![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17490 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.4.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001fbd38c80 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, lxml._elementpath, lxml.etree, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._webp (total: 57)
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"procRole" : "Background",
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"incident" : "17066075-C267-4054-AF61-7A3ABFFC7D8A",
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"procLaunch" : "2025-04-26 15:28:40.0717 +0200",
"procStartAbsTime" : 860536920718,
"procExitAbsTime" : 1341854477037,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "D935C5C0-045E-C264-7256-02B1A9F3C542",
"appleIntelligenceStatus" : {"reasons":["notOptedIn","selectedLanguageDoesNotMatchSelectedSiriLanguage","siriAssetIsNotReady"],"state":"unavailable"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "FFA93159-B7D2-408B-993D-B29EA665412F",
"sleepWakeUUID" : "664E032B-F730-4732-ABAB-746FEE1E0945",
"sip" : "enabled",
"vmRegionInfo" : "0x168 is not in any region. Bytes before following region: 4339990168\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102af0000-102af4000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000168","rawCodes":[1,360],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000168"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":21562},
"vmregioninfo" : "0x168 is not in any region. Bytes before following region: 4339990168\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102af0000-102af4000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/nones_formathandler.cpython-311-darwin.so",
"name" : "nones_formathandler.cpython-311-darwin.so"
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{
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"uuid" : "a55a4181-c446-3fa3-8fd6-27f845527eab",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_osx.abi3.so",
"name" : "_psutil_osx.abi3.so"
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{
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"arch" : "arm64",
"base" : 5778538496,
"size" : 16384,
"uuid" : "a516c5bc-1157-318a-a306-5c9b350e0c09",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_posix.abi3.so",
"name" : "_psutil_posix.abi3.so"
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{
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"size" : 32768,
"uuid" : "8abbdcef-1901-3d4b-9e6b-a38214b79214",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so",
"name" : "_imagingmath.cpython-311-darwin.so"
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{
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"arch" : "arm64",
"base" : 5773312000,
"size" : 737280,
"uuid" : "cc06500d-d418-3365-b197-36b1304a819e",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGL.abi3.so",
"name" : "QtOpenGL.abi3.so"
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{
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"arch" : "arm64",
"base" : 5532631040,
"size" : 49152,
"uuid" : "b32a8c32-a5e0-3a8b-9a0d-00a26b160215",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGLWidgets.abi3.so",
"name" : "QtOpenGLWidgets.abi3.so"
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{
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"arch" : "arm64",
"base" : 5520621568,
"size" : 49152,
"uuid" : "cd4f396b-89fe-36fd-a488-6f5b3d4b0282",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtOpenGLWidgets.framework\/Versions\/A\/QtOpenGLWidgets",
"name" : "QtOpenGLWidgets"
},
{
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"arch" : "arm64",
"base" : 5976031232,
"size" : 475136,
"uuid" : "0c6e9a11-e483-3d7d-a88f-8ad0507af167",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
"name" : "mmcif.cpython-311-darwin.so"
},
{
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"arch" : "arm64",
"base" : 5962203136,
"size" : 409600,
"uuid" : "1ab8e5e2-c699-3efb-8f77-d375e3793c8f",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
"name" : "_mmcif.cpython-311-darwin.so"
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{
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"arch" : "arm64",
"base" : 5174673408,
"size" : 81920,
"uuid" : "3133c77c-8bf7-32a3-b5db-cbfe2e50ce9d",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
"name" : "_ribbons.cpython-311-darwin.so"
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{
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"base" : 5174853632,
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"uuid" : "de871a78-14f2-3e72-9bde-e4f2c7493f1b",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
"name" : "_graphics.cpython-311-darwin.so"
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{
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"uuid" : "1e310bc7-5f96-396b-816d-5b40a3dde12c",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
"name" : "_pdbio.cpython-311-darwin.so"
},
{
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"arch" : "arm64",
"base" : 5172674560,
"size" : 16384,
"uuid" : "90797215-312d-32b5-979a-1ad6584ca6ca",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/mmap.cpython-311-darwin.so",
"name" : "mmap.cpython-311-darwin.so"
},
{
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"base" : 5181095936,
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"uuid" : "8e643d65-26b4-33bb-955a-181387c9c6f8",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_webp.cpython-311-darwin.so",
"name" : "_webp.cpython-311-darwin.so"
},
{
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"uuid" : "a638d617-da17-3d03-9ecf-b5af8a9cffe2",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libwebp.7.dylib",
"name" : "libwebp.7.dylib"
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{
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"uuid" : "2c35f97e-b9a7-3870-9f66-4b252682556c",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libwebpmux.3.dylib",
"name" : "libwebpmux.3.dylib"
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{
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"uuid" : "34221167-6136-38da-95c4-9a3b859d54f9",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libwebpdemux.2.dylib",
"name" : "libwebpdemux.2.dylib"
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{
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"uuid" : "0016bb66-b2b7-386a-8d07-278e6bd2d518",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libsharpyuv.0.dylib",
"name" : "libsharpyuv.0.dylib"
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"uuid" : "225cb279-20a9-381d-a163-d2be263f5327",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
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"legacyInfo" : {
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"queue" : "com.apple.main-thread"
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}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/haoranfu/Downloads/cryosparc_P40_J444_015_volume_map.mrc
Opened cryosparc_P40_J444_015_volume_map.mrc as #1, grid size 440,440,440,
pixel 0.573, shown at level 0.0223, step 2, values float32
> open /Users/haoranfu/Downloads/cryosparc_P40_J443_014_volume_map.mrc
Opened cryosparc_P40_J443_014_volume_map.mrc as #2, grid size 440,440,440,
pixel 0.573, shown at level 0.0224, step 2, values float32
> volume #1 level 0.02949
> volume #2 level 0.03112
> volume #2 level 0.01776
> volume #2 level 0.05186
> volume #1 level 0.03883
> volume #2 level 0.03251
> surface dust #2 size 5.73
> close #1
> close #2
> open /Users/haoranfu/Downloads/cryosparc_P40_J439_011_volume_map.mrc
Opened cryosparc_P40_J439_011_volume_map.mrc as #1, grid size 440,440,440,
pixel 0.573, shown at level 0.0225, step 2, values float32
> open /Users/haoranfu/Downloads/cryosparc_P40_J438_014_volume_map.mrc
Opened cryosparc_P40_J438_014_volume_map.mrc as #2, grid size 440,440,440,
pixel 0.573, shown at level 0.0225, step 2, values float32
> volume #1 level 0.03612
> close #1
> close #2
> open /Users/haoranfu/Downloads/cryosparc_P40_J442_cluster_000.mrc
Opened cryosparc_P40_J442_cluster_000.mrc as #1, grid size 440,440,440, pixel
0.573, shown at level 0.0218, step 2, values float32
> open /Users/haoranfu/Downloads/cryosparc_P40_J442_cluster_001.mrc
Opened cryosparc_P40_J442_cluster_001.mrc as #2, grid size 440,440,440, pixel
0.573, shown at level 0.0221, step 2, values float32
> open /Users/haoranfu/Downloads/cryosparc_P40_J442_cluster_002.mrc
Opened cryosparc_P40_J442_cluster_002.mrc as #3, grid size 440,440,440, pixel
0.573, shown at level 0.0219, step 2, values float32
> volume #3 level 0.02977
> volume #2 level 0.02957
> volume #1 level 0.03002
> close #1
> close #2
> close #3
> open /Users/haoranfu/Downloads/run_it050_class003.mrc
