> ui tool show "Color Actions"
> color bychain
> color #2 #fffc79ff
> color #2 #73fa79ff
> color #2 #76d6ffff
> color #2 #d783ffff
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FV-PSI-LHCII-J6644-coot-7.pdb, chain A (#1) with
FvPSI_J94-230921-coot-2.pdb, chain A (#2), sequence alignment score = 3852.5
RMSD between 742 pruned atom pairs is 0.282 angstroms; (across all 742 pairs:
0.282)
> hide #!2 models
> open /Users/huanggq/Downloads/7f4v.cif
Summary of feedback from opening /Users/huanggq/Downloads/7f4v.cif
---
notes | Fetching CCD CL0 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/0/CL0/CL0.cif
Fetching CCD CLA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CLA/CLA.cif
Fetching CCD 1L3 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/3/1L3/1L3.cif
Fetching CCD SF4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SF4/SF4.cif
Fetching CCD BCR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/BCR/BCR.cif
Fetching CCD LHG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/LHG/LHG.cif
Fetching CCD LMG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/LMG/LMG.cif
7f4v.cif title:
Cryo-EM structure of a primordial cyanobacterial photosystem I [more info...]
Chain information for 7f4v.cif #3
---
Chain | Description | UniProt
aA bA cA | Photosystem I P700 chlorophyll a apoprotein A1 | PSAA_GLOVI 1-783
aB bB cB | Photosystem I P700 chlorophyll a apoprotein A2 | PSAB_GLOVI 1-872
aC bC cC | Photosystem I iron-sulfur center | PSAC_GLOVI 1-81
aD bD cD | Photosystem I reaction center subunit II | PSAD_GLOVI 1-144
aE bE cE | Photosystem I reaction center subunit IV | PSAE_GLOVI 1-65
aF bF cF | Photosystem I reaction center subunit III | PSAF_GLOVI 1-181
aI bI cI | Photosystem I reaction center subunit Z | PSAZ_GLOVI 1-35
aJ bJ cJ | Unknown protein |
aL bL cL | Photosystem I reaction center subunit XI | PSAL_GLOVI 1-147
aM bM cM | Photosystem I reaction center subunit XII | PSAM_GLOVI 1-34
Non-standard residues in 7f4v.cif #3
---
1L3 — Menaquinone-4 (vitamin K2)
BCR — β-carotene
CL0 — chlorophyll A isomer
CLA — chlorophyll A
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
SF4 — iron/sulfur cluster
> hide #!1 models
> hide #!3 atoms
> show #!3 cartoons
> hide #!3 cartoons
> select
> ::name="1L3"::name="BCR"::name="CHL"::name="CL0"::name="CLA"::name="DGD"::name="HOH"::name="HTG"::name="LHG"::name="LMG"::name="LMT"::name="LUT"::name="PQN"::name="SF4"::name="XAT"
40280 atoms, 42365 bonds, 2511 pseudobonds, 1200 residues, 6 models selected
> show sel & #!3 atoms
> select add #3
90179 atoms, 93797 bonds, 2568 pseudobonds, 7635 residues, 6 models selected
> select add #2
116994 atoms, 121479 bonds, 2568 pseudobonds, 11047 residues, 6 models
selected
> select add #1
143800 atoms, 149152 bonds, 2568 pseudobonds, 14458 residues, 6 models
selected
> select subtract #1
105828 atoms, 109655 bonds, 1873 pseudobonds, 10828 residues, 4 models
selected
> select subtract #2
67641 atoms, 69933 bonds, 1170 pseudobonds, 7191 residues, 2 models selected
> select subtract #3
Nothing selected
> ui tool show Matchmaker
> matchmaker #!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 FV-PSI-LHCII-J6644-coot-7.pdb, chain B (#1) with 7f4v.cif, chain aB
(#3), sequence alignment score = 3145.7
RMSD between 680 pruned atom pairs is 0.535 angstroms; (across all 714 pairs:
1.362)
> show #!1 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 #!1 models
> show #!1 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 #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #3/aB
8251 atoms, 8564 bonds, 172 pseudobonds, 842 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #3/aB #3/bB #3/cB
Alignment identifier is 1
> show sel cartoons
> select add #3
67641 atoms, 69933 bonds, 1170 pseudobonds, 7191 residues, 2 models selected
> select subtract #3
Nothing selected
> select #3/aB,bB,cB:717
21 atoms, 21 bonds, 3 residues, 1 model selected
> select #3/aB,bB,cB:717-727
222 atoms, 231 bonds, 33 residues, 1 model selected
> select
