![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 12 months ago
Closed 12 months ago
#16359 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-13.6.7-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Current thread 0x00000001de8be100 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 56)
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{
"uptime" : 170000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,9",
"coalitionID" : 5506,
"osVersion" : {
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"build" : "22G720",
"releaseType" : "User"
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"captureTime" : "2024-11-21 17:29:50.6979 +0000",
"incident" : "39AA4A83-4710-4EE7-A98A-2E7105C48D99",
"pid" : 58361,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-11-17 08:04:01.4740 +0000",
"procStartAbsTime" : 965478063085,
"procExitAbsTime" : 4107893712824,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"89B6C8C4-930E-5610-9016-F2F4E6C6E053","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B97F65CB-AB70-2664-1BC6-992D64AA7B45",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 1,
"sleepWakeUUID" : "C8437E8B-3C7D-4889-B27C-959920D450B7",
"sip" : "enabled",
"vmRegionInfo" : "0x612d65653131 is not in any region. Bytes after previous region: 1292875673906 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO (reserved) 600058000000-600060000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000101, 0x3039612d65653131","rawCodes":[257,3474915435095601457],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"UNKNOWN_0x101 at 0x3039612d65653131 -> 0x0000612d65653131 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":58361},
"vmregioninfo" : "0x612d65653131 is not in any region. Bytes after previous region: 1292875673906 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO (reserved) 600058000000-600060000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)\n---> \n UNUSED SPACE AT END",
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"faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/hmed/Documents/nipah/nipah1/simonus_J97z.mrc
> /Users/hmed/Documents/nipah/nipah1/nipah-inzmap.pdb
Opened simonus_J97z.mrc as #1, grid size 300,300,300, pixel 1.1, shown at
level 0.0882, step 2, values float32
nipah-inzmap.pdb title:
Nipah virus attachment glycoprotein head domain In complex with A broadly
neutralizing antibody 1E5 [more info...]
Chain information for nipah-inzmap.pdb #2
---
Chain | Description | UniProt
A | glycoprotein | Q4VCP5_NIPAV 176-602
B | glycoprotein | Q4VCP5_NIPAV 176-602
> volume #1 step 1
> volume #1 level 0.1539
> set bgColor white
> transparency 50
> volume #1 level 0.2571
> hide #!2 models
> open /Users/hmed/Documents/nipah/nipah1/nipah-inzmap-coot-5.pdb
Summary of feedback from opening /Users/hmed/Documents/nipah/nipah1/nipah-
inzmap-coot-5.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 328 ASN A 331 1 4
End residue of secondary structure not found: SHEET 5 5 5 LEU A 234 ARG A 236
0
Start residue of secondary structure not found: SHEET 25 2525 ILE A 545 GLN A
550 0
Start residue of secondary structure not found: SHEET 50 5050 ILE B 545 GLN B
550 0
nipah-inzmap-coot-5.pdb title:
Nipah virus attachment glycoprotein head domain In complex with A broadly
neutralizing antibody 1E5 [more info...]
Chain information for nipah-inzmap-coot-5.pdb #3
---
Chain | Description | UniProt
A | glycoprotein | Q4VCP5_NIPAV 176-602
B | glycoprotein |
Non-standard residues in nipah-inzmap-coot-5.pdb #3
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-
glucosamine;2-acetamido-2-deoxy-β- D-glucose;2-acetamido-2-deoxy-D-
glucose;2-acetamido- 2-deoxy-glucose;N-acetyl-D-glucosamine)
> lighting soft
> graphics silhouettes true
> lighting full
> lighting soft
> lighting simple
> color #3 bychain
> show #3 atoms
> color #3 byhetero
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> close #3
> open /Users/hmed/Downloads/7dzx.pdb
7dzx.pdb title:
Spike protein from sars-COV2 with fab fragment of enhancing antibody 8D2 [more
info...]