Opened run_it050_class003.mrc as #1, grid size 104,104,104, pixel 2.29, shown
at level 0.0336, step 1, values float32
> open /Users/haoranfu/Downloads/run_it050_class002.mrc
Opened run_it050_class002.mrc as #2, grid size 104,104,104, pixel 2.29, shown
at level 0.0403, step 1, values float32
> open /Users/haoranfu/Downloads/run_it050_class001.mrc
Opened run_it050_class001.mrc as #3, grid size 104,104,104, pixel 2.29, shown
at level 0.0374, step 1, values float32
> volume #2 level 0.001904
> close #1
> close #3
> close #2
> open
> /Users/haoranfu/Desktop/mine/data/Data_processing/2024_04_08_cyddc_CRYO_SPARC/NU_refine__cydDC_box416.mrc
Opened NU_refine__cydDC_box416.mrc as #1, grid size 416,416,416, pixel 0.573,
shown at level 0.0239, step 2, values float32
> open
> /Users/haoranfu/Desktop/mine/data/Data_processing/2024_04_08_cyddc_CRYO_SPARC/NU_refine_nomask_cydDC_box440.mrc
Opened NU_refine_nomask_cydDC_box440.mrc as #2, grid size 440,440,440, pixel
0.573, shown at level 0.0221, step 2, values float32
> fitmap #1 inMap #2
Fit map NU_refine__cydDC_box416.mrc in map NU_refine_nomask_cydDC_box440.mrc
using 89978 points
correlation = 0.5212, correlation about mean = 0.07628, overlap = 67.48
steps = 72, shift = 1.57, angle = 0.924 degrees
Position of NU_refine__cydDC_box416.mrc (#1) relative to
NU_refine_nomask_cydDC_box440.mrc (#2) coordinates:
Matrix rotation and translation
0.99994842 0.00745207 -0.00690046 1.03401953
-0.00736507 0.99989414 0.01254817 0.14514317
0.00699324 -0.01249670 0.99989746 1.51003904
Axis -0.77667264 -0.43086121 -0.45949780
Axis point 0.00000000 63.14443179 42.51338384
Rotation angle (degrees) 0.92383036
Shift along axis -1.55949085
> select add #1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.99995,0.0074521,-0.0069005,2.1576,-0.0073651,0.99989,0.012548,8.1541,0.0069932,-0.012497,0.9999,4.9941
> fitmap #1 inMap #2
Fit map NU_refine__cydDC_box416.mrc in map NU_refine_nomask_cydDC_box440.mrc
using 89978 points
correlation = 0.9937, correlation about mean = 0.9728, overlap = 211.1
steps = 84, shift = 5.6, angle = 0.931 degrees
Position of NU_refine__cydDC_box416.mrc (#1) relative to
NU_refine_nomask_cydDC_box440.mrc (#2) coordinates:
Matrix rotation and translation
0.99999999 0.00011760 -0.00005705 6.86747790
-0.00011761 0.99999996 -0.00025875 6.92014706
0.00005702 0.00025876 0.99999996 6.84229871
Axis 0.89258965 -0.19673289 -0.40568447
Axis point 0.00000000 -29562.65435451 28263.64445210
Rotation angle (degrees) 0.01660981
Shift along axis 1.99260480
> volume #2 level 0.0302
> volume #1 level 0.02344
> surface dust #2 size 5.73
> view matrix models
> #1,1,0.0001176,-5.7047e-05,5.8148,-0.00011761,1,-0.00025875,7.1545,5.7017e-05,0.00025876,1,14.509
> volume #1 level 0.01872
> volume #1 level 0.00738
> volume #1 level 0.03194
> surface dust #1 size 5.73
> volume #2 level 0.03259
> surface dust #2 size 5.73
> volume #2 level 0.07126
> volume #2 level 0.02924
> volume #1 level 0.0173
> fitmap #1 inMap #2
Fit map NU_refine__cydDC_box416.mrc in map NU_refine_nomask_cydDC_box440.mrc
using 138729 points
correlation = 0.6746, correlation about mean = 0.2569, overlap = 124.3
steps = 92, shift = 3.56, angle = 2.24 degrees
Position of NU_refine__cydDC_box416.mrc (#1) relative to
NU_refine_nomask_cydDC_box440.mrc (#2) coordinates:
Matrix rotation and translation
0.99924259 -0.03717572 0.01149869 10.20711285
0.03719033 0.99930764 -0.00105897 4.50098852
-0.01145136 0.00148581 0.99993333 12.84193160
Axis 0.03268045 0.29472855 0.95502202
Axis point -5.79036417 262.44118568 0.00000000
Rotation angle (degrees) 2.23132971
Shift along axis 13.92447041
> open /Users/haoranfu/Downloads/emd_22457.map
Opened emd_22457.map as #3, grid size 256,256,256, pixel 1.05, shown at level
2.36, step 1, values float32
> open
> /Users/haoranfu/Desktop/mine/data/Data_processing/Nact/cryosparc_P42_J212_011_volume_map.mrc
Opened cryosparc_P42_J212_011_volume_map.mrc as #4, grid size 160,160,160,
pixel 1.15, shown at level 0.0861, step 1, values float32
> open
> /Users/haoranfu/Desktop/mine/data/Data_processing/Nact/NaCT_apo_NU_refine.mrc
Opened NaCT_apo_NU_refine.mrc as #5, grid size 320,320,320, pixel 0.573, shown
at level 0.0286, step 2, values float32
> view matrix models
> #1,0.99924,-0.037176,0.011499,-23.02,0.03719,0.99931,-0.001059,0.46276,-0.011451,0.0014858,0.99993,-30.304
> view matrix models
> #1,0.99924,-0.037176,0.011499,-50.176,0.03719,0.99931,-0.001059,-4.0396,-0.011451,0.0014858,0.99993,-66.597
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.99924,-0.037176,0.011499,-79.471,0.03719,0.99931,-0.001059,-7.9812,-0.011451,0.0014858,0.99993,-104.96
> view matrix models
> #1,0.99924,-0.037176,0.011499,-95.589,0.03719,0.99931,-0.001059,-9.1788,-0.011451,0.0014858,0.99993,-125.24
> select subtract #1
Nothing selected
> ui mousemode right "rotate selected models"
> select add #4
2 models selected
> view matrix models
> #4,-0.94342,-0.32747,0.05215,203.24,-0.33159,0.93035,-0.15651,50.989,0.0027364,-0.16495,-0.9863,195.58
> fitmap #4 inMap #5
Fit map cryosparc_P42_J212_011_volume_map.mrc in map NaCT_apo_NU_refine.mrc
using 40890 points
correlation = 0.5083, correlation about mean = 0.01695, overlap = 122
steps = 136, shift = 4.15, angle = 10.9 degrees
Position of cryosparc_P42_J212_011_volume_map.mrc (#4) relative to
NaCT_apo_NU_refine.mrc (#5) coordinates:
Matrix rotation and translation
-0.98693200 -0.16081353 -0.01020943 197.71272290
-0.15514236 0.96542651 -0.20948148 40.51770033
0.04354390 -0.20516006 -0.97775931 195.68536920
Axis 0.07969542 -0.99131735 0.10458752
Axis point 99.14399812 0.00000000 101.33430080
Rotation angle (degrees) 178.44640240
Shift along axis -3.94285474
> volume filp #4
Expected a density maps specifier or a keyword
> volume flip #4
Opened cryosparc_P42_J212_011_volume_map.mrc z flip as #6, grid size
160,160,160, pixel 1.15, shown at step 1, values float32
> fitmap #5 inMap #6
Fit map NaCT_apo_NU_refine.mrc in map cryosparc_P42_J212_011_volume_map.mrc z
flip using 40901 points
correlation = 0.9561, correlation about mean = 0.7806, overlap = 350.6
steps = 112, shift = 8.23, angle = 10.6 degrees
Position of NaCT_apo_NU_refine.mrc (#5) relative to
cryosparc_P42_J212_011_volume_map.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.99904745 -0.01621160 0.04051403 180.80508238
-0.01987401 0.99558866 -0.09169650 14.86628881
-0.03884875 -0.09241433 -0.99496250 195.11226813
Axis -0.00903497 0.99889612 -0.04609678
Axis point 92.41233737 0.00000000 96.10045174
Rotation angle (degrees) 177.72331218
Shift along axis 4.22226231
> volume #5 level 0.0323
> volume #6 level 0.07129
> volume #6 level 0.03084
> volume #4 level 0.1697
> volume #6 level 0.1495
> volume #5 level 0.03719
> volume #6 level 0.1023
> close #4
> volume #3 level 11.24
> surface dust #3 size 10.5
> surface dust #6 size 11.5
> volume #3 level 9.487
> surface dust #3 size 10.5
> surface dust #6 size 11.5
> surface dust #3 size 10.5
> surface dust #6 size 11.5
> surface dust #3 size 10.5
> surface dust #6 size 11.5
> select add #3
2 models selected
> view matrix models
> #3,-0.37518,0.45482,-0.8077,227.11,-0.9239,-0.25419,0.28602,253.23,-0.075223,0.85354,0.51557,-41.051
> view matrix models
> #3,-0.097274,0.67529,-0.73111,150.77,-0.23959,0.6971,0.67576,-15.279,0.96599,0.2409,0.093983,-43.322
> ui mousemode right "move picked models"
> view matrix models
> #3,-0.097274,0.67529,-0.73111,120.33,-0.23959,0.6971,0.67576,-51.339,0.96599,0.2409,0.093983,-82.623
> view matrix models
> #3,-0.097274,0.67529,-0.73111,120.21,-0.23959,0.6971,0.67576,-49.765,0.96599,0.2409,0.093983,-81.33
> view matrix models
> #3,-0.097274,0.67529,-0.73111,116.74,-0.23959,0.6971,0.67576,-58.349,0.96599,0.2409,0.093983,-78.953
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.39972,-0.40734,-0.82115,206.65,0.16149,0.91312,-0.37435,-4.4632,0.9023,0.017033,0.43077,-84.262
> fitmap #3 inMap #6
Fit map emd_22457.map in map cryosparc_P42_J212_011_volume_map.mrc z flip
using 39548 points
correlation = 0.5409, correlation about mean = 0.04596, overlap = 3.031e+04
steps = 328, shift = 3.26, angle = 17.4 degrees
Position of emd_22457.map (#3) relative to
cryosparc_P42_J212_011_volume_map.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.13230601 0.14690715 0.98026191 -44.61575484
-0.04161212 0.98726083 -0.15357243 -22.08476534
-0.99033507 -0.06110933 -0.12450743 241.68696977
Axis 0.04665725 0.99437108 -0.09512757
Axis point 82.36251663 0.00000000 138.41289445
Rotation angle (degrees) 97.74568488
Shift along axis -47.03319477
> close #3
> open /Users/haoranfu/Downloads/7jsk.cif
Summary of feedback from opening /Users/haoranfu/Downloads/7jsk.cif
---
note | Fetching CCD CIT from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/CIT/CIT.cif
7jsk.cif title:
Structure of the NaCT-Citrate complex [more info...]