> #3/aB,bB,cB:9-14,18-27,30-34,38-80,97-105,119-127,131-156,164-181,183-203,211-215,222-227,229-239,257-276,288-296,307-341,350-383,392-432,434-438,443-453,466-471,475-484,495-522,531-535,553-585,587-595,597-615,626-668,684-716
12288 atoms, 12651 bonds, 1530 residues, 1 model selected
> select #3/aB,bB,cB:717-727
222 atoms, 231 bonds, 33 residues, 1 model selected
> select #3/aB,bB,cB:716
36 atoms, 36 bonds, 3 residues, 1 model selected
> select #3/aB,bB,cB:704-716
291 atoms, 297 bonds, 39 residues, 1 model selected
> show #!1 models
> show sel cartoons
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show sel cartoons
> select add #3
67641 atoms, 69933 bonds, 1170 pseudobonds, 7191 residues, 2 models selected
> select subtract #3
Nothing selected
> show #!1,3 cartoons
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> hide #!3 cartoons
> hide #!3 models
> show #!2 models
> show #!1 models
> hide #!1-2 atoms
> show #!1-2 cartoons
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/FV/FVPSI-
> LHCII/map/cryosparc_P124_J6654_007_volume_map_sharp.mrc
Opened cryosparc_P124_J6654_007_volume_map_sharp.mrc as #4, grid size
440,440,440, pixel 0.835, shown at level 0.0629, step 2, values float32
> volume #4 step 1
> volume #4 level 0.1842
> lighting soft
> show #!3 models
> hide #5 models
> hide #!3 atoms
> show #!3 cartoons
> close #3
> open /Users/huanggq/Downloads/8j6z.pdb
8j6z.pdb title:
Cryo-em structure of the arabidopsis thaliana photosystem I(ψ-lhcii- ST2)
[more info...]
Chain information for 8j6z.pdb #3
---
Chain | Description | UniProt
1 | chlorophyll A-B binding protein 6, chloroplastic | CAB6_ARATH 1-241
2 | photosystem I chlorophyll A/B-binding protein 2, chloroplastic |
LHCA2_ARATH 1-257
3 | photosystem I chlorophyll A/B-binding protein 3-1, chloroplastic |
LHCA3_ARATH 1-273
4 | LHCI TYPE III CAB-4 | CA4_ARATH 1-251
A | photosystem I P700 chlorophyll A apoprotein A1 | PSAA_ARATH 1-750
B | photosystem I P700 chlorophyll A apoprotein A2 | PSAB_ARATH 1-734
C | photosystem I iron-sulfur center | PSAC_ARATH 1-81
D | photosystem I reaction center subunit II-2, chloroplastic | PSAD2_ARATH
1-204
E | ψ-E A | PSAE1_ARATH 1-143
F | photosystem I reaction center subunit III, chloroplastic | PSAF_ARATH
1-221
G | PSI-G | PSAG_ARATH 1-160
H | ψ-H1 | PSAH2_ARATH 1-145
I | PSI-I | PSAI_ARATH 1-37
J | PSI-J | PSAJ_ARATH 1-44
K | photosystem I reaction center subunit psak, chloroplastic | PSAK_ARATH
1-130
L | photosystem I reaction center subunit XI, chloroplastic | PSAL_ARATH 1-219
O | PSI-O | PSAO_ARATH 1-140
x y | chlorophyll A-B binding protein 2, chloroplastic | CB1A_ARATH -34-232
z | chlorophyll A-B binding protein 2.1, chloroplastic | CB21_ARATH -36-228
Non-standard residues in 8j6z.pdb #3
---
BCR — β-carotene
CHL — chlorophyll B
CL0 — chlorophyll A isomer
CLA — chlorophyll A
DGD — digalactosyl diacyl glycerol (DGDG)
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol; lutein)
NEX —
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol
((3S,5R,6R,3'S,5'R,6'S)-5',6'-epoxy-6,7-didehydro-
5,6,5',6'-tetrahydro-β,β-carotene-3,5,3'-triol; 9'-cis-
neoxanthin)
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)
SF4 — iron/sulfur cluster
XAT —
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-β,β-carotene-3,3'-diol
(violaxanthin)
> hide #!3 atoms
> show #!3 cartoons
> select add #3
43924 atoms, 45757 bonds, 844 pseudobonds, 4227 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.87356,0.48665,-0.007688,243.94,-0.4306,-0.78013,-0.45386,477.78,-0.22687,-0.39317,0.89104,130.31
> view matrix models
> #3,-0.99851,0.02563,0.048146,335.74,-0.040796,-0.93684,-0.34737,416.03,0.036203,-0.34881,0.93649,67.49
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.99851,0.02563,0.048146,350.15,-0.040796,-0.93684,-0.34737,430.88,0.036203,-0.34881,0.93649,70.616
> fitmap #3 inMap #4
Fit molecule 8j6z.pdb (#3) to map
cryosparc_P124_J6654_007_volume_map_sharp.mrc (#4) using 43924 atoms
average map value = 0.01038, steps = 2000
shifted from previous position = 3.1
rotated from previous position = 3.97 degrees