Chain information for 7dzx.pdb #3
---
Chain | Description | UniProt
A B C | spike glycoprotein | SPIKE_SARS2 27-1147
H | fab heavy chain of enhancing antibody |
L | fab light chain of enhancing antibody |
> delete #3/A-C
> show #3 atoms
> style #3 stick
Changed 1760 atom styles
> select add #3
1760 atoms, 1758 bonds, 440 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,2.4195,0,1,0,9.8361,0,0,1,-55.818
> view matrix models #3,1,0,0,5.93,0,1,0,25.45,0,0,1,-53.576
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.063306,-0.79284,-0.60613,409.5,0.54446,0.48157,-0.68678,99.532,0.8364,-0.37349,0.40118,-68.207
> view matrix models
> #3,0.06868,-0.75418,-0.65306,388.12,0.68771,0.51001,-0.51666,37.27,0.72273,-0.41364,0.55369,-69.604
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.06868,-0.75418,-0.65306,399.01,0.68771,0.51001,-0.51666,45.702,0.72273,-0.41364,0.55369,-72.905
> view matrix models
> #3,0.06868,-0.75418,-0.65306,398.34,0.68771,0.51001,-0.51666,45.477,0.72273,-0.41364,0.55369,-70.961
> view matrix models
> #3,0.06868,-0.75418,-0.65306,400.59,0.68771,0.51001,-0.51666,44.159,0.72273,-0.41364,0.55369,-71.072
> view matrix models
> #3,0.06868,-0.75418,-0.65306,399.35,0.68771,0.51001,-0.51666,44.709,0.72273,-0.41364,0.55369,-71.612
> view matrix models
> #3,0.06868,-0.75418,-0.65306,398.64,0.68771,0.51001,-0.51666,44.496,0.72273,-0.41364,0.55369,-70.062
> view matrix models
> #3,0.06868,-0.75418,-0.65306,399.19,0.68771,0.51001,-0.51666,44.771,0.72273,-0.41364,0.55369,-70.142
> view matrix models
> #3,0.06868,-0.75418,-0.65306,399.18,0.68771,0.51001,-0.51666,44.792,0.72273,-0.41364,0.55369,-70.148
> view matrix models
> #3,0.06868,-0.75418,-0.65306,401.53,0.68771,0.51001,-0.51666,44.055,0.72273,-0.41364,0.55369,-69.965
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #3 inMap #1
Fit molecule 7dzx.pdb (#3) to map simonus_J97z.mrc (#1) using 1760 atoms
average map value = 0.1847, steps = 160
shifted from previous position = 3.61
rotated from previous position = 11.9 degrees
atoms outside contour = 1281, contour level = 0.25708
Position of 7dzx.pdb (#3) relative to simonus_J97z.mrc (#1) coordinates:
Matrix rotation and translation
0.06835338 -0.71145514 -0.69939932 402.18859098
0.81368412 0.44539619 -0.37355105 -0.69852271
0.57727461 -0.54355664 0.60934408 -36.59042108
Axis -0.08516425 -0.63954942 0.76401806
Axis point 227.03392794 260.61146038 0.00000000
Rotation angle (degrees) 86.47139648
Shift along axis -61.76109173
> select subtract #3
Nothing selected
> delete #3/H:127-226
> delete #3/H:127-227
> delete #3/L
> fitmap #3 inMap #1
Fit molecule 7dzx.pdb (#3) to map simonus_J97z.mrc (#1) using 504 atoms
average map value = 0.269, steps = 52
shifted from previous position = 0.241
rotated from previous position = 6.91 degrees
atoms outside contour = 245, contour level = 0.25708
Position of 7dzx.pdb (#3) relative to simonus_J97z.mrc (#1) coordinates:
Matrix rotation and translation
0.05668574 -0.77773561 -0.62603039 397.12432719
0.85484959 0.36173753 -0.37199213 0.22335219
0.51577021 -0.51407517 0.68535232 -42.88112920
Axis -0.07113735 -0.57167039 0.81739369
Axis point 219.91514889 238.07971714 -0.00000000
Rotation angle (degrees) 87.02571249
Shift along axis -63.42882088
> open /Users/hmed/Downloads/7duo.pdb
7duo.pdb title:
Crystal structure of daratumumab fab and CD38 complex [more info...]