Chain information for 7jsk.cif #3
---
Chain | Description | UniProt
A B | Solute carrier family 13 member 5 | S13A5_HUMAN 1-568
Non-standard residues in 7jsk.cif #3
---
CIT — citric acid
NA — sodium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> select add #3
15060 atoms, 15248 bonds, 22 pseudobonds, 944 residues, 4 models selected
> view matrix models
> #3,0.19594,0.66973,-0.71629,116.29,-0.5424,0.68256,0.48982,47.915,0.81695,0.29254,0.497,-79.375
> view matrix models
> #3,-0.96815,0.082762,0.23631,220.15,0.24226,0.54812,0.80055,-81.981,-0.063271,0.83229,-0.55071,109.89
> view matrix models
> #3,0.34338,-0.22732,-0.91127,244.01,-0.53898,0.7469,-0.38941,159.84,0.76915,0.62488,0.13395,-68.064
> hide #!6 models
> open
> /Users/haoranfu/Desktop/mine/data/Data_processing/Nact/cryosparc_P42_J212_011_volume_map.mrc
Opened cryosparc_P42_J212_011_volume_map.mrc as #4, grid size 160,160,160,
pixel 1.15, shown at level 0.0861, step 1, values float32
> volume #4 level 0.1239
> view matrix models
> #3,0.94147,-0.21554,0.25918,1.7328,0.24755,-0.079769,-0.96559,244.58,0.2288,0.97323,-0.021742,-21.052
> view matrix models
> #3,0.23536,0.0029093,0.9719,-31.075,0.90617,-0.36218,-0.21836,91.347,0.35137,0.9321,-0.08788,-22.852
> view matrix models
> #3,0.025251,0.04888,0.99849,-12.755,0.93287,-0.36016,-0.0059607,58.501,0.35933,0.93161,-0.054693,-28.382
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.025251,0.04888,0.99849,-12.668,0.93287,-0.36016,-0.0059607,58.637,0.35933,0.93161,-0.054693,-27.879
> view matrix models
> #3,0.025251,0.04888,0.99849,-21.073,0.93287,-0.36016,-0.0059607,19.813,0.35933,0.93161,-0.054693,-76.037
> fitmap #3 inMap #4
Fit molecule 7jsk.cif (#3) to map cryosparc_P42_J212_011_volume_map.mrc (#4)
using 15060 atoms
average map value = 0.03659, steps = 116
shifted from previous position = 15.1
rotated from previous position = 13.7 degrees
atoms outside contour = 13232, contour level = 0.12388
Position of 7jsk.cif (#3) relative to cryosparc_P42_J212_011_volume_map.mrc
(#4) coordinates:
Matrix rotation and translation
0.17647878 0.20902842 0.96185361 -72.84907273
0.94945420 -0.29387394 -0.11033957 22.39314594
0.25959961 0.93270854 -0.25032542 -34.97682920
Axis 0.71479548 0.48125103 0.50740996
Axis point 0.00000000 37.24100967 23.76758260
Rotation angle (degrees) 133.14604140
Shift along axis -59.04305467
> view matrix models
> #3,0.17648,0.20903,0.96185,-92.639,0.94945,-0.29387,-0.11034,24.648,0.2596,0.93271,-0.25033,-34.611
> fitmap #3 inMap #4
Fit molecule 7jsk.cif (#3) to map cryosparc_P42_J212_011_volume_map.mrc (#4)
using 15060 atoms
average map value = 0.06183, steps = 100
shifted from previous position = 2.97
rotated from previous position = 14.5 degrees
atoms outside contour = 11698, contour level = 0.12388
Position of 7jsk.cif (#3) relative to cryosparc_P42_J212_011_volume_map.mrc
(#4) coordinates:
Matrix rotation and translation
-0.00988354 0.04310257 0.99902176 -52.82350624
0.95559011 -0.29386677 0.02213268 3.85740032
0.29453327 0.95487407 -0.03828395 -71.39147063
Axis 0.62900509 0.47508007 0.61534667
Axis point 0.00000000 30.70927245 4.12459718
Rotation angle (degrees) 132.14561586
Shift along axis -75.32418401
> view matrix models
> #3,-0.0098835,0.043103,0.99902,-51.031,0.95559,-0.29387,0.022133,18.466,0.29453,0.95487,-0.038284,-79.597
> undo
> ui mousemode right "move picked models"
> hide #!3 models
> show #!3 models
> volume #4 level 0.1805
> ui mousemode right "rotate selected models"
> select subtract #3
Nothing selected
> select add #3
15060 atoms, 15248 bonds, 22 pseudobonds, 944 residues, 4 models selected
> view matrix models
> #3,-0.0024823,0.078953,0.99688,-58.323,0.88974,-0.45486,0.038241,32.048,0.45645,0.88706,-0.069119,-79.823
> fitmap #3 inMap #4
Fit molecule 7jsk.cif (#3) to map cryosparc_P42_J212_011_volume_map.mrc (#4)
using 15060 atoms
average map value = 0.1183, steps = 60
shifted from previous position = 4.43
rotated from previous position = 5.93 degrees
atoms outside contour = 11190, contour level = 0.18051
Position of 7jsk.cif (#3) relative to cryosparc_P42_J212_011_volume_map.mrc
(#4) coordinates:
Matrix rotation and translation
-0.01560019 0.00574183 0.99986182 -43.06256486
0.92043462 -0.39054375 0.01660369 20.59816672
0.39058512 0.92056646 0.00080758 -84.80031387
Axis 0.63523563 0.42815288 0.64277586
Axis point 3.50991918 39.62659907 -0.00000000
Rotation angle (degrees) 134.64146656
Shift along axis -73.04330565
> select subtract #3
Nothing selected
> hide #!3 models
> close #4
> close #6
> close #5
> close #2
> open
> /Users/haoranfu/Desktop/mine/data/Data_processing/Nact/Maps_NaCT_Ö/NaCT_inward_high_res.mrc
Opened NaCT_inward_high_res.mrc as #2, grid size 360,360,360, pixel 0.833,
shown at level 0.247, step 2, values float32
> ui mousemode right "move picked models"
> view matrix models #2,1,0,0,-103.86,0,1,0,24.139,0,0,1,48.094
> open
> /Users/haoranfu/Desktop/mine/data/Data_processing/Nact/NaCT_apo_NU_refine.mrc
Opened NaCT_apo_NU_refine.mrc as #4, grid size 320,320,320, pixel 0.573, shown
at level 0.0286, step 2, values float32
> open
> /Users/haoranfu/Desktop/mine/data/Data_processing/Nact/NaCT_inhibitor1_BI_NU_refine.mrc
Opened NaCT_inhibitor1_BI_NU_refine.mrc as #5, grid size 320,320,320, pixel
0.573, shown at level 0.0292, step 2, values float32
> open
> /Users/haoranfu/Desktop/mine/data/Data_processing/Nact/NaCT_inhibitor2_PF4_NU_refine.mrc
Opened NaCT_inhibitor2_PF4_NU_refine.mrc as #6, grid size 160,160,160, pixel
1.15, shown at level 0.0829, step 1, values float32
> set bgColor white
> view matrix models #4,1,0,0,-1.1871,0,1,0,-10.342,0,0,1,124.43
> volume #2 level 0.6793
> volume #2 level 0.5682
> surface dust #2 size 8.33
> surface dust #4 size 5.73
> surface dust #5 size 5.73
> surface dust #6 size 11.5
> view matrix models #4,1,0,0,-30.791,0,1,0,22.922,0,0,1,100.9
> select add #4
2 models selected
> view matrix models #4,1,0,0,-4.9401,0,1,0,33.234,0,0,1,102.95
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.1481,0.36603,-0.91874,123.01,-0.8961,0.4427,0.031921,163.51,0.41841,0.81856,0.39356,44.673
> view matrix models
> #4,0.30782,0.27606,0.91052,-53.125,-0.29735,-0.88113,0.36768,202.67,0.90379,-0.38392,-0.18914,168.1
> view matrix models
> #4,0.21298,0.27903,0.93637,-47.25,-0.034676,-0.95559,0.29265,192.94,0.97644,-0.094798,-0.19385,134.8
> ui mousemode right "move picked models"
> select add #3
15060 atoms, 15248 bonds, 22 pseudobonds, 944 residues, 6 models selected
> select subtract #3
2 models selected
> select add #2
4 models selected
> select subtract #4
2 models selected
> view matrix models #2,1,0,0,-100.16,0,1,0,69.512,0,0,1,67.264
> view matrix models
> #4,0.21298,0.27903,0.93637,-79.483,-0.034676,-0.95559,0.29265,265.94,0.97644,-0.094798,-0.19385,165.43
> view matrix models
> #4,0.21298,0.27903,0.93637,-77.543,-0.034676,-0.95559,0.29265,276.94,0.97644,-0.094798,-0.19385,147.66
> volume #4 level 0.0274
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 4 maps.
> select add #4
4 models selected
> fitmap #2 inMap #4
Fit map NaCT_inward_high_res.mrc in map NaCT_apo_NU_refine.mrc using 12008
points
correlation = 0.4903, correlation about mean = 0.05277, overlap = 265.4
steps = 160, shift = 5.4, angle = 6.62 degrees
Position of NaCT_inward_high_res.mrc (#2) relative to NaCT_apo_NU_refine.mrc
(#4) coordinates:
Matrix rotation and translation
0.17964141 -0.07351372 0.98098149 -71.03340734
0.17451285 -0.97900576 -0.10532318 221.43040313
0.96812924 0.19011428 -0.16304088 -58.75969336
Axis 0.76545998 0.03329938 0.64262133
Axis point 0.00000000 112.53329075 14.70546258
Rotation angle (degrees) 168.87323496
Shift along axis -84.75996698
> volume #4 level 0.03556
> view matrix models
> #4,0.21298,0.27903,0.93637,-22.788,-0.034676,-0.95559,0.29265,256.78,0.97644,-0.094798,-0.19385,148.45
> view matrix models
> #4,0.21298,0.27903,0.93637,-75.887,-0.034676,-0.95559,0.29265,276.78,0.97644,-0.094798,-0.19385,147.78
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.97212,-0.22937,0.04881,-68.489,0.22936,0.97332,0.0057035,36.986,-0.048816,0.0056509,0.99879,68.772,#4,0.23938,0.38906,0.88957,-83.699,-0.024754,-0.91346,0.40617,261.41,0.97061,-0.11925,-0.20903,151.92
> view matrix models
> #2,0.9265,-0.36856,0.075873,-45.045,0.37027,0.92888,-0.0094282,23.717,-0.067002,0.036829,0.99707,67.323,#4,0.26796,0.51451,0.81454,-90.436,-0.011018,-0.84376,0.5366,241.59,0.96337,-0.15276,-0.22043,156.66
> view matrix models
> #2,0.81858,-0.5636,0.11087,-5.0992,0.56774,0.82318,-0.0072013,7.9545,-0.08721,0.068842,0.99381,66.353,#4,0.29725,0.68294,0.66726,-94.462,0.03441,-0.70606,0.70732,208.95,0.95418,-0.18729,-0.23337,161.88
> select subtract #2
2 models selected
> view matrix models
> #4,0.36385,0.75577,0.54444,-95.632,-0.28474,-0.46628,0.83756,203.83,0.88687,-0.45977,0.045539,166.68
> view matrix models
> #4,0.10296,0.73181,0.67368,-81.897,-0.1001,-0.66622,0.73901,214.55,0.98964,-0.14352,0.0046553,132.37
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.10296,0.73181,0.67368,-25.397,-0.1001,-0.66622,0.73901,212.99,0.98964,-0.14352,0.0046553,131.2
> select subtract #4
Nothing selected
> select add #5
2 models selected
> view matrix models #5,1,0,0,-103.74,0,1,0,121.29,0,0,1,85.619
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.3792,-0.92008,0.098335,28.861,0.2971,0.22171,0.92875,81.833,-0.87632,-0.32297,0.35742,253.58
> view matrix models
> #5,0.21638,-0.88766,-0.40649,86.599,-0.058048,-0.42732,0.90224,176.58,-0.97458,-0.17163,-0.14399,294.14
> select subtract #5
Nothing selected
> select add #6
2 models selected
> view matrix models
> #6,0.40652,-0.89106,0.20189,120.72,0.91106,0.41195,-0.016353,-26.133,-0.068595,0.19058,0.97927,-9.9396
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.40652,-0.89106,0.20189,-60.672,0.91106,0.41195,-0.016353,36.715,-0.068595,0.19058,0.97927,104.23
> view matrix models
> #6,0.40652,-0.89106,0.20189,-62.907,0.91106,0.41195,-0.016353,20.796,-0.068595,0.19058,0.97927,90.701
> view matrix models
> #6,0.40652,-0.89106,0.20189,-60.159,0.91106,0.41195,-0.016353,22.186,-0.068595,0.19058,0.97927,91.068
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.67724,-0.14292,0.72175,-203.81,0.38073,0.90748,-0.17754,38.463,-0.6296,0.39503,0.669,151.51
> view matrix models
> #6,0.67631,-0.13663,0.72384,-204.52,0.37634,0.90881,-0.18009,38.973,-0.63322,0.3942,0.66606,152.2
> view matrix models
> #6,-0.72985,0.30168,0.61344,-107.1,0.61012,-0.11726,0.78358,26.838,0.30832,0.94617,-0.098477,83.365
> view matrix models
> #6,0.0064758,0.93772,0.34732,-210.78,-0.44459,-0.30841,0.84097,136.52,0.89571,-0.15986,0.4149,87.662
> select subtract #6
Nothing selected
> hide #!4 models
> hide #!6 models
> volume flip #4
Opened NaCT_apo_NU_refine.mrc z flip as #7, grid size 320,320,320, pixel
0.573, shown at step 1, values float32
> volume flip #6
Opened NaCT_inhibitor2_PF4_NU_refine.mrc z flip as #8, grid size 160,160,160,
pixel 1.15, shown at step 1, values float32
> select add #5
2 models selected
> view matrix models
> #5,0.19995,-0.88133,-0.4281,89.472,-0.070029,-0.44866,0.89095,180.68,-0.9773,-0.14817,-0.15143,292.89
> ui mousemode right "move picked models"
> view matrix models
> #5,0.19995,-0.88133,-0.4281,137.21,-0.070029,-0.44866,0.89095,190.06,-0.9773,-0.14817,-0.15143,285.39
> view matrix models
> #5,0.19995,-0.88133,-0.4281,147.1,-0.070029,-0.44866,0.89095,190.88,-0.9773,-0.14817,-0.15143,324.87
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 4 maps.