atoms outside contour = 42437, contour level = 0.18421
Position of 8j6z.pdb (#3) relative to
cryosparc_P124_J6654_007_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.99974337 -0.02262472 -0.00115075 371.65491292
0.02155579 -0.93442770 -0.35549996 420.03457161
0.00696780 -0.35543353 0.93467559 77.22770514
Axis 0.00147882 -0.18073222 0.98353123
Axis point 183.37048266 219.23497155 0.00000000
Rotation angle (degrees) 178.71302014
Shift along axis 0.59168741
> view matrix models
> #3,-0.99974,-0.022625,-0.0011507,372.21,0.021556,-0.93443,-0.3555,417.74,0.0069678,-0.35543,0.93468,79.894
> fitmap #3 inMap #4
Fit molecule 8j6z.pdb (#3) to map
cryosparc_P124_J6654_007_volume_map_sharp.mrc (#4) using 43924 atoms
average map value = 0.05212, steps = 2000
shifted from previous position = 6.34
rotated from previous position = 4.61 degrees
atoms outside contour = 38702, contour level = 0.18421
Position of 8j6z.pdb (#3) relative to
cryosparc_P124_J6654_007_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.99965611 0.01150550 -0.02356463 371.58596757
-0.00417225 -0.95694569 -0.29023706 408.29780183
-0.02588939 -0.29003893 0.95666460 68.42175606
Axis 0.01249992 0.14666902 -0.98910664
Axis point 187.04413431 208.47741559 0.00000000
Rotation angle (degrees) 179.54591442
Shift along axis -3.14698238
> select subtract #3
Nothing selected
> volume #4 level 0.2419
> volume #4 level 0.1553
> hide #!4 models
Drag select of 1793 residues
> select up
15493 atoms, 15972 bonds, 1964 residues, 1 model selected
> select up
21710 atoms, 22407 bonds, 2751 residues, 1 model selected
> select up
30465 atoms, 31742 bonds, 2926 residues, 1 model selected
> select up
43924 atoms, 45757 bonds, 4227 residues, 1 model selected
> select up
120083 atoms, 124976 bonds, 11494 residues, 6 models selected
> select down
43924 atoms, 45757 bonds, 4227 residues, 1 model selected
> select down
30465 atoms, 31742 bonds, 2926 residues, 1 model selected
> select down
21710 atoms, 22407 bonds, 2751 residues, 1 model selected
> select up
30465 atoms, 31742 bonds, 2926 residues, 1 model selected
> select up
43924 atoms, 45757 bonds, 4227 residues, 1 model selected
> select down
30465 atoms, 31742 bonds, 2926 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 58 residues
Drag select of 7 residues
> select add #3/K:55
510 atoms, 7 bonds, 66 residues, 1 model selected
> select add #3/O:133
519 atoms, 15 bonds, 67 residues, 1 model selected
> select up
1322 atoms, 1358 bonds, 171 residues, 1 model selected
> select up
4152 atoms, 4270 bonds, 548 residues, 1 model selected
> select up
5520 atoms, 5735 bonds, 579 residues, 1 model selected
> select up
13459 atoms, 14015 bonds, 1301 residues, 1 model selected
> select down
5520 atoms, 5735 bonds, 579 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> fitmap #3 inMap #4
Fit molecule 8j6z.pdb (#3) to map
cryosparc_P124_J6654_007_volume_map_sharp.mrc (#4) using 7939 atoms
average map value = 0.2731, steps = 48
shifted from previous position = 0.178
rotated from previous position = 0.627 degrees
atoms outside contour = 2536, contour level = 0.15534
Position of 8j6z.pdb (#3) relative to
cryosparc_P124_J6654_007_volume_map_sharp.mrc (#4) coordinates:
Matrix rotation and translation
-0.99977180 0.01414902 -0.01600518 369.10214140
-0.00903866 -0.95901961 -0.28319552 407.71505227
-0.01935622 -0.28298623 0.95892864 65.29507485
Axis 0.00893289 0.14302655 -0.98967854
Axis point 186.05358754 207.48331356 0.00000000
Rotation angle (degrees) 179.32877884
Shift along axis -3.00990756
> save /Users/huanggq/Desktop/1/HGQ_MAC/project/FV/FVPSI-
> LHCII/PDB/8j6z_LHCII_J6654.pdb models #3 relModel #4
> close #5#1-4
> open /Users/huanggq/Downloads/cryosparc_P124_J6737_003_volume_map.mrc
Opened cryosparc_P124_J6737_003_volume_map.mrc as #1, grid size 220,220,220,
pixel 2.3, shown at level 0.181, step 1, values float32
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/轮藻PSI/4xk8_J258.pdb
4xk8_J258.pdb title:
Crystal structure of plant photosystem I-LHCI super-complex At 2.8 angstrom
resolution [more info...]
