![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17134 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 (last modified by )
The following bug report has been submitted:
Platform: macOS-15.3.2-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 0x00000002082f8840 (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, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.dssp._dssp (total: 53)
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"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 2195,
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"build" : "24D81",
"releaseType" : "User"
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"captureTime" : "2025-03-19 16:18:49.5124 +0100",
"codeSigningMonitor" : 1,
"incident" : "442AEC30-C71E-4B8D-9713-7962AA24FADF",
"pid" : 2976,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-19 10:05:04.6060 +0100",
"procStartAbsTime" : 22607304214,
"procExitAbsTime" : 445990291587,
"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"},
"storeInfo" : {"deviceIdentifierForVendor":"6B169C76-CA35-514E-8B10-F8F8A1295F79","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "9575A0BD-1234-9581-1E01-974F4B4A7465",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "B527D14B-73D5-4ED3-9230-DA9FEB14A940",
"wakeTime" : 1,
"sleepWakeUUID" : "4DC6BF73-8AFD-467F-A640-B1CDCEDB4C6F",
"sip" : "enabled",
"vmRegionInfo" : "0x212ea5f763c8 is not in any region. Bytes after previous region: 36003200328649 Bytes before following region: 69068879600696\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000212ea5f763c8","rawCodes":[1,36484236665800],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000212ea5f763c8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":2976},
"vmregioninfo" : "0x212ea5f763c8 is not in any region. Bytes after previous region: 36003200328649 Bytes before following region: 69068879600696\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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[deleted to fit within ticket limits]
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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/u0159610/SwitchLab Dropbox/brajabandhu
> pradhan/Heterotypic_Abeta_medin_manuscript/Data/Morphology_1_maps/Morpholgy_1_Processed_Job101.mrc"
Opened Morpholgy_1_Processed_Job101.mrc as #1, grid size 400,400,400, pixel
0.71, shown at level 0.0164, step 2, values float32
> volume #1 step 1
> volume #1 level 0.133
> set bgColor white
> volume #1 level 0.1089
> lighting soft
> save /Users/u0159610/Desktop/image18.png supersample 3
> color #1 #73fdffff models
> color #1 #7a81ffff models
> color #1 #0433ffff models
> color #1 #7a81ffff models
> color #1 #ff8ad8ff models
> color #1 #d783ffff models
> color #1 #7a81ffff models
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> color #1 #945200ff models
> color #1 #009051ff models
> color #1 #8efa00ff models
> color #1 #00f900ff models
> color #1 #ff7e79ff models
> color #1 #ff85ffff models
> color #1 #7a81ffff models
> color #1 #ff7e79ff models
> color #1 #ff85ffff models
> color #1 #d783ffff models
> color #1 #ff7e79ff models
> color #1 #7a81ffff models
> color #1 #0433ffff models
> color #1 #7a81ffff models
> color #1 #6c72e2ff models
> color #1 #6e75e6ff models
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> color #1 #d0e6b1ff models
> color #1 #cce6d4ff models
> color #1 #ac82e6ff models
> color #1 #3d2e51ff models
> color #1 #00f900ff models
> color #1 #fffc79ff models
> color #1 #ff7e79ff models
> color #1 #ff2600ff models
> color #1 #941100ff models
> color #1 #ff7e79ff models
> color #1 #d783ffff models
> color #1 #7a81ffff models
> color #1 #0433ffff models
> color #1 #7a81ffff models
> color #1 #d783ffff models
> color #1 #7a81ffff models
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> color #1 #d783ffff models
> color #1 #7a81ffff models
> ui tool show "Map Statistics"
> measure mapstats
Map Morpholgy_1_Processed_Job101.mrc #1, minimum -0.001785, maximum 2.237,
mean 0.003323, SD 0.04851, RMS 0.04862
> ui tool show Toolbar
> ui tool show "Scale Bar"
> set bgColor black
> set bgColor white
> scalebar
> scalebar 50
> scalebar ypos 0.9
> scalebar xpos 0.9
> scalebar xpos 0.1
> scalebar xpos 0.2
> scalebar ypos 0.1
> save /Users/u0159610/Desktop/PopulationA.png supersample 20
> transparentBackground true
> volume #1 level 0.04265
> volume #1 color #7a81ff28
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> ui tool show "Side View"
> open "/Users/u0159610/SwitchLab Dropbox/brajabandhu
> pradhan/Heterotypic_Abeta_medin_manuscript/Data/Morphology_1_Models/morphology1_extradenisty_8layersMerged.pdb"
Chain information for morphology1_extradenisty_8layersMerged.pdb #3
---
Chain | Description
A B C D E F G H I J K L M N O P | No description available
q r s t u v w x | No description available
> style stick
Changed 3352 atom styles
> color #3 #7a81ffff
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> color #3 #4f54a5ff
> color #3 #6338a5ff
> color #3 #4765a5ff
> color #3 #5173bbff
> color #3 #89bb3aff
> color #3 #bb5b46ff
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> preset "molecular surfaces" "chain id coloring (opaque)"
Using preset: Molecular Surfaces / Chain ID Coloring (Opaque)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color bychain targ s trans 0
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
Computing secondary structure
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> scalebar off
> scalebar 50 xpos 0.2
> scalebar 1
> scalebar 10
> scalebar off
> volume #1 level 0.291
> color #1#!3 byelement
> hide #!1 models
> select /E
185 atoms, 186 bonds, 26 residues, 1 model selected
> hide sel atoms
> select /M
185 atoms, 186 bonds, 26 residues, 1 model selected
> hide sel atoms
> select /M/K
370 atoms, 372 bonds, 52 residues, 1 model selected
> hide sel atoms
> select /M/K/s/C
604 atoms, 606 bonds, 88 residues, 1 model selected
> hide sel atoms
> show #!1 models
> stereo
Unknown command: stereo
> mono
Unknown command: mono
> camera stereo
Could not switch graphics mode. Graphics driver did not create OpenGL context.