> select add #2
4 models selected
> fitmap #2 inMap #5
Fit map NaCT_inward_high_res.mrc in map NaCT_inhibitor1_BI_NU_refine.mrc using
12008 points
correlation = 0.4427, correlation about mean = -0.004388, overlap = 254.9
steps = 108, shift = 2.49, angle = 6.52 degrees
Position of NaCT_inward_high_res.mrc (#2) relative to
NaCT_inhibitor1_BI_NU_refine.mrc (#5) coordinates:
Matrix rotation and translation
0.17645051 -0.13283431 -0.97530522 229.61167585
-0.97475664 0.11412985 -0.19189549 248.01435641
0.13680174 0.98454529 -0.10934285 -69.48523532
Axis 0.64472159 -0.60946490 -0.46139637
Axis point 0.00000000 260.71553975 180.78607152
Rotation angle (degrees) 114.16597137
Shift along axis 28.93979300
> ui mousemode right "rotate selected models"
> select subtract #5
2 models selected
> select subtract #2
Nothing selected
> select add #7
2 models selected
> view matrix models
> #7,-0.38725,0.89133,-0.23571,86.311,0.048509,0.275,0.96022,93.909,0.9207,0.36041,-0.14973,105.45
> ui mousemode right "move picked models"
> view matrix models
> #7,-0.38725,0.89133,-0.23571,24.357,0.048509,0.275,0.96022,114.33,0.9207,0.36041,-0.14973,97.53
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 4 maps.
> select add #5
4 models selected
> fitmap #5 inMap #7
Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_apo_NU_refine.mrc z flip
using 40947 points
correlation = 0.7424, correlation about mean = 0.3079, overlap = 78.33
steps = 184, shift = 7.91, angle = 23.2 degrees
Position of NaCT_inhibitor1_BI_NU_refine.mrc (#5) relative to
NaCT_apo_NU_refine.mrc z flip (#7) coordinates:
Matrix rotation and translation
-0.98626494 -0.16456688 0.01411378 195.96537239
0.16443637 -0.98633735 -0.00996488 164.49166856
0.01556083 -0.00750720 0.99985074 -2.65333105
Axis 0.00746981 -0.00439814 0.99996243
Axis point 91.18124786 90.35563259 0.00000000
Rotation angle (degrees) 170.53135694
Shift along axis -1.91286420
> select subtract #7
2 models selected
> select subtract #5
Nothing selected
> select add #8
2 models selected
> view matrix models
> #8,0.0064758,0.93772,0.34732,-75.69,-0.44459,-0.30841,0.84097,194.15,0.89571,-0.15986,0.4149,178.98
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.3745,0.925,0.064171,-14.262,-0.67465,-0.31931,0.66549,231.95,0.63607,0.20593,0.74364,138.54
> view matrix models
> #8,-0.15425,0.95382,0.25776,-54.491,-0.54199,-0.29981,0.78509,207.25,0.82611,-0.018605,0.5632,158.64
> view matrix models
> #8,-0.12189,0.84826,-0.51536,21.598,-0.22728,0.48159,0.84642,98.311,0.96617,0.2203,0.13409,161.27
> ui mousemode right "move picked models"
> view matrix models
> #8,-0.12189,0.84826,-0.51536,38.745,-0.22728,0.48159,0.84642,109.42,0.96617,0.2203,0.13409,85.666
> view matrix models
> #8,-0.12189,0.84826,-0.51536,39.692,-0.22728,0.48159,0.84642,118.09,0.96617,0.2203,0.13409,83.622
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 4 maps.
> select add #7
4 models selected
> fitmap #7 inMap #8
Fit map NaCT_apo_NU_refine.mrc z flip in map NaCT_inhibitor2_PF4_NU_refine.mrc
z flip using 230090 points
correlation = 0.5338, correlation about mean = 0.04985, overlap = 653.8
steps = 72, shift = 3.86, angle = 6.23 degrees
Position of NaCT_apo_NU_refine.mrc z flip (#7) relative to
NaCT_inhibitor2_PF4_NU_refine.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.89404027 0.26672644 -0.35992918 14.62442750
-0.15992037 0.94052072 0.29974368 -13.53301131
0.41847041 -0.21042291 0.88351838 5.62180082
Axis -0.49829811 -0.76029095 -0.41672133
Axis point -2.33529441 0.00000000 42.23120260
Rotation angle (degrees) 30.79107172
Shift along axis 0.65897709
> close #6
> close #4
> hide #!5 models
> hide #!8 models
> select subtract #8
2 models selected
> select add #2
4 models selected
> fitmap #2 inMap #7
Fit map NaCT_inward_high_res.mrc in map NaCT_apo_NU_refine.mrc z flip using
12008 points
correlation = 0.4951, correlation about mean = 0.0409, overlap = 258.1
steps = 120, shift = 2.18, angle = 5.49 degrees
Position of NaCT_inward_high_res.mrc (#2) relative to NaCT_apo_NU_refine.mrc z
flip (#7) coordinates:
Matrix rotation and translation
-0.44502245 0.29811526 0.84444201 -7.39893197
0.82320705 -0.23503466 0.51680641 -69.93255855
0.35254101 0.92514107 -0.14081488 -93.96021817
Axis 0.49357512 0.59458604 0.63470547
Axis point 34.12697982 16.61103225 0.00000000
Rotation angle (degrees) 155.56567282
Shift along axis -104.86991660
> view matrix models
> #2,0.86869,-0.48801,0.085002,-17.425,0.48678,0.87278,0.036035,15.185,-0.091774,0.010074,0.99573,65.213
> fitmap #2 inMap #7
Fit map NaCT_inward_high_res.mrc in map NaCT_apo_NU_refine.mrc z flip using
12008 points
correlation = 0.4675, correlation about mean = 0.01479, overlap = 256.7
steps = 188, shift = 3.8, angle = 10.8 degrees
Position of NaCT_inward_high_res.mrc (#2) relative to NaCT_apo_NU_refine.mrc z
flip (#7) coordinates:
Matrix rotation and translation
-0.36229365 0.14858152 0.92014501 -14.93075464
0.88733739 -0.24716039 0.38928665 -58.60017223
0.28526420 0.95751515 -0.04229730 -89.82926893
Axis 0.50388066 0.56298506 0.65509701
Axis point 27.70885466 17.58059101 0.00000000
Rotation angle (degrees) 145.67737156
Shift along axis -99.36122595
> select subtract #2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.21802,0.97462,-0.050922,-17.168,-0.0015979,0.051821,0.99866,132.43,0.97594,0.21781,-0.0097406,93.376
> fitmap #7 inMap #2
Fit map NaCT_apo_NU_refine.mrc z flip in map NaCT_inward_high_res.mrc using
230090 points
correlation = 0.4186, correlation about mean = 0.06045, overlap = 5144
steps = 124, shift = 2.84, angle = 10.6 degrees
Position of NaCT_apo_NU_refine.mrc z flip (#7) relative to
NaCT_inward_high_res.mrc (#2) coordinates:
Matrix rotation and translation
-0.02246715 0.87576604 0.48221268 25.61585958
0.01574908 -0.48196455 0.87604917 115.85248715
0.99962353 0.02727673 -0.00296415 52.78691291
Axis -0.64572832 -0.39363535 -0.65428292
Axis point 9.03943566 52.59056906 0.00000000
Rotation angle (degrees) 138.91172646
Shift along axis -96.68209645
> view matrix models
> #7,-0.081456,0.9815,-0.17329,-18.811,0.084578,0.18004,0.98002,115.97,0.99308,0.065171,-0.097679,111.3
> fitmap #7 inMap #2
Fit map NaCT_apo_NU_refine.mrc z flip in map NaCT_inward_high_res.mrc using
230090 points
correlation = 0.8805, correlation about mean = 0.5675, overlap = 1.683e+04
steps = 80, shift = 5.99, angle = 1.29 degrees
Position of NaCT_apo_NU_refine.mrc z flip (#7) relative to
NaCT_inward_high_res.mrc (#2) coordinates:
Matrix rotation and translation
-0.00217585 0.96004447 0.27983904 38.90453703
-0.03835313 -0.27971392 0.95931703 92.00569805
0.99926188 -0.00864537 0.03742933 54.95624878
Axis -0.61824220 -0.45949880 -0.63768130
Axis point 9.99940642 35.19629234 0.00000000
Rotation angle (degrees) 128.47918081
Shift along axis -101.37350627
> volume #7 level 0.03133
> surface dust #7 size 5.73
> volume #5 level 0.03014
> volume #2 level 0.5435
> surface dust #7 size 5.73
> fitmap #7 inMap #2
Fit map NaCT_apo_NU_refine.mrc z flip in map NaCT_inward_high_res.mrc using
275715 points
correlation = 0.8714, correlation about mean = 0.5951, overlap = 1.759e+04
steps = 28, shift = 0.0175, angle = 0.0128 degrees
Position of NaCT_apo_NU_refine.mrc z flip (#7) relative to
NaCT_inward_high_res.mrc (#2) coordinates:
Matrix rotation and translation
-0.00236598 0.96005064 0.27981632 38.92968904
-0.03846887 -0.27969737 0.95931722 92.02372475
0.99925700 -0.00849449 0.03759382 54.91449750
Axis -0.61814880 -0.45951230 -0.63776211
Axis point 10.04374223 35.20779535 0.00000000