Chain information for 4xk8_J258.pdb #2
---
Chain | Description | UniProt
1 | chlorophyll A-B binding protein 6, chloroplastic |
2 | type II chlorophyll A/B binding protein from photosystem I | Q41038_PEA
52-257
3 | lhcii TYPE III CAB-3 | CB23_PEA 49-266
4 | LHCI TYPE III CAB-P4 |
A | photosystem I P700 chlorophyll A apoprotein A1 |
B | photosystem I P700 chlorophyll A apoprotein A2 |
C | photosystem I iron-sulfur center | PSAC_PEA 2-81
D | uncharacterized protein | I1NGD2_SOYBN 70-210
E | putative uncharacterized protein |
F | photosystem I reaction center subunit III, chloroplastic |
G | photosystem I reaction center subunit V, chloroplastic |
H | putative uncharacterized protein |
I | PSI-I | PSAI_PEA 2-31
J | PSI-J | PSAJ_PHAVU 1-39
K | photosystem I reaction center subunit X psak | B6TR16_MAIZE 1-134
L | putative uncharacterized protein | E1C9L1_PEA 4-156
N | No description available | B6TXS5_MAIZE 1-145
O | No description available |
Non-standard residues in 4xk8_J258.pdb #2
---
BCR — β-carotene
CHL — chlorophyll B
CLA — chlorophyll A
DGD — digalactosyl diacyl glycerol (DGDG)
HTG — heptyl 1-thio-β-D-glucopyranoside
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
LMT — dodecyl-β-D-maltoside
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol; lutein)
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)
SF4 — iron/sulfur cluster
XAT —
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-β,β-carotene-3,3'-diol
(violaxanthin)
> hide atoms
> show cartoons
> select add #1
2 models selected
> select subtract #1
Nothing selected
> select add #2
38341 atoms, 39755 bonds, 853 pseudobonds, 3747 residues, 2 models selected
> view matrix models #2,1,0,0,157.8,0,1,0,91.689,0,0,1,192.09
> ui mousemode right "rotate selected models"
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/huanggq/Downloads/cryosparc_P124_J6737_003_volume_map.mrc
Opened cryosparc_P124_J6737_003_volume_map.mrc as #1, grid size 220,220,220,
pixel 2.3, shown at level 0.181, step 1, values float32
> set bgColor white
> lighting soft
> open /Users/huanggq/Desktop/1/HGQ_MAC/project/轮藻PSI/4xk8_J258.pdb
4xk8_J258.pdb title:
Crystal structure of plant photosystem I-LHCI super-complex At 2.8 angstrom
resolution [more info...]