Chain information for 7duo.pdb #4
---
Chain | Description | UniProt
B | adp-ribosyl cyclase/cyclic adp-ribose hydrolase 1 | CD38_HUMAN 13-241
H | fab heavy chain |
L | fab light chain |
> mmaker #4/H to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7dzx.pdb, chain H (#3) with 7duo.pdb, chain H (#4), sequence
alignment score = 810.2
RMSD between 111 pruned atom pairs is 0.638 angstroms; (across all 120 pairs:
1.734)
> delete #4/B #4/H
> delete #4/L:108-213
> fitmap #4 inMap #1
Fit molecule 7duo.pdb (#4) to map simonus_J97z.mrc (#1) using 820 atoms
average map value = 0.2598, steps = 64
shifted from previous position = 2.23
rotated from previous position = 12 degrees
atoms outside contour = 419, contour level = 0.25708
Position of 7duo.pdb (#4) relative to simonus_J97z.mrc (#1) coordinates:
Matrix rotation and translation
-0.57337704 0.33780233 0.74641031 190.70776058
-0.03565061 -0.92046768 0.38918927 162.75297494
0.81851561 0.19654221 0.53981789 85.57826238
Axis -0.45184589 -0.16912006 -0.87591877
Axis point 81.33481903 66.62335957 0.00000000
Rotation angle (degrees) 167.69135314
Shift along axis -188.65491718
> open /Users/hmed/Documents/nipah/nipah1/nipah-inzmap-coot-6.pdb
Summary of feedback from opening /Users/hmed/Documents/nipah/nipah1/nipah-
inzmap-coot-6.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY A 328 ASN A 331 1 4
End residue of secondary structure not found: SHEET 5 5 5 LEU A 234 ARG A 236
0
Start residue of secondary structure not found: SHEET 25 2525 ILE A 545 GLN A
550 0
Start residue of secondary structure not found: SHEET 50 5050 ILE B 545 GLN B
550 0
nipah-inzmap-coot-6.pdb title:
Nipah virus attachment glycoprotein head domain In complex with A broadly
neutralizing antibody 1E5 [more info...]
Chain information for nipah-inzmap-coot-6.pdb #5
---
Chain | Description | UniProt
A | glycoprotein | Q4VCP5_NIPAV 176-602
B | glycoprotein |
Non-standard residues in nipah-inzmap-coot-6.pdb #5
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-
glucosamine;2-acetamido-2-deoxy-β- D-glucose;2-acetamido-2-deoxy-D-
glucose;2-acetamido- 2-deoxy-glucose;N-acetyl-D-glucosamine)
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/hmed/Documents/nipah/nipah1/7dzx_H.pdb models #3 relModel #1
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/hmed/Documents/nipah/nipah1/7duo_L.pdb models #4 relModel #1
> open /Users/hmed/Downloads/3ghe.pdb
3ghe.pdb title:
Crystal structure of ANTI-hiv-1 fab 537-10D In complex with V3 peptide Mn
[more info...]
Chain information for 3ghe.pdb #6
---
Chain | Description | UniProt
H | fab 537-10D, heavy chain |
L | fab 537-10D, light chain |
P | envelope glycoprotein | P88403_9HIV1 304-320
> mmaker #6 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7dzx.pdb, chain H (#3) with 3ghe.pdb, chain H (#6), sequence
alignment score = 818.1
RMSD between 111 pruned atom pairs is 0.544 angstroms; (across all 126 pairs:
3.717)
> hide #!3 models
> delete #6/H:127-227
> delete #6/L