Rotation angle (degrees) 128.47951280
Shift along axis -101.37275987
> close #5
> open
> /Users/haoranfu/Desktop/mine/data/Data_processing/Nact/NaCT_inhibitor1_BI_NU_refine.mrc
Opened NaCT_inhibitor1_BI_NU_refine.mrc as #4, grid size 320,320,320, pixel
0.573, shown at level 0.0292, step 2, values float32
> view matrix models
> #7,-0.1165,0.99163,-0.055563,-21.902,0.10693,0.068143,0.99193,122.85,0.98742,0.10962,-0.11398,112.14
> undo
> select subtract #7
Nothing selected
> save /Users/haoranfu/Desktop/1.tif width 1140 height 765 supersample 3
> transparentBackground true
> select add #2
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.89722,-0.43487,-0.076749,-18.192,0.44112,0.89065,0.11027,103.99,0.020402,-0.1328,0.99093,66.392
> view matrix models
> #2,0.89722,-0.43487,-0.076749,-24.508,0.44112,0.89065,0.11027,108.57,0.020402,-0.1328,0.99093,63.662
> select subtract #2
Nothing selected
> volume #2 step 1
> volume #2 level 0.611
> select add #2
2 models selected
> view matrix models
> #2,0.89722,-0.43487,-0.076749,-4.0299,0.44112,0.89065,0.11027,12.761,0.020402,-0.1328,0.99093,76.182
> fitmap #2 inMap #7
Fit map NaCT_inward_high_res.mrc in map NaCT_apo_NU_refine.mrc z flip using
89648 points
correlation = 0.5704, correlation about mean = 0.08965, overlap = 2750
steps = 68, shift = 3.31, angle = 1.35 degrees
Position of NaCT_inward_high_res.mrc (#2) relative to NaCT_apo_NU_refine.mrc z
flip (#7) coordinates:
Matrix rotation and translation
-0.00137119 -0.06128358 0.99811945 -42.33647981
0.96165872 -0.27381114 -0.01549065 -11.42941657
0.27424555 0.95982904 0.05930934 -103.10400215
Axis 0.61419226 0.45584822 0.64418186
Axis point 15.30699972 37.52157774 0.00000000
Rotation angle (degrees) 127.44044721
Shift along axis -97.63054498
> view matrix models
> #2,0.89968,-0.42775,-0.08723,-7.1165,0.436,0.89046,0.1303,10.364,0.02194,-0.15526,0.98763,78.403
> fitmap #2 inMap #7
Fit map NaCT_inward_high_res.mrc in map NaCT_apo_NU_refine.mrc z flip using
89648 points
correlation = 0.9135, correlation about mean = 0.6255, overlap = 6177
steps = 84, shift = 3.51, angle = 1.37 degrees
Position of NaCT_inward_high_res.mrc (#2) relative to NaCT_apo_NU_refine.mrc z
flip (#7) coordinates:
Matrix rotation and translation
-0.00242723 -0.03813507 0.99926964 -51.29429941
0.96012555 -0.27944497 -0.00833230 -11.24037149
0.27955863 0.95940410 0.03729274 -101.16223106
Axis 0.61813520 0.45971063 0.63763235
Axis point 10.00656396 35.14956439 0.00000000
Rotation angle (degrees) 128.48353636
Shift along axis -101.37844122
> select subtract #2
Nothing selected
> surface dust #2 size 8.33
> surface dust #7 size 5.73
> volume #2 level 0.7459
> volume #7 level 0.03048
> surface dust #2 size 8.33
> surface dust #7 size 5.73
> volume #7 level 0.03217
> volume #7 level 0.03683
> save /Users/haoranfu/Desktop/1.tif width 1140 height 765 supersample 3
> hide #!2 models
> show #!2 models
> show #!4 models
> hide #!7 models
> volume #4 level 0.03417
> select add #4
2 models selected
> view matrix models #4,1,0,0,7.1755,0,1,0,32.071,0,0,1,88.88
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.068747,-0.92809,0.36595,144.01,-0.0001924,0.36681,0.9303,5.0854,-0.99763,-0.064026,0.025039,275.16
> view matrix models
> #4,0.18382,-0.98263,0.025599,170,-0.36701,-0.044449,0.92916,76.611,-0.91188,-0.18019,-0.3688,314.46
> ui mousemode right "move picked models"
> view matrix models
> #4,0.18382,-0.98263,0.025599,173.87,-0.36701,-0.044449,0.92916,187.63,-0.91188,-0.18019,-0.3688,335.75
> view matrix models
> #4,0.18382,-0.98263,0.025599,131.18,-0.36701,-0.044449,0.92916,192.68,-0.91188,-0.18019,-0.3688,335.86
> fitmap #4 inMap #2
Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_inward_high_res.mrc using
32734 points
correlation = 0.3699, correlation about mean = 0.03798, overlap = 543.2
steps = 104, shift = 1.95, angle = 6.54 degrees
Position of NaCT_inhibitor1_BI_NU_refine.mrc (#4) relative to
NaCT_inward_high_res.mrc (#2) coordinates:
Matrix rotation and translation
-0.00651287 -0.92834552 0.37166137 214.64282044
-0.19184472 0.36592529 0.91065597 55.87858123
-0.98140368 -0.06537029 -0.18048141 263.02772364
Axis -0.53519303 0.74193802 0.40385194
Axis point 236.29173317 0.00000000 15.14706755
Rotation angle (degrees) 114.23841547
Shift along axis 32.80735822
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.19837,-0.91909,0.34049,95.13,-0.21102,0.29919,0.93057,144.97,-0.95714,-0.25645,-0.1346,326.88
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.19837,-0.91909,0.34049,89.389,-0.21102,0.29919,0.93057,132.33,-0.95714,-0.25645,-0.1346,325.81
> fitmap #4 inMap #2
Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_inward_high_res.mrc using
32734 points
correlation = 0.3616, correlation about mean = 0.04613, overlap = 580.9
steps = 124, shift = 3.61, angle = 6.71 degrees
Position of NaCT_inhibitor1_BI_NU_refine.mrc (#4) relative to
NaCT_inward_high_res.mrc (#2) coordinates:
Matrix rotation and translation
0.16207205 -0.71992036 0.67486838 140.44597548
-0.09276325 0.66976630 0.73675511 29.51839288
-0.98240910 -0.18201040 0.04176824 251.81448512
Axis -0.46030286 0.83029843 0.31420662
Axis point 213.82367910 0.00000000 30.78940695
Rotation angle (degrees) 93.62331921
Shift along axis 38.98317074
> volume flip #4
Opened NaCT_inhibitor1_BI_NU_refine.mrc z flip as #5, grid size 320,320,320,
pixel 0.573, shown at step 1, values float32
> select subtract #4
Nothing selected
> select add #5
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.079183,-0.9604,-0.26714,171.51,-0.70227,-0.13645,0.69871,241.09,-0.70749,0.24293,-0.66366,304.82
> hide #!5 models
> select subtract #5
Nothing selected
> show #!4 models
> select add #4
2 models selected
> view matrix models
> #4,0.12299,-0.97718,-0.17319,146.66,0.026711,-0.17119,0.98488,152.08,-0.99205,-0.12576,0.0050476,303.88
> fitmap #4 inMap #2
Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_inward_high_res.mrc using
32734 points
correlation = 0.6266, correlation about mean = 0.2456, overlap = 1381
steps = 68, shift = 3.18, angle = 7.48 degrees
Position of NaCT_inhibitor1_BI_NU_refine.mrc (#4) relative to
NaCT_inward_high_res.mrc (#2) coordinates:
Matrix rotation and translation
0.16117904 -0.95104108 0.26370853 196.75946006
-0.01094773 0.26546279 0.96405895 38.17398261
-0.98686446 -0.15827311 0.03237530 251.15157306
Axis -0.58289496 0.64949824 0.48824737
Axis point 252.69468206 0.00000000 -14.67837111
Rotation angle (degrees) 105.69351205
Shift along axis 32.72793151
> close #5
> view matrix models
> #4,-0.14823,-0.98633,-0.071919,160.18,0.085799,-0.085274,0.99266,136.27,-0.98522,0.14097,0.097266,270.29
> undo
> ui mousemode right "move picked models"
> select subtract #4
Nothing selected
> volume #2 color #fbd8b4
> undo
> volume #2 color #f3d1af4d
> select subtract #4
Nothing selected
> undo
> ui mousemode right "rotate selected models"
> volume #2 color #f3d1af00
> volume #2 color #f3d1af
> view matrix models
> #4,-0.018278,-0.88212,-0.47068,178.07,-0.068217,-0.46856,0.8808,197.87,-0.9975,0.048207,-0.051611,293.46
> fitmap #4 inMap #2
Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_inward_high_res.mrc using
32734 points
correlation = 0.4075, correlation about mean = 0.04414, overlap = 684.2
steps = 84, shift = 6.07, angle = 4.23 degrees
Position of NaCT_inhibitor1_BI_NU_refine.mrc (#4) relative to
NaCT_inward_high_res.mrc (#2) coordinates:
Matrix rotation and translation
0.00554612 -0.99959269 -0.02799449 249.99940977