Chain information for 4xk8_J258.pdb #2
---
Chain | Description | UniProt
1 | chlorophyll A-B binding protein 6, chloroplastic |
2 | type II chlorophyll A/B binding protein from photosystem I | Q41038_PEA
52-257
3 | lhcii TYPE III CAB-3 | CB23_PEA 49-266
4 | LHCI TYPE III CAB-P4 |
A | photosystem I P700 chlorophyll A apoprotein A1 |
B | photosystem I P700 chlorophyll A apoprotein A2 |
C | photosystem I iron-sulfur center | PSAC_PEA 2-81
D | uncharacterized protein | I1NGD2_SOYBN 70-210
E | putative uncharacterized protein |
F | photosystem I reaction center subunit III, chloroplastic |
G | photosystem I reaction center subunit V, chloroplastic |
H | putative uncharacterized protein |
I | PSI-I | PSAI_PEA 2-31
J | PSI-J | PSAJ_PHAVU 1-39
K | photosystem I reaction center subunit X psak | B6TR16_MAIZE 1-134
L | putative uncharacterized protein | E1C9L1_PEA 4-156
N | No description available | B6TXS5_MAIZE 1-145
O | No description available |
Non-standard residues in 4xk8_J258.pdb #2
---
BCR — β-carotene
CHL — chlorophyll B
CLA — chlorophyll A
DGD — digalactosyl diacyl glycerol (DGDG)
HTG — heptyl 1-thio-β-D-glucopyranoside
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
LMT — dodecyl-β-D-maltoside
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol; lutein)
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)
SF4 — iron/sulfur cluster
XAT —
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-β,β-carotene-3,3'-diol
(violaxanthin)
> hide atoms
> show cartoons
> select add #2
38341 atoms, 39755 bonds, 853 pseudobonds, 3747 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,135.97,0,1,0,113.38,0,0,1,196.39
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.89347,-0.39089,0.22116,383.11,0.33723,-0.90913,-0.24444,334.26,0.29662,-0.14382,0.94411,185.13
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule 4xk8_J258.pdb (#2) to map cryosparc_P124_J6737_003_volume_map.mrc
(#1) using 38341 atoms
average map value = 0.2567, steps = 116
shifted from previous position = 18.1
rotated from previous position = 15.9 degrees
atoms outside contour = 12275, contour level = 0.18079
Position of 4xk8_J258.pdb (#2) relative to
cryosparc_P124_J6737_003_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.98080667 -0.18536092 0.06049463 386.63611238
0.16565321 -0.95580135 -0.24290492 368.56173266
0.10284593 -0.22822164 0.96816197 200.27023090
Axis 0.04149407 -0.11968222 0.99194476
Axis point 171.64595645 213.42249599 0.00000000
Rotation angle (degrees) 169.80887457
Shift along axis 170.58982776
> select subtract #2
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!1 models
Drag select of 258 residues
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select up
3187 atoms, 3294 bonds, 403 residues, 1 model selected
> select up
4753 atoms, 4918 bonds, 605 residues, 1 model selected
> select up
7756 atoms, 8093 bonds, 679 residues, 1 model selected
> select up
38341 atoms, 39755 bonds, 3747 residues, 1 model selected
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select down
7756 atoms, 8093 bonds, 679 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 3 residues
> select up
260 atoms, 265 bonds, 35 residues, 1 model selected
> select up
1727 atoms, 1791 bonds, 220 residues, 1 model selected
> select up
2603 atoms, 2727 bonds, 243 residues, 1 model selected
> select up
30585 atoms, 31662 bonds, 3068 residues, 1 model selected
> select down
2603 atoms, 2727 bonds, 243 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!1 models
> volume #1 level 0.2498
> select add /F:89
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /N:126
17 atoms, 15 bonds, 2 residues, 1 model selected
> select up
234 atoms, 234 bonds, 29 residues, 1 model selected
> select up
1879 atoms, 1925 bonds, 235 residues, 1 model selected
> hide #!1 models
> select up
1895 atoms, 1940 bonds, 237 residues, 1 model selected
> select up
2248 atoms, 2309 bonds, 251 residues, 1 model selected
> select up
27982 atoms, 28935 bonds, 2825 residues, 1 model selected
> select down
2248 atoms, 2309 bonds, 251 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!1 models
> transparency 50
> hide #!1 models
> show #!1 models
> transparency 0
> volume #1 level 0.3027
> select add /J:18
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
257 atoms, 263 bonds, 32 residues, 1 model selected
> select up
311 atoms, 319 bonds, 39 residues, 1 model selected
> select up
412 atoms, 425 bonds, 42 residues, 1 model selected
> select up
25734 atoms, 26626 bonds, 2574 residues, 1 model selected
> select down
412 atoms, 425 bonds, 42 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add /O:50
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
115 atoms, 118 bonds, 16 residues, 1 model selected
> select up
720 atoms, 746 bonds, 90 residues, 1 model selected
> select up
956 atoms, 994 bonds, 97 residues, 1 model selected
> select up
25322 atoms, 26201 bonds, 2532 residues, 1 model selected
> select down
956 atoms, 994 bonds, 97 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save /Users/huanggq/Desktop/4xk8-J6737.pdb relModel #1
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,1
Model Number: MK193CH/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 8419.60.44
OS Loader Version: 8419.60.44
Software:
System Software Overview:
System Version: macOS 13.1 (22C65)
Kernel Version: Darwin 22.2.0
Time since boot: 4天19小时59分钟
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
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: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 16 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 16 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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