> camera mono
> camera ortho
> volume #1 level 0.2868
> volume #1 level 0.1668
> hide #!1 models
> hide /t
> show #!1 models
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting simple
> lighting full
> hide /tu
> hide /t/u
> save /Users/u0159610/Desktop/PopulationA_topview.png supersample 20
> transparentBackground true
> volume #1 level 0.4731
Unsupported scale factor (0.000000) detected on Display1
> volume #1 level 0.2399
> hide #!1 models
> hide /r
> hide /r/q
> show #!1 models
> volume #1 level 0.07913
> hide #!3 models
> open "/Users/u0159610/SwitchLab Dropbox/brajabandhu
> pradhan/Heterotypic_Abeta_medin_manuscript/Data/Morphology_1_Models/morphology1UNit_corrrectedt-0.pdb"
Chain information for morphology1UNit_corrrectedt-0.pdb #5
---
Chain | Description
M | No description available
Computing secondary structure
> dssp #5
Computing secondary structure
> style #5 stick
Changed 185 atom styles
> style #5 stick
Changed 185 atom styles
> select add #5
789 atoms, 792 bonds, 114 residues, 6 models selected
> style sel & #5 stick
Changed 185 atom styles
> style sel & #5 stick
Changed 185 atom styles
> show sel & #5 atoms
> select subtract #5
604 atoms, 606 bonds, 88 residues, 5 models selected
> color #5 #eb27fdff
> color #5 #aefd4dff
> color #5 #426ffdff
> select add #5
789 atoms, 792 bonds, 114 residues, 6 models selected
> color (#5 & sel) byelement
> select clear
> color #5 byatom
> ui tool show "Color Actions"
> color byelement
> color byhetero
> color light gray
> color white
> color magenta
> color purple
> color cornflower blue
> color yellow
> color red
> color byelement
> color byhetero
> color light sea green
> color medium blue
> color cornflower blue
> color byhetero
> color byelement
> color byhetero
> color bynucleotide
> color bychain
> color bypolymer
> color byhetero
> color byelement
> color byelement target a
> color byhetero target a
Cannot color background by het
> color byelement target a
> color byhetero target a
> color forest green target a
> color byelement target a
> color light sea green target a
> hide #5 cartoons
> show #5 cartoons
> hide #5 cartoons
> color byelement target a
> color magenta target a
> color byelement target a
> select add #5
185 atoms, 186 bonds, 26 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.66404,-0.71791,-0.20895,375.27,-0.70605,0.69403,-0.14074,166.66,0.24606,0.054072,-0.96775,229.78
> view matrix models
> #5,0.70752,0.65113,0.27469,-88.788,0.66238,-0.74649,0.063393,144.79,0.24633,0.13709,-0.95944,216.68
> view matrix models
> #5,0.64818,0.71358,0.26583,-87.838,0.72173,-0.68701,0.084345,124.67,0.24282,0.13719,-0.96032,217.31
> view matrix models
> #5,0.68496,0.65314,0.32286,-92.475,0.67043,-0.73851,0.071643,141.32,0.28523,0.16738,-0.94373,204.47
> view matrix models
> #5,0.98614,0.019482,0.16477,-23.67,-0.040699,0.99114,0.12639,-10.348,-0.16085,-0.13135,0.9782,45.381
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.98614,0.019482,0.16477,-34.026,-0.040699,0.99114,0.12639,-18.512,-0.16085,-0.13135,0.9782,46
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.99592,0.030301,0.085001,265.29,-0.035085,-0.99785,-0.055357,291.14,0.083141,-0.058114,0.99484,-2.486
> view matrix models
> #5,-0.99724,0.030601,0.067692,267.84,-0.03645,-0.99555,-0.08693,295.4,0.06473,-0.089157,0.99391,4.7864
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.99724,0.030601,0.067692,269.92,-0.03645,-0.99555,-0.08693,297.85,0.06473,-0.089157,0.99391,4.9295
> ui tool show "Fit in Map"
> fitmap #5 inMap #1
Fit molecule morphology1UNit_corrrectedt-0.pdb (#5) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 185 atoms
average map value = 0.3618, steps = 76
shifted from previous position = 1.06
rotated from previous position = 2.13 degrees
atoms outside contour = 67, contour level = 0.07913
Position of morphology1UNit_corrrectedt-0.pdb (#5) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99817084 -0.00414635 0.06031350 276.34192556
-0.00191319 -0.99497910 -0.10006447 295.44684437
0.06042557 -0.09999683 0.99315123 6.73438554
Axis 0.03023637 -0.05009989 0.99828641
Axis point 137.98621669 147.96980980 0.00000000
Rotation angle (degrees) 179.93591497
Shift along axis 0.27656870
[deleted to fit within ticket limits]
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7656, correlation about mean = 0.7479, overlap = 66.33
steps = 28, shift = 0.0164, angle = 0.0274 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982707 -0.01858489 -0.00065507 2.71805464
0.01858140 0.99981496 -0.00497766 -1.95402146
0.00074745 0.00496463 0.99998740 -5.64894959
Axis 0.25824996 -0.03643035 0.96539100
Axis point 116.42950310 210.20378158 0.00000000
Rotation angle (degrees) 1.10297434
Shift along axis -4.68032191
Average map value = 0.5722 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7655, correlation about mean = 0.7478, overlap = 66.31
steps = 60, shift = 0.00128, angle = 0.0155 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982763 -0.01856229 -0.00039408 2.68299887
0.01856007 0.99981503 -0.00504214 -1.94343366
0.00048760 0.00503395 0.99998721 -5.62116856
Axis 0.26188233 -0.02291522 0.96482772
Axis point 112.57159427 209.46947180 0.00000000
Rotation angle (degrees) 1.10231393
Shift along axis -4.67629504
Average map value = 0.5721 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7653, correlation about mean = 0.7473, overlap = 66.28
steps = 44, shift = 0.00145, angle = 0.0167 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982806 -0.01854265 -0.00012217 2.64830006
0.01854178 0.99981484 -0.00514577 -1.92883525
0.00021757 0.00514262 0.99998675 -5.59909258
Axis 0.26732349 -0.00882742 0.96356641
Axis point 108.33830056 209.14511033 0.00000000
Rotation angle (degrees) 1.10262896
Shift along axis -4.67011807
Average map value = 0.5718 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7652, correlation about mean = 0.7473, overlap = 66.3
steps = 44, shift = 0.00261, angle = 0.00977 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982729 -0.01858401 -0.00015909 2.65722322
0.01858299 0.99981490 -0.00498444 -1.95362071
0.00025169 0.00498062 0.99998756 -5.58402025
Axis 0.25895432 -0.01067469 0.96583058
Axis point 109.88455156 207.23484921 0.00000000
Rotation angle (degrees) 1.10249353
Shift along axis -4.68426380
Average map value = 0.5717 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7667, correlation about mean = 0.7495, overlap = 66.24
steps = 48, shift = 0.0165, angle = 0.0264 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982658 -0.01862024 -0.00032098 2.68258555
0.01861823 0.99981200 -0.00541480 -1.90644765
0.00042175 0.00540788 0.99998529 -5.64902585
Axis 0.27903269 -0.01914924 0.96009066
Axis point 109.31400094 212.56079530 0.00000000
Rotation angle (degrees) 1.11121832
Shift along axis -4.63854085
Average map value = 0.5732 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7656, correlation about mean = 0.7479, overlap = 66.3
steps = 28, shift = 0.0126, angle = 0.0225 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982697 -0.01858935 -0.00068137 2.72226990
0.01858551 0.99981343 -0.00526171 -1.92054237
0.00077906 0.00524814 0.99998592 -5.68933931