0.09183041 -0.02736752 0.99539851 49.93733654
-0.99575921 -0.00809134 0.09164122 230.79333088
Axis -0.56677476 0.54659707 0.61643978
Axis point 214.09141949 52.91431331 0.00000000
Rotation angle (degrees) 117.71605268
Shift along axis 27.87243665
> ui mousemode right "move picked models"
> view matrix models
> #2,0.89734,-0.43465,-0.07654,-0.25786,0.44087,0.8908,0.11001,16.859,0.020366,-0.13246,0.99098,70.827
> fitmap #4 inMap #2
Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_inward_high_res.mrc using
32734 points
correlation = 0.4069, correlation about mean = 0.05245, overlap = 721.4
steps = 144, shift = 4.01, angle = 7.14 degrees
Position of NaCT_inhibitor1_BI_NU_refine.mrc (#4) relative to
NaCT_inward_high_res.mrc (#2) coordinates:
Matrix rotation and translation
0.12039552 -0.99262752 0.01398293 223.64944107
0.06587221 0.02204238 0.99758458 46.16343842
-0.99053812 -0.11918363 0.06804037 244.98964968
Axis -0.60774258 0.54665795 0.57603302
Axis point 0.00000000 246.93866058 212.48367192
Rotation angle (degrees) 113.25106078
Shift along axis 30.43644874
> view matrix models
> #4,0.15522,-0.89118,-0.42627,163.07,0.0027916,-0.4311,0.9023,185.81,-0.98788,-0.14124,-0.064427,313.26
> fitmap #4 inMap #2
Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_inward_high_res.mrc using
32734 points
correlation = 0.6266, correlation about mean = 0.2455, overlap = 1381
steps = 120, shift = 3.35, angle = 14.9 degrees
Position of NaCT_inhibitor1_BI_NU_refine.mrc (#4) relative to
NaCT_inward_high_res.mrc (#2) coordinates:
Matrix rotation and translation
0.16132111 -0.95098679 0.26381741 196.72640529
-0.01093279 0.26558029 0.96402676 38.15428550
-0.98684141 -0.15840213 0.03244677 251.15258244
Axis -0.58291710 0.64951145 0.48820336
Axis point 252.69501788 0.00000000 -14.66724141
Rotation angle (degrees) 105.68366153
Shift along axis 32.71999395
> save /Users/haoranfu/Desktop/side-view-BI.tif width 1140 height 765
> supersample 3
> save /Users/haoranfu/Desktop/TOP-VIEW-BI.tif width 1140 height 765
> supersample 3
> volume #2 color #e1c1a1
> select subtract #4
Nothing selected
> save /Users/haoranfu/Desktop/SIDE-viw.tif width 1140 height 765 supersample
> 3
> save /Users/haoranfu/Desktop/side-view.tif width 1140 height 765 supersample
> 3
> save /Users/haoranfu/Desktop/bottom.tif width 1140 height 765 supersample 3
> volume #4 level 0.04044
> surface dust #4 size 5.73
> view
> undo
> ui tool show "Side View"
> save /Users/haoranfu/Desktop/inhibitor-bi.tif width 1140 height 765
> supersample 3
> show #!3 models
> hide #!3 models
> open
> /Users/haoranfu/Desktop/mine/data/Data_processing/Nact/NaCT_PF4_daneng.map
Opened NaCT_PF4_daneng.map as #5, grid size 256,256,256, pixel 0.825, shown at
level 0.131, step 1, values float32
> volume #5 level 0.3265
> select add #5
3 models selected
> view matrix models #5,1,0,0,-35.327,0,1,0,20.771,0,0,1,81.446
> view matrix models #5,1,0,0,-83.4,0,1,0,115.01,0,0,1,90.111
> view matrix models #5,1,0,0,-57.914,0,1,0,119.24,0,0,1,87.364
> view matrix models #5,1,0,0,21.36,0,1,0,154.67,0,0,1,113.03
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.85881,-0.48073,0.17705,67.29,0.49969,0.86225,-0.082626,124.47,-0.11294,0.15943,0.98073,110.62
> view matrix models
> #5,0.85904,-0.48107,0.17497,67.521,0.49998,0.86185,-0.08511,124.74,-0.10985,0.16059,0.98089,110.16
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.85904,-0.48107,0.17497,10.614,0.49998,0.86185,-0.08511,107.03,-0.10985,0.16059,0.98089,129.44
> view matrix models
> #5,0.85904,-0.48107,0.17497,2.2088,0.49998,0.86185,-0.08511,98.616,-0.10985,0.16059,0.98089,91.451
> fitmap #5 inMap #4
Fit map NaCT_PF4_daneng.map in map NaCT_inhibitor1_BI_NU_refine.mrc using
50301 points
correlation = 0.4556, correlation about mean = 0.07124, overlap = 735.2
steps = 192, shift = 7.19, angle = 15.3 degrees
Position of NaCT_PF4_daneng.map (#5) relative to
NaCT_inhibitor1_BI_NU_refine.mrc (#4) coordinates:
Matrix rotation and translation
0.14390330 -0.11731788 -0.98261302 187.95624798
-0.89799614 0.40173540 -0.17947590 161.30384834
0.41580617 0.90820988 -0.04753996 -43.48613100
Axis 0.56182123 -0.72232405 -0.40324295
Axis point 178.57204019 0.00000000 31.91720460
Rotation angle (degrees) 104.53377251
Shift along axis 6.61963813
> open
> /Users/haoranfu/Desktop/mine/data/Data_processing/Nact/NaCT_PF4_daneng.cif
NaCT_PF4_daneng.cif title:
Structure of NaCT-PF4a complex [more info...]
Chain information for NaCT_PF4_daneng.cif #6
---
Chain | Description | UniProt
A B | Solute carrier family 13 member 5 | S13A5_HUMAN 1-568
Non-standard residues in NaCT_PF4_daneng.cif #6
---
NA — sodium ion
XKC — (2R)-2-hydroxy-2-[2-(2-methoxy-5-methylpyridin-3-yl)ethyl]butanedioic
acid
> select add #6
7202 atoms, 7386 bonds, 28 pseudobonds, 924 residues, 7 models selected
> view matrix models
> #5,0.81464,-0.57854,-0.040648,27.637,0.57983,0.81395,0.035747,82.038,0.012405,-0.05269,0.99853,118.34,#6,1,0,0,-8.8477,0,1,0,0.53453,0,0,1,12.796
> ui mousemode right "move picked models"
> view matrix models #6,1,0,0,-57.517,0,1,0,52.131,0,0,1,62.792
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.51805,-0.62833,-0.58037,103.22,0.80459,0.58823,0.081362,78.802,0.29027,-0.50911,0.81028,147.17,#6,0.80912,-0.23179,-0.53999,71.252,0.31184,0.94822,0.06023,20.543,0.49807,-0.21712,0.83951,64.613
> ui mousemode right "move picked models"
> view matrix models
> #6,0.80912,-0.23179,-0.53999,7.821,0.31184,0.94822,0.06023,80.549,0.49807,-0.21712,0.83951,68.951
> view matrix models
> #6,0.80912,-0.23179,-0.53999,34.654,0.31184,0.94822,0.06023,95.981,0.49807,-0.21712,0.83951,92.407
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.50751,-0.62332,-0.5949,105.33,0.80736,0.58519,0.075608,79.433,0.301,-0.51867,0.80024,148.05,#6,0.79824,-0.23435,-0.55489,37.613,0.31608,0.94715,0.054679,96.28,0.51275,-0.21904,0.83013,92.136
> view matrix models
> #5,0.52014,-0.62516,-0.58192,102.7,0.805,0.5865,0.089448,78.091,0.28538,-0.51497,0.80831,148.41,#6,0.80906,-0.22806,-0.54167,34.314,0.31283,0.94734,0.068399,95.089,0.49755,-0.22479,0.8378,93.366
> view matrix models
> #5,0.8816,-0.36788,0.2957,-55.502,0.25017,0.89546,0.36818,75.695,-0.40024,-0.25062,0.88148,186.24,#6,0.91901,0.22231,0.32559,-119.41,-0.32922,0.88708,0.32357,137.71,-0.21689,-0.40455,0.88843,178.17
> select subtract #5
7202 atoms, 7386 bonds, 28 pseudobonds, 924 residues, 4 models selected
> view matrix models
> #6,0.94287,-0.33053,-0.041868,-23.152,0.3101,0.8247,0.47298,60.13,-0.12181,-0.45894,0.88008,174.76
> fitmap #6 inMap #5
Fit molecule NaCT_PF4_daneng.cif (#6) to map NaCT_PF4_daneng.map (#5) using
7202 atoms
average map value = 0.07183, steps = 72
shifted from previous position = 2.35
rotated from previous position = 2.07 degrees
atoms outside contour = 6091, contour level = 0.32651
Position of NaCT_PF4_daneng.cif (#6) relative to NaCT_PF4_daneng.map (#5)
coordinates:
Matrix rotation and translation
0.96418056 0.06985697 -0.25588251 30.20411527
-0.01073472 0.97418247 0.22550673 -24.61022187
0.26502947 -0.21468237 0.94003769 -1.41537716
Axis -0.64098436 -0.75852953 -0.11735414
Axis point 30.99943641 0.00000000 112.38023244
Rotation angle (degrees) 20.08230240
Shift along axis -0.52668516
> view matrix models
> #6,0.75867,-0.62102,-0.19686,44.144,0.62874,0.61881,0.47092,50.736,-0.17063,-0.48105,0.85993,185
> fitmap #6 inMap #5
Fit molecule NaCT_PF4_daneng.cif (#6) to map NaCT_PF4_daneng.map (#5) using
7202 atoms
average map value = 0.07665, steps = 128
shifted from previous position = 3.56