> delete #6/H:115-127
> fitmap #6 inMap #1
Fit molecule 3ghe.pdb (#6) to map simonus_J97z.mrc (#1) using 1303 atoms
average map value = 0.1836, steps = 44
shifted from previous position = 0.245
rotated from previous position = 1.79 degrees
atoms outside contour = 854, contour level = 0.25708
Position of 3ghe.pdb (#6) relative to simonus_J97z.mrc (#1) coordinates:
Matrix rotation and translation
-0.94997927 -0.13407243 -0.28207086 230.60090282
-0.04482579 -0.83528299 0.54798994 124.74430407
-0.30907933 0.53322313 0.78749162 123.21191942
Axis -0.15641822 0.28608877 0.94534997
Axis point 124.35060738 46.83549507 0.00000000
Rotation angle (degrees) 177.29446396
Shift along axis 116.09614429
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/hmed/Documents/nipah/nipah1/3ghe_H.pdb models #6 relModel #1
> show #5#!4,6 atoms
> select ::name="HOH"
140 atoms, 140 residues, 1 model selected
> delete sel
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/hmed/Documents/nipah/nipah1/3ghe_H.pdb models #6 relModel #6
> open /Users/hmed/Downloads/cryosparc_P1027_J174_003_volume_map_sharp.mrc
Opened cryosparc_P1027_J174_003_volume_map_sharp.mrc as #7, grid size
240,240,240, pixel 1.46, shown at level 0.0252, step 1, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #7 level 0.1527
> open /Users/hmed/Downloads/cryosparc_P1027_J174_003_volume_map_sharp.mrc
Opened cryosparc_P1027_J174_003_volume_map_sharp.mrc as #8, grid size
240,240,240, pixel 1.46, shown at level 0.0252, step 1, values float32
> volume #8 level 0.1099
> open /Users/hmed/Downloads/cryosparc_P1027_J176_002_volume_map_sharp.mrc
Opened cryosparc_P1027_J176_002_volume_map_sharp.mrc as #9, grid size
240,240,240, pixel 1.46, shown at level 0.022, step 1, values float32
> volume #9 level 0.1037
> open /Users/hmed/Downloads/cryosparc_P1027_J154_005_volume_map_sharp.mrc
Opened cryosparc_P1027_J154_005_volume_map_sharp.mrc as #10, grid size
240,240,240, pixel 1.46, shown at level 0.0394, step 1, values float32
> volume #10 level 0.1904
> volume #10 level -0.1803
> volume #10 level 0.3551
> open
> /Users/hmed/Downloads/fold_2024_11_19_11_37/fold_2024_11_19_11_37_model_0.cif
Chain information for fold_2024_11_19_11_37_model_0.cif #11
---
Chain | Description
A | .
B | .
> open
> /Users/hmed/Downloads/fold_2024_11_19_11_37/fold_2024_11_19_11_37_model_1.cif
Chain information for fold_2024_11_19_11_37_model_1.cif #12
---
Chain | Description
A | .
B | .
> open
> /Users/hmed/Downloads/fold_2024_11_19_11_37/fold_2024_11_19_11_37_model_2.cif
Chain information for fold_2024_11_19_11_37_model_2.cif #13
---
Chain | Description
A | .
B | .
> open
> /Users/hmed/Downloads/fold_2024_11_19_11_37/fold_2024_11_19_11_37_model_3.cif
Chain information for fold_2024_11_19_11_37_model_3.cif #14
---
Chain | Description
A | .
B | .
> open
> /Users/hmed/Downloads/fold_2024_11_19_11_37/fold_2024_11_19_11_37_model_4.cif
Chain information for fold_2024_11_19_11_37_model_4.cif #15
---
Chain | Description
A | .
B | .