Axis 0.27185655 -0.03777672 0.96159604
Axis point 114.94689108 213.49590113 0.00000000
Rotation angle (degrees) 1.10758338
Shift along axis -4.65822744
Average map value = 0.5722 for 185 atoms, 29 outside contour
> style sel stick
Changed 185 atom styles
> style sel stick
Changed 185 atom styles
> hide sel atoms
> show sel atoms
> hide sel cartoons
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.765, correlation about mean = 0.7469, overlap = 66.27
steps = 48, shift = 0.00362, angle = 0.026 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99983086 -0.01838953 -0.00027530 2.64511899
0.01838782 0.99981697 -0.00528301 -1.89053085
0.00037240 0.00527706 0.99998601 -5.64061933
Axis 0.27594394 -0.01692499 0.96102471
Axis point 109.22013791 212.74245256 0.00000000
Rotation angle (degrees) 1.09638976
Shift along axis -4.65887275
Average map value = 0.5716 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7655, correlation about mean = 0.7477, overlap = 66.3
steps = 40, shift = 0.00266, angle = 0.0137 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982934 -0.01847239 -0.00024099 2.65229082
0.01847094 0.99981659 -0.00506060 -1.92924987
0.00033443 0.00505529 0.99998717 -5.60265192
Axis 0.26407005 -0.01502100 0.96438653
Axis point 110.32768940 209.37519060 0.00000000
Rotation angle (degrees) 1.09749883
Shift along axis -4.67375221
Average map value = 0.572 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7669, correlation about mean = 0.75, overlap = 66.3
steps = 44, shift = 0.0132, angle = 0.0119 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982584 -0.01866038 -0.00028300 2.68147870
0.01865874 0.99981350 -0.00498194 -1.96540373
0.00037591 0.00497579 0.99998755 -5.58465357
Axis 0.25776923 -0.01705693 0.96605594
Axis point 111.67442851 207.17186729 0.00000000
Rotation angle (degrees) 1.10674778
Shift along axis -4.67036131
Average map value = 0.5735 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7655, correlation about mean = 0.7477, overlap = 66.31
steps = 28, shift = 0.0139, angle = 0.0106 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982717 -0.01858597 -0.00042657 2.69068456
0.01858357 0.99981445 -0.00507061 -1.94353852
0.00052073 0.00506181 0.99998705 -5.63007317
Axis 0.26292380 -0.02458120 0.96450342
Axis point 112.86277359 209.85444386 0.00000000
Rotation angle (degrees) 1.10408631
Shift along axis -4.67500527
Average map value = 0.5721 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7661, correlation about mean = 0.7487, overlap = 66.26
steps = 44, shift = 0.00877, angle = 0.0176 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982643 -0.01862921 -0.00026377 2.67726022
0.01862754 0.99981229 -0.00532837 -1.91847052
0.00036298 0.00532253 0.99998577 -5.63487308
Axis 0.27483104 -0.01617233 0.96135652
Axis point 109.15767797 211.30045601 0.00000000
Rotation angle (degrees) 1.11029996
Shift along axis -4.65030159
Average map value = 0.5727 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7652, correlation about mean = 0.7473, overlap = 66.31
steps = 44, shift = 0.0122, angle = 0.0229 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982777 -0.01854992 -0.00057764 2.70364492
0.01854674 0.99981502 -0.00509451 -1.93526352
0.00067203 0.00508292 0.99998686 -5.65725892
Axis 0.26443311 -0.03246937 0.96385729
Axis point 114.63744033 211.32869188 0.00000000
Rotation angle (degrees) 1.10265991
Shift along axis -4.67502019
Average map value = 0.5717 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7664, correlation about mean = 0.7491, overlap = 66.25
steps = 40, shift = 0.0148, angle = 0.0211 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982662 -0.01861706 -0.00037946 2.68926053
0.01861474 0.99981216 -0.00539782 -1.90790437
0.00047988 0.00538982 0.99998536 -5.65751373
Axis 0.27822794 -0.02216343 0.96025934
Axis point 110.16878053 212.80157414 0.00000000
Rotation angle (degrees) 1.11082426
Shift along axis -4.64216727
Average map value = 0.573 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7666, correlation about mean = 0.7493, overlap = 66.26
steps = 36, shift = 0.00127, angle = 0.0112 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982668 -0.01860872 -0.00057440 2.71289734
0.01860534 0.99981227 -0.00540926 -1.90515226
0.00067495 0.00539764 0.99998520 -5.68476450
Axis 0.27873237 -0.03222332 0.95982807
Axis point 112.59380150 214.22088613 0.00000000
Rotation angle (degrees) 1.11079366
Shift along axis -4.63883389
Average map value = 0.5731 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7666, correlation about mean = 0.7494, overlap = 66.26
steps = 40, shift = 0.00139, angle = 0.027 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982695 -0.01860224 -0.00015237 2.65918117
0.01860119 0.99981345 -0.00520126 -1.93001873
0.00024910 0.00519753 0.99998646 -5.59832625
Axis 0.26917924 -0.01039218 0.96303403
Axis point 108.45783392 209.30725652 0.00000000
Rotation angle (degrees) 1.10677930
Shift along axis -4.65552522
Average map value = 0.5731 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7657, correlation about mean = 0.748, overlap = 66.3
steps = 28, shift = 0.0108, angle = 0.0272 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982757 -0.01855924 -0.00062269 2.70969491
0.01855579 0.99981457 -0.00514900 -1.92999004
0.00071814 0.00513656 0.99998655 -5.66568244
Axis 0.26689941 -0.03479303 0.96309613
Axis point 114.87849569 212.03997166 0.00000000
Rotation angle (degrees) 1.10407783
Shift along axis -4.66623063
Average map value = 0.5723 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7655, correlation about mean = 0.7476, overlap = 66.27
steps = 44, shift = 0.000448, angle = 0.0168 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982884 -0.01849497 -0.00047971 2.68359563
0.01849211 0.99981444 -0.00539764 -1.89095318
0.00057945 0.00538784 0.99998532 -5.68024092
Axis 0.27983652 -0.02748087 0.95965427
Axis point 111.31624296 214.39673735 0.00000000
Rotation angle (degrees) 1.10421772
Shift along axis -4.64813439
Average map value = 0.572 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7654, correlation about mean = 0.7476, overlap = 66.31
steps = 48, shift = 0.00279, angle = 0.0239 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982733 -0.01857958 -0.00034519 2.67959664
0.01857762 0.99981486 -0.00501251 -1.94963781
0.00043826 0.00500523 0.99998738 -5.61155085
Axis 0.26025595 -0.02035365 0.96532511
Axis point 112.15308101 208.73478575 0.00000000
Rotation angle (degrees) 1.10277975
Shift along axis -4.67990770
Average map value = 0.572 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7662, correlation about mean = 0.7488, overlap = 66.27
steps = 40, shift = 0.00871, angle = 0.0142 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982825 -0.01852843 -0.00041020 2.68030961
0.01852602 0.99981461 -0.00524654 -1.91401148
0.00050733 0.00523804 0.99998615 -5.64395581
Axis 0.27218466 -0.02381960 0.96195017
Axis point 111.42009132 211.99539254 0.00000000
Rotation angle (degrees) 1.10358866
Shift along axis -4.65407414
Average map value = 0.5728 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7667, correlation about mean = 0.7496, overlap = 66.23