rotated from previous position = 10.5 degrees
atoms outside contour = 6093, contour level = 0.32651
Position of NaCT_PF4_daneng.cif (#6) relative to NaCT_PF4_daneng.map (#5)
coordinates:
Matrix rotation and translation
0.88841813 -0.02778485 -0.45819344 67.51213013
0.20848766 0.91369683 0.34884238 -53.89617338
0.40895736 -0.40544557 0.81753763 15.10992979
Axis -0.64285569 -0.73904511 0.20136756
Axis point 25.43974788 0.00000000 140.41065908
Rotation angle (degrees) 35.92103683
Shift along axis -0.52620380
> ui mousemode right "move picked models"
> view matrix models
> #6,0.82746,-0.48052,-0.29053,90.323,0.55952,0.66195,0.49875,13.249,-0.047341,-0.57526,0.8166,175.35
> view matrix models
> #6,0.82746,-0.48052,-0.29053,66.082,0.55952,0.66195,0.49875,73.589,-0.047341,-0.57526,0.8166,191.37
> view matrix models
> #6,0.82746,-0.48052,-0.29053,74.943,0.55952,0.66195,0.49875,51.153,-0.047341,-0.57526,0.8166,198.64
> view matrix models
> #6,0.82746,-0.48052,-0.29053,32.734,0.55952,0.66195,0.49875,45.094,-0.047341,-0.57526,0.8166,192.31
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.8163,-0.28529,0.50226,-72.157,0.27,0.95714,0.10485,86.6,-0.51064,0.050019,0.85834,170.15
> ui mousemode right "move picked models"
> view matrix models
> #5,0.8816,-0.36788,0.2957,-54.624,0.25017,0.89546,0.36818,66.911,-0.40024,-0.25062,0.88148,192.07
> view matrix models
> #6,0.8163,-0.28529,0.50226,-78.41,0.27,0.95714,0.10485,88.718,-0.51064,0.050019,0.85834,172.53
> fitmap #6 inMap #5
Fit molecule NaCT_PF4_daneng.cif (#6) to map NaCT_PF4_daneng.map (#5) using
7202 atoms
average map value = 0.08076, steps = 252
shifted from previous position = 2.97
rotated from previous position = 12.5 degrees
atoms outside contour = 5935, contour level = 0.32651
Position of NaCT_PF4_daneng.cif (#6) relative to NaCT_PF4_daneng.map (#5)
coordinates:
Matrix rotation and translation
0.98915417 -0.05099570 0.13774421 -5.14990174
0.06422743 0.99355594 -0.09338865 5.89485707
-0.13209416 0.10122273 0.98605532 6.62171535
Axis 0.55274230 0.76640475 0.32726092
Axis point 34.75767894 -0.00000000 55.52663058
Rotation angle (degrees) 10.13928373
Shift along axis 3.83830658
> view matrix models
> #6,0.80935,-0.38054,0.44737,-60.747,0.25634,0.9142,0.31388,70.333,-0.52843,-0.13936,0.83746,202.62
> fitmap #6 inMap #5
Fit molecule NaCT_PF4_daneng.cif (#6) to map NaCT_PF4_daneng.map (#5) using
7202 atoms
average map value = 0.6612, steps = 84
shifted from previous position = 4.17
rotated from previous position = 10.2 degrees
atoms outside contour = 1506, contour level = 0.32651
Position of NaCT_PF4_daneng.cif (#6) relative to NaCT_PF4_daneng.map (#5)
coordinates:
Matrix rotation and translation
0.99999938 0.00016146 -0.00110330 0.09457846
-0.00016136 0.99999998 0.00008808 -0.00265260
0.00110331 -0.00008791 0.99999939 -0.08745726
Axis -0.07867179 -0.98640109 -0.14430395
Axis point 78.29591777 0.00000000 86.23500145
Rotation angle (degrees) 0.06408640
Shift along axis 0.00779630
> view matrix models
> #6,0.88199,-0.36777,0.29469,-43.365,0.25044,0.89547,0.36799,84.559,-0.39922,-0.25076,0.8819,188.95
> view matrix models
> #6,0.88199,-0.36777,0.29469,-37.757,0.25044,0.89547,0.36799,70.733,-0.39922,-0.25076,0.8819,185.76
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.69538,-0.65796,0.28902,13.922,0.70718,0.69805,-0.11235,94.752,-0.12783,0.28251,0.95071,92.154
> ui mousemode right "move picked models"
> view matrix models
> #4,0.22504,-0.95667,-0.18477,132.87,-0.047177,-0.20011,0.97864,163.04,-0.97321,-0.21152,-0.090166,322.46
> view matrix models
> #6,0.69538,-0.65796,0.28902,14.565,0.70718,0.69805,-0.11235,95.412,-0.12783,0.28251,0.95071,87.274
> fitmap #6 inMap #4
Fit molecule NaCT_PF4_daneng.cif (#6) to map NaCT_inhibitor1_BI_NU_refine.mrc
(#4) using 7202 atoms
average map value = 0.01791, steps = 172
shifted from previous position = 3.38
rotated from previous position = 14.4 degrees
atoms outside contour = 5619, contour level = 0.04044
Position of NaCT_PF4_daneng.cif (#6) relative to
NaCT_inhibitor1_BI_NU_refine.mrc (#4) coordinates:
Matrix rotation and translation
0.28239059 -0.22147292 -0.93338379 183.11002982
-0.81886620 0.45119115 -0.35480232 165.24220382
0.49971361 0.86450927 -0.05394455 -46.02230615
Axis 0.61763090 -0.72592210 -0.30260399
Axis point 187.56736746 0.00000000 47.29514365
Rotation angle (degrees) 99.21742580
Shift along axis 7.06797705
> view matrix models
> #6,0.7546,-0.64122,0.13934,22.902,0.63958,0.7662,0.062241,77.52,-0.14667,0.042153,0.98829,112.85
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.74988,-0.65469,0.095189,29.594,0.6451,0.7555,0.11429,72.49,-0.14674,-0.024299,0.98888,119.93
> fitmap #6 inMap #4
Fit molecule NaCT_PF4_daneng.cif (#6) to map NaCT_inhibitor1_BI_NU_refine.mrc
(#4) using 7202 atoms
average map value = 0.02009, steps = 212
shifted from previous position = 4.47
rotated from previous position = 10.6 degrees
atoms outside contour = 5407, contour level = 0.04044
Position of NaCT_PF4_daneng.cif (#6) relative to
NaCT_inhibitor1_BI_NU_refine.mrc (#4) coordinates:
Matrix rotation and translation
0.14294565 -0.09788775 -0.98487793 186.77354041
-0.89437526 0.41338507 -0.17089669 158.79340772
0.42386252 0.90527939 -0.02845678 -46.11747583
Axis 0.55373792 -0.72485630 -0.40982637
Axis point 177.44399129 0.00000000 31.16696950
Rotation angle (degrees) 103.65429324
Shift along axis 7.22134852
> volume #4 level 0.05388
> view matrix models
> #6,0.90058,-0.29224,-0.3218,19.252,0.40221,0.841,0.36186,60.306,0.16489,-0.45532,0.87493,149.01
> undo
> ui mousemode right "move picked models"
> ui tool show "Side View"
> select subtract #6
Nothing selected
> save /Users/haoranfu/Desktop/bi-and-pf4a.tif width 1140 height 765
> supersample 3
> save /Users/haoranfu/Desktop/expand.tif width 1140 height 765 supersample 3
> select add #6
7202 atoms, 7386 bonds, 28 pseudobonds, 924 residues, 4 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.91653,-0.39954,-0.018614,-3.4849,0.39988,0.91632,0.021201,89.045,0.0085851,-0.026875,0.9996,106.31
> view matrix models
> #6,0.80258,-0.59616,0.021582,25.469,0.59642,0.80263,-0.0081523,83.425,-0.012462,0.019414,0.99973,103.57
> fitmap #6 inMap #4
Fit molecule NaCT_PF4_daneng.cif (#6) to map NaCT_inhibitor1_BI_NU_refine.mrc
(#4) using 7202 atoms
average map value = 0.02, steps = 96
shifted from previous position = 0.498
rotated from previous position = 4.72 degrees
atoms outside contour = 5997, contour level = 0.053878
Position of NaCT_PF4_daneng.cif (#6) relative to
NaCT_inhibitor1_BI_NU_refine.mrc (#4) coordinates:
Matrix rotation and translation
0.12957825 -0.13138116 -0.98282678 191.53602301
-0.91053385 0.37668501 -0.17040103 164.94876921
0.39260359 0.91697731 -0.07081681 -39.41459482
Axis 0.56673665 -0.71686805 -0.40609084
Axis point 180.20016292 0.00000000 31.65342933
Rotation angle (degrees) 106.39613688
Shift along axis 6.30988657
> show #!5 models
> select subtract #6
Nothing selected
> select add #5
3 models selected
> ui mousemode right "move picked models"
> view matrix models
> #5,0.8816,-0.36788,0.2957,-48.563,0.25017,0.89546,0.36818,65.502,-0.40024,-0.25062,0.88148,189.58
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.62203,-0.78139,0.050116,47.833,0.78284,0.62192,-0.019621,78.173,-0.015836,0.051437,0.99855,105.03
> ui mousemode right "move picked models"
> view matrix models
> #5,0.62203,-0.78139,0.050116,59.056,0.78284,0.62192,-0.019621,78.532,-0.015836,0.051437,0.99855,103.76
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.