> show #!1 models
> hide #!4 models
> show #!10 models
> hide #!10 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> mmaker #11-15 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7duo.pdb, chain L (#4) with fold_2024_11_19_11_37_model_0.cif,
chain B (#11), sequence alignment score = 509.3
RMSD between 105 pruned atom pairs is 0.448 angstroms; (across all 107 pairs:
0.545)
Matchmaker 7duo.pdb, chain L (#4) with fold_2024_11_19_11_37_model_1.cif,
chain B (#12), sequence alignment score = 516.5
RMSD between 107 pruned atom pairs is 0.409 angstroms; (across all 107 pairs:
0.409)
Matchmaker 7duo.pdb, chain L (#4) with fold_2024_11_19_11_37_model_2.cif,
chain B (#13), sequence alignment score = 509.3
RMSD between 106 pruned atom pairs is 0.474 angstroms; (across all 107 pairs:
0.518)
Matchmaker 7duo.pdb, chain L (#4) with fold_2024_11_19_11_37_model_3.cif,
chain B (#14), sequence alignment score = 509.3
RMSD between 106 pruned atom pairs is 0.470 angstroms; (across all 107 pairs:
0.514)
Matchmaker 7duo.pdb, chain L (#4) with fold_2024_11_19_11_37_model_4.cif,
chain B (#15), sequence alignment score = 509.3
RMSD between 106 pruned atom pairs is 0.470 angstroms; (across all 107 pairs:
0.520)
> hide #13 models
> show #13 models
> hide #12 models
> hide #11 models
> hide #14 models
> fitmap #13 inMap #1
Fit molecule fold_2024_11_19_11_37_model_2.cif (#13) to map simonus_J97z.mrc
(#1) using 1833 atoms
average map value = 0.2104, steps = 48
shifted from previous position = 1
rotated from previous position = 5.52 degrees
atoms outside contour = 1121, contour level = 0.25708
Position of fold_2024_11_19_11_37_model_2.cif (#13) relative to
simonus_J97z.mrc (#1) coordinates:
Matrix rotation and translation
0.80069766 -0.56638708 0.19516387 197.63373490
-0.18405445 0.07744073 0.97986065 142.10736848
-0.57009404 -0.82049291 -0.04223945 134.90982390
Axis -0.90322229 0.38392348 0.19181307
Axis point 0.00000000 191.43486060 -3.21399292
Rotation angle (degrees) 94.70644026
Shift along axis -98.07137072
> hide #15 models
> show #15 models
> hide #15 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/hmed/Downloads/model2.pdb models #13 relModel #1
> hide #13 models
> hide #5 models
> hide #!6 models
> open /Users/hmed/Downloads/cryosparc_P22_J263_011_volume_map_sharp.mrc
Opened cryosparc_P22_J263_011_volume_map_sharp.mrc as #16, grid size
270,270,270, pixel 0.976, shown at level 0.0826, step 2, values float32
> volume #16 level 0.1594
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #16 step 1
> view orient
> volume #16 level 0.2943
> show #5 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> delete #5/B
> select add #5
3584 atoms, 3681 bonds, 450 residues, 1 model selected
> hide sel atoms
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,-11.596,0,1,0,-27.013,0,0,1,-24.957
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.36512,0.93093,0.0074457,55.835,0.53464,0.20313,0.8203,-97.837,0.76213,0.30349,-0.57189,21.98
> view matrix models
> #5,-0.15234,0.86788,0.47285,-29.321,0.55021,-0.32296,0.77004,-13.933,0.82101,0.37747,-0.42831,-17.389
> view matrix models
> #5,-0.41979,0.21269,0.88235,56.166,0.55688,-0.7073,0.43545,87.815,0.7167,0.67416,0.17847,-127.22
> view matrix models
> #5,0.36032,0.76311,0.5365,-100.55,-0.19079,-0.50269,0.84315,117.08,0.91311,-0.40616,-0.035539,34.648
> view matrix models
> #5,0.21472,0.31646,0.92399,-62.345,-0.020455,-0.94439,0.3282,226.48,0.97646,-0.089369,-0.1963,-1.5418