steps = 48, shift = 0.00681, angle = 0.0128 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982652 -0.01862274 -0.00033732 2.68512474
0.01862063 0.99981185 -0.00543533 -1.90439842
0.00043848 0.00542811 0.99998517 -5.65345130
Axis 0.27996280 -0.01999304 0.95980264
Axis point 109.40258500 212.86674545 0.00000000
Rotation angle (degrees) 1.11169837
Shift along axis -4.63638774
Average map value = 0.5732 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7657, correlation about mean = 0.748, overlap = 66.29
steps = 28, shift = 0.0126, angle = 0.0215 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982715 -0.01858013 -0.00067373 2.71962956
0.01857633 0.99981354 -0.00527354 -1.91799975
0.00077159 0.00526011 0.99998587 -5.68934090
Axis 0.27255524 -0.03739716 0.96141307
Axis point 114.76883287 213.61711452 0.00000000
Rotation angle (degrees) 1.10724573
Shift along axis -4.65682968
Average map value = 0.5723 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7661, correlation about mean = 0.7486, overlap = 66.27
steps = 40, shift = 0.00469, angle = 0.00571 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982693 -0.01859407 -0.00060457 2.71353216
0.01859058 0.99981290 -0.00534398 -1.91139375
0.00070382 0.00533181 0.99998554 -5.68502395
Axis 0.27579649 -0.03380058 0.96062158
Axis point 113.41825141 213.82359027 0.00000000
Rotation angle (degrees) 1.10899903
Shift along axis -4.64816780
Average map value = 0.5727 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7651, correlation about mean = 0.747, overlap = 66.27
steps = 40, shift = 0.00819, angle = 0.0117 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982880 -0.01849851 -0.00042818 2.67910523
0.01849594 0.99981446 -0.00538003 -1.89345310
0.00052762 0.00537119 0.99998544 -5.67416129
Axis 0.27898522 -0.02480210 0.95997505
Axis point 110.75670628 213.97223656 0.00000000
Rotation angle (degrees) 1.10406865
Shift along axis -4.65266091
Average map value = 0.5716 for 185 atoms, 29 outside contour
> fitmap #7 inMap #1 resolution 5
Fit map morphology1UNit_corrrectedt-13.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 935 points
correlation = 0.7665, correlation about mean = 0.7492, overlap = 66.25
steps = 36, shift = 0.0131, angle = 0.0127 degrees
Position of morphology1UNit_corrrectedt-13.pdb map 5 (#10) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
0.99982636 -0.01863277 -0.00026188 2.67733643
0.01863111 0.99981226 -0.00532304 -1.91922242
0.00036102 0.00531724 0.99998580 -5.63076750
Axis 0.27452962 -0.01607150 0.96144433
Axis point 109.14875392 211.15207095 0.00000000
Rotation angle (degrees) 1.11041087
Shift along axis -4.64781653
Average map value = 0.573 for 185 atoms, 29 outside contour
> save "/Users/u0159610/SwitchLab Dropbox/brajabandhu
> pradhan/Heterotypic_Abeta_medin_manuscript/Data/Morphology_1_Models/morphology1UNit_corrrectedt-18.pdb"
> models #7 relModel #1
> close #2-9#10-11
> open "/Users/u0159610/SwitchLab Dropbox/brajabandhu
> pradhan/Heterotypic_Abeta_medin_manuscript/Data/Morphology_1_Models/morphology1_protofibril_1.pdb"
Chain information for morphology1_protofibril_1.pdb #2
---
Chain | Description
A B C D E F G M | No description available
> show atoms
> style stick
Changed 1480 atom styles
> select add #2
1480 atoms, 1488 bonds, 208 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.99712,0.011368,-0.075002,284.09,-0.012056,-0.99989,0.0087208,277.74,-0.074895,0.0095999,0.99715,9.3875
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.99712,0.011368,-0.075002,290.59,-0.012056,-0.99989,0.0087208,283.16,-0.074895,0.0095999,0.99715,9.6066
Opened morphology1_protofibril_1.pdb map 5 as #3, grid size 41,59,42, pixel
1.67, shown at level 0.0872, step 1, values float32
Opened morphology1_protofibril_1.pdb map 5 as #4, grid size 41,59,42, pixel
1.67, shown at level 0.0872, step 1, values float32
> fitmap #2 inMap #1 resolution 5
Fit map morphology1_protofibril_1.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 5811 points
correlation = 0.7421, correlation about mean = 0.7363, overlap = 541.4
steps = 80, shift = 2.55, angle = 4.2 degrees
Position of morphology1_protofibril_1.pdb map 5 (#4) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99995626 -0.00781806 -0.00513678 286.10152571
0.00782294 -0.99996898 -0.00093033 280.91408265
-0.00512935 -0.00097048 0.99998640 3.37116897
Axis -0.00256655 -0.00047517 0.99999659
Axis point 142.50585215 141.01723168 0.00000000
Rotation angle (degrees) 179.55191207
Shift along axis 2.50338328
Average map value = 0.578 for 1480 atoms, 249 outside contour
> fitmap #2 inMap #1 resolution 5
Fit map morphology1_protofibril_1.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 5811 points
correlation = 0.7421, correlation about mean = 0.7362, overlap = 540.6
steps = 40, shift = 0.0117, angle = 0.00481 degrees
Position of morphology1_protofibril_1.pdb map 5 (#3) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99995625 -0.00780104 -0.00516443 286.10308444
0.00780634 -0.99996904 -0.00100774 280.92597963
-0.00515641 -0.00104801 0.99998618 3.39716076
Axis -0.00258023 -0.00051390 0.99999654
Axis point 142.50784539 141.02205278 0.00000000
Rotation angle (degrees) 179.55287534
Shift along axis 2.51456918
Average map value = 0.5775 for 1480 atoms, 248 outside contour
> fitmap #2 inMap #1 resolution 5
Fit map morphology1_protofibril_1.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 5811 points
correlation = 0.7421, correlation about mean = 0.7363, overlap = 540.4
steps = 36, shift = 0.00142, angle = 0.0142 degrees
Position of morphology1_protofibril_1.pdb map 5 (#3) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99995674 -0.00781719 -0.00504326 286.09077048
0.00782345 -0.99996866 -0.00122230 280.94919131
-0.00503354 -0.00126170 0.99998656 3.40790841
Axis -0.00251922 -0.00062097 0.99999663
Axis point 142.50038467 141.03500871 0.00000000
Rotation angle (degrees) 179.55192266
Shift along axis 2.51271210
Average map value = 0.5775 for 1480 atoms, 247 outside contour
> fitmap #2 inMap #1 resolution 5
Fit map morphology1_protofibril_1.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 5811 points
correlation = 0.7421, correlation about mean = 0.7362, overlap = 540.2
steps = 40, shift = 0.0036, angle = 0.00163 degrees
Position of morphology1_protofibril_1.pdb map 5 (#3) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99995676 -0.00780803 -0.00505321 286.09110371
0.00781418 -0.99996877 -0.00119724 280.94764772
-0.00504370 -0.00123667 0.99998654 3.40947031
Axis -0.00252424 -0.00060844 0.99999663
Axis point 142.50121213 141.03355766 0.00000000
Rotation angle (degrees) 179.55245063
Shift along axis 2.51635444
Average map value = 0.5774 for 1480 atoms, 247 outside contour
> fitmap #2 inMap #1 resolution 5
Fit map morphology1_protofibril_1.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 5811 points
correlation = 0.7421, correlation about mean = 0.7363, overlap = 540.3
steps = 44, shift = 0.00182, angle = 0.00125 degrees
Position of morphology1_protofibril_1.pdb map 5 (#3) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99995677 -0.00781777 -0.00503622 286.09024756