> select add #4
6 models selected
> fitmap #4 inMap #5
Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_PF4_daneng.map using
16959 points
correlation = 0.2194, correlation about mean = 0.05495, overlap = 100.4
steps = 100, shift = 2.89, angle = 7.58 degrees
Position of NaCT_inhibitor1_BI_NU_refine.mrc (#4) relative to
NaCT_PF4_daneng.map (#5) coordinates:
Matrix rotation and translation
-0.00937606 -0.75750504 0.65276198 118.86565169
-0.28782334 0.62720880 0.72371738 11.93407458
-0.95763762 -0.18109451 -0.22390838 222.77778194
Axis -0.47472837 0.84492963 0.24642827
Axis point 158.28884611 0.00000000 56.44756915
Rotation angle (degrees) 107.64015346
Shift along axis 8.55329959
> hide #!6 models
> undo
> view matrix models
> #5,0.62203,-0.78139,0.050116,55.689,0.78284,0.62192,-0.019621,81.26,-0.015836,0.051437,0.99855,105.32
> view matrix models
> #5,0.62203,-0.78139,0.050116,58.483,0.78284,0.62192,-0.019621,78.791,-0.015836,0.051437,0.99855,101.3
> view matrix models
> #5,0.62203,-0.78139,0.050116,61.9,0.78284,0.62192,-0.019621,81.582,-0.015836,0.051437,0.99855,101.33
> select add #6
7202 atoms, 7386 bonds, 28 pseudobonds, 924 residues, 7 models selected
> fitmap #6 inMap #5
Fit molecule NaCT_PF4_daneng.cif (#6) to map NaCT_PF4_daneng.map (#5) using
7202 atoms
average map value = 0.07301, steps = 80
shifted from previous position = 2.31
rotated from previous position = 3.24 degrees
atoms outside contour = 6001, contour level = 0.32651
Position of NaCT_PF4_daneng.cif (#6) relative to NaCT_PF4_daneng.map (#5)
coordinates:
Matrix rotation and translation
0.93622815 0.34552280 -0.06395973 -20.30498607
-0.33791562 0.93520690 0.10583525 32.31214349
0.09638407 -0.07747295 0.99232457 -2.30568729
Axis -0.25265267 -0.22100097 -0.94197941
Axis point 81.59424250 73.70779532 0.00000000
Rotation angle (degrees) 21.27023524
Shift along axis 0.16100402
> hide #!4 models
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.57484,-0.81744,0.036626,72.078,0.81819,0.57483,-0.011917,81.867,-0.011312,0.036817,0.99926,102.28,#6,0.81794,-0.5687,-0.086936,33.908,0.57062,0.82121,-0.0033193,83.855,0.073281,-0.046892,0.99621,101.4
> view matrix models
> #5,0.52462,-0.85089,0.027741,81.823,0.85121,0.52368,-0.034629,86.048,0.014938,0.04178,0.99902,99.002,#6,0.78136,-0.61664,-0.09608,43.613,0.61663,0.78655,-0.033382,85.765,0.096156,-0.033162,0.99481,97.745
> select subtract #5
7202 atoms, 7386 bonds, 28 pseudobonds, 924 residues, 4 models selected
> view matrix models
> #6,0.58782,-0.79612,-0.14373,88.654,0.79645,0.60066,-0.069746,90.432,0.14186,-0.073472,0.98716,98.017
> fitmap #6 inMap #5
Fit molecule NaCT_PF4_daneng.cif (#6) to map NaCT_PF4_daneng.map (#5) using
7202 atoms
average map value = 0.6613, steps = 100
shifted from previous position = 3.43
rotated from previous position = 11.1 degrees
atoms outside contour = 1504, contour level = 0.32651
Position of NaCT_PF4_daneng.cif (#6) relative to NaCT_PF4_daneng.map (#5)
coordinates:
Matrix rotation and translation
0.99999928 0.00019541 -0.00118212 0.09624853
-0.00019524 0.99999997 0.00014340 0.00390135
0.00118215 -0.00014317 0.99999929 -0.09049126
Axis -0.11873948 -0.97964280 -0.16186696
Axis point 76.67943902 0.00000000 81.31311248
Rotation angle (degrees) 0.06913881
Shift along axis -0.00060288
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!7 models
> select subtract #6
Nothing selected
> select add #7
2 models selected
> view matrix models
> #7,-0.11445,0.75543,-0.64515,52.398,0.084644,0.65447,0.75133,93.088,0.98982,0.031385,-0.13885,121.31
> view matrix models
> #7,0.071953,0.8597,-0.50571,13.441,0.05422,0.50291,0.86264,99.645,0.99593,-0.089489,-0.010427,120.22
> fitmap #7 inMap #5
Fit map NaCT_apo_NU_refine.mrc z flip in map NaCT_PF4_daneng.map using 219319
points
correlation = 0.2179, correlation about mean = 0.05573, overlap = 1072
steps = 108, shift = 2.31, angle = 5.94 degrees
Position of NaCT_apo_NU_refine.mrc z flip (#7) relative to NaCT_PF4_daneng.map
(#5) coordinates:
Matrix rotation and translation
0.00052605 0.87578287 0.48270499 -16.15807808
0.03823494 -0.48236972 0.87513290 64.78700313
0.99926865 0.01799584 -0.03373925 9.70572934
Axis -0.65681319 -0.39583614 -0.64180229
Axis point 0.00000000 36.14910919 -3.18196835
Rotation angle (degrees) 139.26988212
Shift along axis -21.26135782
> hide #!5 models
> hide #!7 models
> show #!5 models
> show #!4 models
> select add #4
4 models selected
> view matrix models
> #7,-0.02912,0.65231,-0.75739,64.851,0.080278,0.75679,0.64871,95.555,0.99635,-0.041912,-0.074404,124.11,#4,0.24629,-0.84154,-0.48079,144.76,-0.19113,-0.5285,0.82714,219.66,-0.95016,-0.11183,-0.29101,329.48
> fitmap #4 inMap #5
Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_PF4_daneng.map using
16959 points
correlation = 0.2009, correlation about mean = 0.0192, overlap = 91.7
steps = 60, shift = 1.52, angle = 3.76 degrees
Position of NaCT_inhibitor1_BI_NU_refine.mrc (#4) relative to
NaCT_PF4_daneng.map (#5) coordinates:
Matrix rotation and translation
-0.05416137 -0.87813800 0.47533167 146.12958841
-0.40066211 0.45514067 0.79518353 33.00785917
-0.91462365 -0.14737916 -0.37648767 231.34571047
Axis -0.53985291 0.79609710 0.27347439
Axis point 168.44130562 -0.00000000 54.02964318
Rotation angle (degrees) 119.19307708
Shift along axis 10.65610329
> view matrix models
> #7,0.1163,0.73397,-0.66915,36.001,-0.23254,0.67511,0.70011,126.33,0.96561,0.074183,0.24919,85.822,#4,0.12708,-0.92183,-0.36617,151.19,0.054535,-0.36211,0.93054,172.45,-0.99039,-0.13822,0.0042549,307.45
> view matrix models
> #7,0.14363,0.69949,-0.70006,39.406,-0.21837,0.71236,0.66698,125.06,0.96524,0.057077,0.25506,86.746,#4,0.10813,-0.90416,-0.41329,155.63,0.05285,-0.40991,0.91059,178.82,-0.99273,-0.1203,0.0034614,306.1
> fitmap #4 inMap #5
Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_PF4_daneng.map using
16959 points
correlation = 0.2171, correlation about mean = 0.02131, overlap = 102
steps = 88, shift = 3.25, angle = 5.74 degrees
Position of NaCT_inhibitor1_BI_NU_refine.mrc (#4) relative to
NaCT_PF4_daneng.map (#5) coordinates:
Matrix rotation and translation
0.16634675 -0.78249500 0.60002528 108.30083016
-0.09921204 0.59213404 0.79970885 -5.07453912
-0.98106357 -0.19255870 0.02086665 204.93816356
Axis -0.49918107 0.79540000 0.34373987
Axis point 165.48787126 0.00000000 39.15681814
Rotation angle (degrees) 96.33412445
Shift along axis 12.34740450
> ui mousemode right "move picked models"
> view matrix models
> #4,0.14447,-0.91969,-0.3651,153.48,0.12361,-0.34931,0.92882,163.42,-0.98176,-0.17932,0.063221,308.08
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.034577,0.56533,-0.82414,73.111,-0.10668,0.82201,0.55939,114.82,0.99369,0.068576,0.088732,98.519,#4,0.26403,-0.81897,-0.50949,146.68,0.060617,-0.5131,0.85619,190.84,-0.96261,-0.25694,-0.085828,327.18
> fitmap #4 inMap #5
Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_PF4_daneng.map using
16959 points
correlation = 0.2591, correlation about mean = 0.06695, overlap = 134
steps = 176, shift = 1.72, angle = 7.2 degrees
Position of NaCT_inhibitor1_BI_NU_refine.mrc (#4) relative to
NaCT_PF4_daneng.map (#5) coordinates:
Matrix rotation and translation
0.15206260 -0.89697867 0.41509786 135.17317197
-0.11694582 0.40070302 0.90871380 -3.25614042
-0.98142786 -0.18672534 -0.04396597 212.20325818
Axis -0.56502562 0.72032555 0.40233959
Axis point 179.49458021 0.00000000 31.95919307
Rotation angle (degrees) 104.21730485
Shift along axis 6.65598668
> hide #!4 models
> hide #!5 models
> select subtract #4
2 models selected
> select subtract #7
Nothing selected
> volume #8 level 0.1162
> surface dust #8 size 11.5
> show #!7 models
> select add #7
2 models selected
> view matrix models
> #7,-0.12196,0.7327,-0.66954,58.16,-0.22042,0.63773,0.73805,125.86,0.96775,0.23759,0.083722,85.926
> ui mousemode right "move picked models"
> view matrix models
> #7,-0.12196,0.7327,-0.66954,65.819,-0.22042,0.63773,0.73805,113.73,0.96775,0.23759,0.083722,83.622
> view matrix models
> #7,-0.12196,0.7327,-0.66954,64.945,-0.22042,0.63773,0.73805,113.33,0.96775,0.23759,0.083722,88.927
> fitmap #7 inMap #8
Fit map NaCT_apo_NU_refine.mrc z flip in map NaCT_inhibitor2_PF4_NU_refine.mrc
z flip using 219319 points
correlation = 0.9678, correlation about mean = 0.7446, overlap = 2277
steps = 76, shift = 2.46, angle = 10.9 degrees
Position of NaCT_apo_NU_refine.mrc z flip (#7) relative to
NaCT_inhibitor2_PF4_NU_refine.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.99979866 -0.01060064 0.01703819 0.00080321
0.01071757 0.99991956 -0.00678627 1.28540241
-0.01696488 0.00696750 0.99983184 -0.71161149
Axis 0.32419360 0.80149553 0.50249719
Axis point -61.99720868 0.00000000 12.02417600
Rotation angle (degrees) 1.21546438
Shift along axis 0.67292190
> select subtract #7
Nothing selected
> volume #8 level 0.1335
> save /Users/haoranfu/Desktop/PF4a.tif width 1140 height 765 supersample 3
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/haoranfu/Downloads/7jsk.cif
7jsk.cif title:
Structure of the NaCT-Citrate complex [more info...]
Chain information for 7jsk.cif #1
---
Chain | Description | UniProt
A B | Solute carrier family 13 member 5 | S13A5_HUMAN 1-568
Non-standard residues in 7jsk.cif #1
---
CIT — citric acid
NA — sodium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac mini
Model Identifier: Mac16,10
Model Number: Z1CF0005RD/A
Chip: Apple M4
Total Number of Cores: 10 (4 performance and 6 efficiency)
Memory: 16 GB
System Firmware Version: 11881.101.1
OS Loader Version: 11881.101.1
Software:
System Software Overview:
System Version: macOS 15.4.1 (24E263)
Kernel Version: Darwin 24.4.0
Time since boot: 2 days, 15 hours, 39 minutes
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL U2715H:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Dell S2716DG:
Resolution: 1440 x 2560
UI Looks like: 720 x 1280 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: 270
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 6 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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