> view matrix models
> #5,0.30539,0.80165,0.5139,-94.941,0.25183,-0.58846,0.76831,72.198,0.91833,-0.10522,-0.38159,34.481
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.30539,0.80165,0.5139,-55.432,0.25183,-0.58846,0.76831,39.667,0.91833,-0.10522,-0.38159,52.61
> view matrix models
> #5,0.30539,0.80165,0.5139,-55.238,0.25183,-0.58846,0.76831,39.92,0.91833,-0.10522,-0.38159,50.517
> show sel surfaces
> view matrix models
> #5,0.30539,0.80165,0.5139,-56.864,0.25183,-0.58846,0.76831,42.731,0.91833,-0.10522,-0.38159,42.614
> show sel cartoons
> hide sel surfaces
> view matrix models
> #5,0.30539,0.80165,0.5139,-66.333,0.25183,-0.58846,0.76831,39.783,0.91833,-0.10522,-0.38159,36.589
> view matrix models
> #5,0.30539,0.80165,0.5139,-101.33,0.25183,-0.58846,0.76831,68.852,0.91833,-0.10522,-0.38159,27.6
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.92112,0.31073,0.2345,-84.176,0.054143,-0.69879,0.71328,123.18,0.3855,-0.64432,-0.66049,228.03
> view matrix models
> #5,0.99992,0.011068,0.0063597,-20.493,0.0050803,-0.80208,0.59719,161.82,0.011711,-0.59711,-0.80207,297.07
> view matrix models
> #5,0.97219,-0.20275,0.11722,1.3155,-0.21021,-0.53472,0.81846,124.86,-0.10326,-0.82034,-0.56247,316.5
> view matrix models
> #5,0.96889,-0.21251,0.12687,2.0122,-0.2219,-0.51885,0.82556,123.3,-0.10962,-0.82803,-0.54987,316.96
> view matrix models
> #5,0.97739,-0.18041,0.11028,-1.9361,-0.19603,-0.57766,0.79239,132.66,-0.079246,-0.79609,-0.59997,314.15
> view matrix models
> #5,0.96291,-0.2606,0.069998,17.788,-0.21826,-0.59965,0.76992,142.39,-0.15867,-0.75664,-0.63428,324.94
> view matrix models
> #5,0.94955,-0.28418,0.13262,15.049,-0.28295,-0.594,0.75306,153.7,-0.13522,-0.7526,-0.64445,322.09
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.94955,-0.28418,0.13262,14.864,-0.28295,-0.594,0.75306,154.97,-0.13522,-0.7526,-0.64445,328.46
> view matrix models
> #5,0.94955,-0.28418,0.13262,9.8668,-0.28295,-0.594,0.75306,157.2,-0.13522,-0.7526,-0.64445,328.5
> view matrix models
> #5,0.94955,-0.28418,0.13262,9.7352,-0.28295,-0.594,0.75306,156.81,-0.13522,-0.7526,-0.64445,326.82
> view matrix models
> #5,0.94955,-0.28418,0.13262,11.923,-0.28295,-0.594,0.75306,156.38,-0.13522,-0.7526,-0.64445,327.57
> view matrix models
> #5,0.94955,-0.28418,0.13262,10.6,-0.28295,-0.594,0.75306,155.02,-0.13522,-0.7526,-0.64445,325.63
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #5 inMap #16
Fit molecule nipah-inzmap-coot-6.pdb (#5) to map
cryosparc_P22_J263_011_volume_map_sharp.mrc (#16) using 3584 atoms
average map value = 0.09614, steps = 104
shifted from previous position = 4.25
rotated from previous position = 6.28 degrees
atoms outside contour = 2912, contour level = 0.29427
Position of nipah-inzmap-coot-6.pdb (#5) relative to
cryosparc_P22_J263_011_volume_map_sharp.mrc (#16) coordinates:
Matrix rotation and translation
0.97211289 -0.19483107 0.13052733 -7.53290057
-0.22786728 -0.65316452 0.72211675 162.29048434
-0.05543496 -0.73172191 -0.67934528 317.44736412
Axis -0.99166652 0.12684528 -0.02253407
Axis point 0.00000000 150.59611967 123.69338518
Rotation angle (degrees) 132.85915333
Shift along axis 20.90252801
> view matrix models
> #5,0.97211,-0.19483,0.13053,-2.8348,-0.22787,-0.65316,0.72212,164.07,-0.055435,-0.73172,-0.67935,315.7
> fitmap #5 inMap #16
Fit molecule nipah-inzmap-coot-6.pdb (#5) to map
cryosparc_P22_J263_011_volume_map_sharp.mrc (#16) using 3584 atoms