0.00782394 -0.99996868 -0.00120685 280.94737346
-0.00502663 -0.00124620 0.99998661 3.40659334
Axis -0.00251573 -0.00061323 0.99999665
Axis point 142.50008162 141.03412344 0.00000000
Rotation angle (degrees) 179.55189200
Shift along axis 2.51457190
Average map value = 0.5774 for 1480 atoms, 247 outside contour
> fitmap #2 inMap #1 resolution 5
Fit map morphology1_protofibril_1.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 5811 points
correlation = 0.7421, correlation about mean = 0.7362, overlap = 540
steps = 44, shift = 0.00328, angle = 0.00163 degrees
Position of morphology1_protofibril_1.pdb map 5 (#3) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99995691 -0.00781010 -0.00502164 286.08770944
0.00781637 -0.99996871 -0.00123003 280.95131065
-0.00501187 -0.00126923 0.99998666 3.41096782
Axis -0.00250839 -0.00062478 0.99999666
Axis point 142.49933303 141.03556307 0.00000000
Rotation angle (degrees) 179.55232859
Shift along axis 2.51780327
Average map value = 0.5773 for 1480 atoms, 247 outside contour
> fitmap #2 inMap #1 resolution 5
Fit map morphology1_protofibril_1.pdb map 5 in map
Morpholgy_1_Processed_Job101.mrc using 5811 points
correlation = 0.7421, correlation about mean = 0.7363, overlap = 540.8
steps = 40, shift = 0.0102, angle = 0.00857 degrees
Position of morphology1_protofibril_1.pdb map 5 (#3) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99995670 -0.00776828 -0.00512700 286.09378473
0.00777419 -0.99996915 -0.00113273 280.94529717
-0.00511804 -0.00117254 0.99998624 3.40234733
Axis -0.00256128 -0.00057628 0.99999655
Axis point 142.50541169 141.02947923 0.00000000
Rotation angle (degrees) 179.55473496
Shift along axis 2.50766607
Average map value = 0.5778 for 1480 atoms, 248 outside contour
> view matrix models
> #2,-0.99996,-0.0077683,-0.005127,294.34,0.0077742,-0.99997,-0.0011327,248.55,-0.005118,-0.0011725,0.99999,0.5517
> undo
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5792, steps = 48
shifted from previous position = 0.0576
rotated from previous position = 0.123 degrees
atoms outside contour = 246, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997007 -0.00573243 -0.00519930 285.82903142
0.00573480 -0.99998347 -0.00044034 281.19550317
-0.00519669 -0.00047014 0.99998641 3.28690324
Axis -0.00259898 -0.00022756 0.99999660
Axis point 142.51571327 141.00784959 0.00000000
Rotation angle (degrees) 179.67148497
Shift along axis 2.48003732
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5792, steps = 44
shifted from previous position = 0.00322
rotated from previous position = 0.0182 degrees
atoms outside contour = 246, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997093 -0.00547606 -0.00530924 285.80734630
0.00547769 -0.99998497 -0.00029148 281.21275085
-0.00530756 -0.00032056 0.99998589 3.28504061
Axis -0.00265418 -0.00015295 0.99999647
Axis point 142.52298469 140.99797428 0.00000000
Rotation angle (degrees) 179.68619539
Shift along axis 2.48343229
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5793, steps = 40
shifted from previous position = 0.00277
rotated from previous position = 0.00923 degrees
atoms outside contour = 246, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997034 -0.00555959 -0.00533205 285.82105151
0.00556049 -0.99998454 -0.00015511 281.18426212
-0.00533110 -0.00018475 0.99998580 3.26711551
Axis -0.00266577 -0.00008490 0.99999644
Axis point 142.52402544 140.98957896 0.00000000
Rotation angle (degrees) 179.68143041
Shift along axis 2.48129621
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5787, steps = 40
shifted from previous position = 0.0155
rotated from previous position = 0.0242 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997169 -0.00542940 -0.00521320 285.79271700
0.00543229 -0.99998511 -0.00053972 281.25043116
-0.00521020 -0.00056802 0.99998629 3.31748221
Axis -0.00260583 -0.00027687 0.99999657
Axis point 142.51881750 141.01371336 0.00000000
Rotation angle (degrees) 179.68883277
Shift along axis 2.49487162
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5788, steps = 40
shifted from previous position = 0.0043
rotated from previous position = 0.00653 degrees
atoms outside contour = 246, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997146 -0.00546598 -0.00521904 285.79706178
0.00546831 -0.99998497 -0.00043172 281.23274521
-0.00521660 -0.00046025 0.99998631 3.29957890
Axis -0.00260889 -0.00022293 0.99999657
Axis point 142.51844379 141.00737829 0.00000000
Rotation angle (degrees) 179.68675309
Shift along axis 2.49125819
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5787, steps = 48
shifted from previous position = 0.00429
rotated from previous position = 0.00899 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997210 -0.00535497 -0.00521145 285.78226175
0.00535787 -0.99998551 -0.00054295 281.26070992
-0.00520846 -0.00057086 0.99998630 3.31761272
Axis -0.00260496 -0.00027839 0.99999657
Axis point 142.51880821 141.01352325 0.00000000
Rotation angle (degrees) 179.69309725
Shift along axis 2.49484973
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5791, steps = 44
shifted from previous position = 0.0112
rotated from previous position = 0.0208 degrees
atoms outside contour = 246, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997073 -0.00548505 -0.00533790 285.81256237
0.00548634 -0.99998494 -0.00022683 281.20405975
-0.00533658 -0.00025610 0.99998575 3.28157715
Axis -0.00266860 -0.00012067 0.99999643
Axis point 142.52500364 140.99421303 0.00000000
Rotation angle (degrees) 179.68568998
Shift along axis 2.48491184
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5787, steps = 44
shifted from previous position = 0.0101
rotated from previous position = 0.0173 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997144 -0.00547308 -0.00521489 285.79852385
0.00547577 -0.99998490 -0.00050197 281.23978161
-0.00521206 -0.00053051 0.99998630 3.31144457
Axis -0.00260672 -0.00025806 0.99999657
Axis point 142.51866518 141.01147807 0.00000000
Rotation angle (degrees) 179.68633605
Shift along axis 2.49385941
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5791, steps = 44
shifted from previous position = 0.0105
rotated from previous position = 0.0186 degrees
atoms outside contour = 246, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997071 -0.00549109 -0.00533461 285.81296892
0.00549224 -0.99998491 -0.00020128 281.20008446
-0.00533343 -0.00023058 0.99998577 3.27728030
Axis -0.00266699 -0.00010790 0.99999644
Axis point 142.52478468 140.99263101 0.00000000
Rotation angle (degrees) 179.68534819
Shift along axis 2.48466494
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5787, steps = 44
shifted from previous position = 0.00995
rotated from previous position = 0.0177 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997141 -0.00547821 -0.00521466 285.79911132
0.00548082 -0.99998488 -0.00048634 281.23710081
-0.00521192 -0.00051491 0.99998631 3.30880499
Axis -0.00260663 -0.00025025 0.99999657
Axis point 142.51860088 141.01048918 0.00000000
Rotation angle (degrees) 179.68604419
Shift along axis 2.49344132
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5786, steps = 48
shifted from previous position = 0.00283
rotated from previous position = 0.000413 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997145 -0.00547507 -0.00521148 285.79912485
0.00547770 -0.99998489 -0.00049201 281.23863067
-0.00520870 -0.00052054 0.99998632 3.31180079
Axis -0.00260503 -0.00025308 0.99999657
Axis point 142.51882696 141.01103544 0.00000000
Rotation angle (degrees) 179.68622360
Shift along axis 2.49609969
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5792, steps = 44
shifted from previous position = 0.0161
rotated from previous position = 0.0188 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997065 -0.00550757 -0.00532952 285.81366129
0.00550865 -0.99998482 -0.00018777 281.19565799
-0.00532840 -0.00021712 0.99998580 3.27159509
Axis -0.00266447 -0.00010116 0.99999645
Axis point 142.52396879 140.99158284 0.00000000
Rotation angle (degrees) 179.68440566
Shift along axis 2.48159723
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5793, steps = 44
shifted from previous position = 0.00106
rotated from previous position = 0.000728 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997066 -0.00551379 -0.00532000 285.81328805
0.00551484 -0.99998479 -0.00018207 281.19391481
-0.00531892 -0.00021140 0.99998586 3.26845818
Axis -0.00265972 -0.00009831 0.99999646
Axis point 142.52333678 140.99114893 0.00000000
Rotation angle (degrees) 179.68405042
Shift along axis 2.48062122
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5786, steps = 40
shifted from previous position = 0.0183
rotated from previous position = 0.0204 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997163 -0.00543685 -0.00521542 285.79451310
0.00543960 -0.99998509 -0.00051407 281.24712352
-0.00521255 -0.00054243 0.99998629 3.31636988
Axis -0.00260697 -0.00026406 0.99999657
Axis point 142.51920162 141.01256790 0.00000000
Rotation angle (degrees) 179.68840992
Shift along axis 2.49703204
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5791, steps = 36
shifted from previous position = 0.0123
rotated from previous position = 0.0125 degrees
atoms outside contour = 245, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997091 -0.00549098 -0.00529745 285.80870867
0.00549274 -0.99998488 -0.00031826 281.21417063
-0.00529562 -0.00034735 0.99998594 3.28956553
Axis -0.00264825 -0.00016634 0.99999648
Axis point 142.52260656 140.99977920 0.00000000
Rotation angle (degrees) 179.68533677
Shift along axis 2.48588293
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5791, steps = 44
shifted from previous position = 0.00174
rotated from previous position = 0.00201 degrees
atoms outside contour = 246, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997106 -0.00545755 -0.00530357 285.80434808
0.00545927 -0.99998507 -0.00030994 281.21774690
-0.00530180 -0.00033889 0.99998591 3.28761910
Axis -0.00265132 -0.00016215 0.99999647
Axis point 142.52277567 140.99916406 0.00000000
Rotation angle (degrees) 179.68725341
Shift along axis 2.48424927
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5786, steps = 48
shifted from previous position = 0.0129
rotated from previous position = 0.0135 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997148 -0.00546826 -0.00521155 285.79810682
0.00547107 -0.99998491 -0.00052608 281.24358372
-0.00520859 -0.00055458 0.99998631 3.31647707
Axis -0.00260502 -0.00027010 0.99999657
Axis point 142.51878980 141.01305910 0.00000000
Rotation angle (degrees) 179.68660874
Shift along axis 2.49599183
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5792, steps = 44
shifted from previous position = 0.0159
rotated from previous position = 0.0203 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997066 -0.00550547 -0.00532931 285.81337430
0.00550658 -0.99998483 -0.00019458 281.19679464
-0.00532816 -0.00022392 0.99998580 3.27271288
Axis -0.00266435 -0.00010457 0.99999645
Axis point 142.52397171 140.99200730 0.00000000
Rotation angle (degrees) 179.68452521
Shift along axis 2.48179026
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5792, steps = 40
shifted from previous position = 0.00119
rotated from previous position = 0.00259 degrees
atoms outside contour = 246, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997044 -0.00553904 -0.00533541 285.81907960
0.00553999 -0.99998466 -0.00016485 281.18883978
-0.00533442 -0.00019440 0.99998578 3.27064228
Axis -0.00266744 -0.00008975 0.99999644
Axis point 142.52448337 140.99040651 0.00000000
Rotation angle (degrees) 179.68260637
Shift along axis 2.48298781
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5792, steps = 40
shifted from previous position = 0.000196
rotated from previous position = 0.0052 degrees
atoms outside contour = 246, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997017 -0.00562184 -0.00529981 285.82618470
0.00562274 -0.99998420 -0.00015448 281.17617465
-0.00529886 -0.00018428 0.99998597 3.26445272
Axis -0.00264965 -0.00008463 0.99999649
Axis point 142.52219741 140.98999022 0.00000000
Rotation angle (degrees) 179.67786361
Shift along axis 2.48330521
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5787, steps = 44
shifted from previous position = 0.0133
rotated from previous position = 0.022 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997145 -0.00546953 -0.00521654 285.79857251
0.00547220 -0.99998492 -0.00049855 281.23999553
-0.00521374 -0.00052708 0.99998629 3.31219617
Axis -0.00260755 -0.00025635 0.99999657
Axis point 142.51894163 141.01132826 0.00000000
Rotation angle (degrees) 179.68653980
Shift along axis 2.49485442
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5792, steps = 44
shifted from previous position = 0.0122
rotated from previous position = 0.0182 degrees
atoms outside contour = 246, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997070 -0.00549372 -0.00533315 285.81291481
0.00549489 -0.99998490 -0.00020366 281.19991373
-0.00533195 -0.00023295 0.99998578 3.27671658
Axis -0.00266626 -0.00010909 0.99999644
Axis point 142.52457021 140.99273622 0.00000000
Rotation angle (degrees) 179.68519686
Shift along axis 2.48397702
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5786, steps = 44
shifted from previous position = 0.014
rotated from previous position = 0.0194 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997149 -0.00545835 -0.00521981 285.79789135
0.00546115 -0.99998497 -0.00052179 281.24465593
-0.00521688 -0.00055028 0.99998626 3.31752343
Axis -0.00260916 -0.00026796 0.99999656
Axis point 142.51938599 141.01288306 0.00000000
Rotation angle (degrees) 179.68717684
Shift along axis 2.49645949
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5786, steps = 40
shifted from previous position = 0.000298
rotated from previous position = 0.00752 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997196 -0.00533670 -0.00525548 285.78559855
0.00533969 -0.99998560 -0.00055616 281.26563998
-0.00525244 -0.00058421 0.99998606 3.32739241
Axis -0.00262696 -0.00028503 0.99999651
Axis point 142.52180095 141.01470299 0.00000000
Rotation angle (degrees) 179.69414155
Shift along axis 2.49646357
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5793, steps = 48