average map value = 0.08462, steps = 56
shifted from previous position = 1.62
rotated from previous position = 4.45 degrees
atoms outside contour = 2994, contour level = 0.29427
Position of nipah-inzmap-coot-6.pdb (#5) relative to
cryosparc_P22_J263_011_volume_map_sharp.mrc (#16) coordinates:
Matrix rotation and translation
0.97575287 -0.14112013 0.16730641 -15.20901311
-0.21886788 -0.62287366 0.75108271 154.06480357
-0.00178213 -0.76948912 -0.63865743 308.55802907
Axis -0.99259315 0.11037698 -0.05075189
Axis point 0.00000000 148.84853267 118.91146025
Rotation angle (degrees) 130.00759239
Shift along axis 16.44166871
> view matrix models
> #5,0.97575,-0.14112,0.16731,16.108,-0.21887,-0.62287,0.75108,204.82,-0.0017821,-0.76949,-0.63866,302.6
> view matrix models
> #5,0.97575,-0.14112,0.16731,0.49905,-0.21887,-0.62287,0.75108,184.68,-0.0017821,-0.76949,-0.63866,308.18
> view matrix models
> #5,0.97575,-0.14112,0.16731,10.04,-0.21887,-0.62287,0.75108,197.83,-0.0017821,-0.76949,-0.63866,306.81
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.69251,0.72139,0.0043097,157.02,0.46316,0.44918,-0.76402,133.21,-0.5531,-0.5271,-0.64518,355.52
> view matrix models
> #5,0.74602,0.45265,-0.48844,42.9,0.29665,-0.88256,-0.3648,306.94,-0.5962,0.12726,-0.79268,282.81
> view matrix models
> #5,0.80358,0.57737,-0.14454,-30.663,0.58859,-0.80695,0.048931,195.57,-0.088388,-0.1244,-0.98829,269.13
> view matrix models
> #5,0.67667,0.70629,-0.20804,-22.241,0.72341,-0.69035,0.0092437,162.55,-0.13709,-0.15675,-0.97808,280.13
> view matrix models
> #5,0.53539,0.80291,-0.26209,-7.9927,0.82129,-0.56732,-0.060269,138.21,-0.19708,-0.18299,-0.96316,291.3
> view matrix models
> #5,0.19925,0.95992,0.19711,-41.471,0.919,-0.11321,-0.37766,96.876,-0.34021,0.25639,-0.90472,238.98
> view matrix models
> #5,-0.077988,0.87553,0.47682,-23.519,0.82027,0.32819,-0.46846,57.347,-0.56663,0.35459,-0.74377,237.36
> view matrix models
> #5,-0.10432,0.89213,0.43958,-17.026,0.78258,0.34639,-0.51728,66.884,-0.61375,0.29004,-0.7343,253.09
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.10432,0.89213,0.43958,-47.386,0.78258,0.34639,-0.51728,27.186,-0.61375,0.29004,-0.7343,262.65
> view matrix models
> #5,-0.10432,0.89213,0.43958,-39.714,0.78258,0.34639,-0.51728,21.201,-0.61375,0.29004,-0.7343,261.32
> volume flip #16
Opened cryosparc_P22_J263_011_volume_map_sharp.mrc z flip as #17, grid size
270,270,270, pixel 0.976, shown at step 1, values float32
> view matrix models
> #5,-0.10432,0.89213,0.43958,-52.06,0.78258,0.34639,-0.51728,18.928,-0.61375,0.29004,-0.7343,332.69
> view matrix models
> #5,-0.10432,0.89213,0.43958,-63.57,0.78258,0.34639,-0.51728,79.628,-0.61375,0.29004,-0.7343,293.89
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.29593,0.84061,-0.45366,2.019,0.81179,0.028974,0.58324,-23.626,0.50342,-0.54087,-0.67382,240.28
> view matrix models
> #5,0.71298,-0.61974,-0.32799,142.25,0.48988,0.10559,0.86537,-23.506,-0.50168,-0.77767,0.37888,289.75
> view matrix models
> #5,-0.18072,-0.88272,-0.43375,333.12,0.50081,-0.46215,0.73185,78.512,-0.84648,-0.084971,0.52559,218.24
> view matrix models
> #5,-0.24396,-0.94256,-0.22817,324.45,0.66347,-0.33382,0.6696,42.47,-0.70731,0.011967,0.7068,158.07
> view matrix models
> #5,0.49065,-0.6338,0.59796,54.942,0.31458,0.7688,0.55676,-55.799,-0.81259,-0.085068,0.57659,206.26
> view matrix models