shifted from previous position = 0.0186
rotated from previous position = 0.0257 degrees
atoms outside contour = 246, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997056 -0.00551274 -0.00534083 285.81528373
0.00551363 -0.99998480 -0.00015148 281.19034734
-0.00533992 -0.00018093 0.99998575 3.26662491
Axis -0.00267017 -0.00008304 0.99999643
Axis point 142.52443350 140.98926237 0.00000000
Rotation angle (degrees) 179.68411504
Shift along axis 2.48008691
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5786, steps = 40
shifted from previous position = 0.0177
rotated from previous position = 0.0245 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997174 -0.00541563 -0.00521659 285.79147244
0.00541857 -0.99998518 -0.00054872 281.25358844
-0.00521354 -0.00057697 0.99998627 3.32006684
Axis -0.00260751 -0.00028136 0.99999656
Axis point 142.51916361 141.01431597 0.00000000
Rotation angle (degrees) 179.68962035
Shift along axis 2.49571679
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5791, steps = 44
shifted from previous position = 0.0126
rotated from previous position = 0.0194 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997078 -0.00548312 -0.00532925 285.81113129
0.00548445 -0.99998495 -0.00023659 281.20544779
-0.00532788 -0.00026581 0.99998580 3.28140297
Axis -0.00266427 -0.00012554 0.99999644
Axis point 142.52441335 140.99477633 0.00000000
Rotation angle (degrees) 179.68579961
Shift along axis 2.48461185
> save "/Users/u0159610/SwitchLab Dropbox/brajabandhu
> pradhan/Heterotypic_Abeta_medin_manuscript/Data/Morphology_1_Models/morphology1_protofibril_0.pdb"
> relModel #1
Computing secondary structure
> dssp
Computing secondary structure
> close #4
> close #3
> dssp #2
Computing secondary structure
> view matrix models
> #2,-0.99997,-0.0054831,-0.0053293,284.67,0.0054845,-0.99998,-0.00023659,299.41,-0.0053279,-0.00026581,0.99999,13.64
> undo
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5787, steps = 44
shifted from previous position = 0.0114
rotated from previous position = 0.0153 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997218 -0.00526409 -0.00528835 285.77895882
0.00526620 -0.99998607 -0.00038462 281.25430592
-0.00528625 -0.00041246 0.99998597 3.30669901
Axis -0.00264363 -0.00019921 0.99999649
Axis point 142.52363328 141.00366316 0.00000000
Rotation angle (degrees) 179.69832696
Shift along axis 2.49516562
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5787, steps = 44
shifted from previous position = 0.0016
rotated from previous position = 0.0145 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997144 -0.00547511 -0.00521306 285.79844310
0.00547780 -0.99998489 -0.00050206 281.23944336
-0.00521023 -0.00053060 0.99998631 3.31075673
Axis -0.00260580 -0.00025811 0.99999657
Axis point 142.51847979 141.01145421 0.00000000
Rotation angle (degrees) 179.68621946
Shift along axis 2.49342098
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5791, steps = 44
shifted from previous position = 0.00967
rotated from previous position = 0.0186 degrees
atoms outside contour = 246, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997072 -0.00548976 -0.00533500 285.81293917
0.00549091 -0.99998492 -0.00020210 281.20039404
-0.00533381 -0.00023139 0.99998577 3.27774731
Axis -0.00266719 -0.00010831 0.99999644
Axis point 142.52486366 140.99269157 0.00000000
Rotation angle (degrees) 179.68542427
Shift along axis 2.48496276
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5791, steps = 44
shifted from previous position = 0.000769
rotated from previous position = 0.0132 degrees
atoms outside contour = 245, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997071 -0.00556961 -0.00525247 285.81403894
0.00557180 -0.99998441 -0.00040236 281.21376204
-0.00525015 -0.00043162 0.99998615 3.29379557
Axis -0.00262564 -0.00020843 0.99999653
Axis point 142.51969760 141.00528549 0.00000000
Rotation angle (degrees) 179.68081948
Shift along axis 2.48472449
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5786, steps = 48
shifted from previous position = 0.014
rotated from previous position = 0.0103 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997157 -0.00545658 -0.00520816 285.79665814
0.00545944 -0.99998497 -0.00053536 281.24671605
-0.00520516 -0.00056378 0.99998632 3.31914774
Axis -0.00260331 -0.00027473 0.99999657
Axis point 142.51888133 141.01379852 0.00000000
Rotation angle (degrees) 179.68727655
Shift along axis 2.49785310
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5787, steps = 40
shifted from previous position = 0.00268
rotated from previous position = 0.00198 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997171 -0.00542357 -0.00521439 285.79218066
0.00542648 -0.99998514 -0.00054393 281.25182380
-0.00521137 -0.00057221 0.99998628 3.31863634
Axis -0.00260642 -0.00027897 0.99999656
Axis point 142.51895906 141.01399683 0.00000000
Rotation angle (degrees) 179.68916616
Shift along axis 2.49526842
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5792, steps = 44
shifted from previous position = 0.0149
rotated from previous position = 0.0206 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997068 -0.00550090 -0.00532938 285.81281724
0.00550211 -0.99998486 -0.00021141 281.19944342
-0.00532814 -0.00024073 0.99998580 3.27535821
Axis -0.00266437 -0.00011297 0.99999644
Axis point 142.52401103 140.99302163 0.00000000
Rotation angle (degrees) 179.68478436
Shift along axis 2.48206900
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5792, steps = 40
shifted from previous position = 0.000486
rotated from previous position = 0.00463 degrees
atoms outside contour = 246, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997037 -0.00555592 -0.00533157 285.82082945
0.00555681 -0.99998456 -0.00015206 281.18493164
-0.00533065 -0.00018169 0.99998580 3.26798775
Axis -0.00266554 -0.00008338 0.99999644
Axis point 142.52417272 140.98964824 0.00000000
Rotation angle (degrees) 179.68164106
Shift along axis 2.48266512
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5792, steps = 40
shifted from previous position = 9.2e-05
rotated from previous position = 0.00792 degrees
atoms outside contour = 246, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997006 -0.00567262 -0.00526612 285.82894502
0.00567368 -0.99998390 -0.00018580 281.17274239
-0.00526499 -0.00021568 0.99998614 3.26353546
Axis -0.00263276 -0.00010031 0.99999653
Axis point 142.51997835 140.99193797 0.00000000
Rotation angle (degrees) 179.67494948
Shift along axis 2.48279938
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5787, steps = 44
shifted from previous position = 0.0132
rotated from previous position = 0.0199 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997139 -0.00547796 -0.00521995 285.80003455
0.00548049 -0.99998489 -0.00047076 281.23542549
-0.00521729 -0.00049935 0.99998629 3.30834221
Axis -0.00260929 -0.00024247 0.99999657
Axis point 142.51908905 141.00961909 0.00000000
Rotation angle (degrees) 179.68606085
Shift along axis 2.49440448
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5791, steps = 44
shifted from previous position = 0.0102
rotated from previous position = 0.016 degrees
atoms outside contour = 246, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997074 -0.00548586 -0.00533437 285.81238437
0.00548709 -0.99998494 -0.00021526 281.20258805
-0.00533311 -0.00024452 0.99998577 3.27979953
Axis -0.00266685 -0.00011488 0.99999644
Axis point 142.52485661 140.99352306 0.00000000
Rotation angle (degrees) 179.68564530
Shift along axis 2.48526278
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.579, steps = 40
shifted from previous position = 0.00345
rotated from previous position = 0.00645 degrees
atoms outside contour = 245, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997093 -0.00546794 -0.00531756 285.80813260
0.00546975 -0.99998500 -0.00032513 281.21844890
-0.00531570 -0.00035421 0.99998583 3.29577979
Axis -0.00265830 -0.00016977 0.99999645
Axis point 142.52395589 141.00027885 0.00000000
Rotation angle (degrees) 179.68665575
Shift along axis 2.48826058
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.579, steps = 40
shifted from previous position = 0.00233
rotated from previous position = 0.0121 degrees
atoms outside contour = 246, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997110 -0.00554616 -0.00520318 285.80548854
0.00554876 -0.99998450 -0.00048522 281.22643773
-0.00520040 -0.00051407 0.99998637 3.29926127
Axis -0.00260088 -0.00024976 0.99999659
Axis point 142.51700542 141.01001896 0.00000000
Rotation angle (degrees) 179.68215146
Shift along axis 2.48566454
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5792, steps = 48
shifted from previous position = 0.00668
rotated from previous position = 0.00415 degrees
atoms outside contour = 244, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997106 -0.00559063 -0.00516336 285.80607510
0.00559342 -0.99998423 -0.00052598 281.22543878
-0.00516034 -0.00055484 0.99998656 3.29261874
Axis -0.00258091 -0.00027014 0.99999663
Axis point 142.51412518 141.01273735 0.00000000
Rotation angle (degrees) 179.67959800
Shift along axis 2.47899662
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5791, steps = 44
shifted from previous position = 0.00546
rotated from previous position = 0.00663 degrees
atoms outside contour = 246, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997110 -0.00552146 -0.00522947 285.80502446
0.00552395 -0.99998465 -0.00046120 281.22735829
-0.00522684 -0.00049007 0.99998624 3.29846891
Axis -0.00261406 -0.00023776 0.99999656
Axis point 142.51853309 141.00869013 0.00000000
Rotation angle (degrees) 179.68356964
Shift along axis 2.48448211
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5791, steps = 44
shifted from previous position = 0.000437
rotated from previous position = 0.000214 degrees
atoms outside contour = 246, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997111 -0.00551890 -0.00522997 285.80481105
0.00552140 -0.99998466 -0.00046389 281.22798982
-0.00522733 -0.00049275 0.99998624 3.29933099
Axis -0.00261431 -0.00023910 0.99999655
Axis point 142.51860688 141.00882515 0.00000000
Rotation angle (degrees) 179.68371619
Shift along axis 2.48489598
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5788, steps = 44
shifted from previous position = 0.00765
rotated from previous position = 0.00324 degrees
atoms outside contour = 246, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997142 -0.00547974 -0.00521147 285.79850374
0.00548242 -0.99998486 -0.00050038 281.23849483
-0.00520865 -0.00052893 0.99998632 3.30919534
Axis -0.00260501 -0.00025727 0.99999657
Axis point 142.51818312 141.01130866 0.00000000
Rotation angle (degrees) 179.68595466
Shift along axis 2.49232183
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5791, steps = 36
shifted from previous position = 0.00665
rotated from previous position = 0.0149 degrees
atoms outside contour = 245, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997080 -0.00547980 -0.00532958 285.81115177
0.00548131 -0.99998496 -0.00026831 281.21018507
-0.00532803 -0.00029752 0.99998579 3.28775870
Axis -0.00266439 -0.00014140 0.99999644
Axis point 142.52465288 140.99694057 0.00000000
Rotation angle (degrees) 179.68598475
Shift along axis 2.48647375
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5789, steps = 40
shifted from previous position = 0.00481
rotated from previous position = 0.0087 degrees
atoms outside contour = 246, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997126 -0.00548481 -0.00523614 285.80189802
0.00548692 -0.99998489 -0.00038787 281.22418624
-0.00523394 -0.00041659 0.99998624 3.29556460
Axis -0.00261750 -0.00020106 0.99999655
Axis point 142.51956619 141.00440685 0.00000000
Rotation angle (degrees) 179.68568028
Shift along axis 2.49092433
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5792, steps = 44
shifted from previous position = 0.00976
rotated from previous position = 0.0123 degrees
atoms outside contour = 247, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997066 -0.00550389 -0.00532995 285.81334422
0.00550500 -0.99998484 -0.00019521 281.19715368
-0.00532879 -0.00022455 0.99998580 3.27318560
Axis -0.00266467 -0.00010488 0.99999644
Axis point 142.52406853 140.99207428 0.00000000
Rotation angle (degrees) 179.68461585
Shift along axis 2.48208404
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5792, steps = 40
shifted from previous position = 0.00159
rotated from previous position = 0.0191 degrees
atoms outside contour = 246, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997075 -0.00563902 -0.00517089 285.81360148
0.00564145 -0.99998400 -0.00045534 281.21009017
-0.00516824 -0.00048450 0.99998655 3.28739503
Axis -0.00258477 -0.00023490 0.99999663
Axis point 142.51451992 141.00846014 0.00000000
Rotation angle (degrees) 179.67683553
Shift along axis 2.48256583
> fitmap #2 inMap #1
Fit molecule morphology1_protofibril_1.pdb (#2) to map
Morpholgy_1_Processed_Job101.mrc (#1) using 1480 atoms
average map value = 0.5791, steps = 44
shifted from previous position = 0.000887
rotated from previous position = 0.00734 degrees
atoms outside contour = 245, contour level = 0.07913
Position of morphology1_protofibril_1.pdb (#2) relative to
Morpholgy_1_Processed_Job101.mrc (#1) coordinates:
Matrix rotation and translation
-0.99997109 -0.00552429 -0.00522768 285.80502118
0.00552674 -0.99998464 -0.00045484 281.22630251
-0.00522509 -0.00048372 0.99998626 3.29599487
Axis -0.00261318 -0.00023458 0.99999656
Axis point 142.51833063 141.00835752 0.00000000
Rotation angle (degrees) 179.68340861
Shift along axis 2.48315396
> select subtract #2
Nothing selected
===== 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
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: 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: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16S000UNFN/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.2 (24D81)
Kernel Version: Darwin 24.3.0
Time since boot: 6 hours, 30 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
S24R65x:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
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 , 7 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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