> #5,0.85055,-0.18755,0.49131,-53.507,0.0029338,0.93592,0.35219,-6.0233,-0.52588,-0.29812,0.7966,165.19
> view matrix models
> #5,0.7365,-0.23367,0.6348,-48.187,-0.12966,0.87227,0.47152,8.0136,-0.66389,-0.42958,0.61213,230.84
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.7365,-0.23367,0.6348,-38.654,-0.12966,0.87227,0.47152,-46.58,-0.66389,-0.42958,0.61213,236.89
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.7984,-0.25676,0.54464,-32.623,-0.32884,0.57179,0.75161,-7.9544,-0.50441,-0.77918,0.37208,297.35
> view matrix models
> #5,0.81906,-0.53129,-0.21649,107.26,0.43192,0.32268,0.84221,-98.967,-0.3776,-0.78333,0.49377,262.31
> view matrix models
> #5,0.87704,-0.4001,-0.26593,85.125,0.42615,0.39234,0.81515,-105.01,-0.2218,-0.82825,0.5146,242.44
> fitmap #5 inMap #16
Fit molecule nipah-inzmap-coot-6.pdb (#5) to map
cryosparc_P22_J263_011_volume_map_sharp.mrc (#16) using 3584 atoms
average map value = 0.0723, steps = 68
shifted from previous position = 3.82
rotated from previous position = 8.24 degrees
atoms outside contour = 3151, contour level = 0.29427
Position of nipah-inzmap-coot-6.pdb (#5) relative to
cryosparc_P22_J263_011_volume_map_sharp.mrc (#16) coordinates:
Matrix rotation and translation
0.90331393 -0.39823675 -0.15947232 67.77304548
0.36108855 0.50515960 0.78385511 -109.05507216
-0.23160094 -0.76565087 0.60011644 226.25716707
Axis -0.89719140 0.04176374 0.43966280
Axis point 0.00000000 152.14309288 236.99082724
Rotation angle (degrees) 59.71543669
Shift along axis 34.11691780
> view matrix models
> #5,0.89233,-0.39781,-0.21328,76.569,0.40847,0.51062,0.75658,-113.51,-0.19207,-0.76224,0.61814,217.28
> fitmap #5 inMap #16
Fit molecule nipah-inzmap-coot-6.pdb (#5) to map
cryosparc_P22_J263_011_volume_map_sharp.mrc (#16) using 3584 atoms
average map value = 0.0723, steps = 56
shifted from previous position = 0.206
rotated from previous position = 3.6 degrees
atoms outside contour = 3152, contour level = 0.29427
Position of nipah-inzmap-coot-6.pdb (#5) relative to
cryosparc_P22_J263_011_volume_map_sharp.mrc (#16) coordinates:
Matrix rotation and translation
0.90321049 -0.39844516 -0.15953766 67.83375654
0.36130360 0.50521440 0.78372069 -109.08466504
-0.23166899 -0.76550627 0.60027462 226.22604465
Axis -0.89706307 0.04176686 0.43992428
Axis point 0.00000000 152.13637439 237.05439132
Rotation angle (degrees) 59.71180285
Shift along axis 34.11504803
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.90153,-0.36756,-0.22835,72.598,0.37458,0.39869,0.8371,-102.13,-0.21664,-0.8402,0.49711,248.98
> view matrix models
> #5,0.91579,-0.31539,-0.2487,65.233,0.37076,0.4257,0.82542,-104.07,-0.15446,-0.84812,0.50678,239.36
> fitmap #5 inMap #16
Fit molecule nipah-inzmap-coot-6.pdb (#5) to map
cryosparc_P22_J263_011_volume_map_sharp.mrc (#16) using 3584 atoms
average map value = 0.0723, steps = 104
shifted from previous position = 0.517
rotated from previous position = 8.56 degrees
atoms outside contour = 3151, contour level = 0.29427
Position of nipah-inzmap-coot-6.pdb (#5) relative to
cryosparc_P22_J263_011_volume_map_sharp.mrc (#16) coordinates:
Matrix rotation and translation
0.90328495 -0.39825501 -0.15959088 67.79574185
0.36120950 0.50517832 0.78378732 -109.06977445
-0.23152537 -0.76562903 0.60017346 226.23432689
Axis -0.89715369 0.04165201 0.43975035
Axis point 0.00000000 152.12058201 237.00756148
Rotation angle (degrees) 59.71388583
Shift along axis 34.12044931
> view matrix models
> #5,0.87172,-0.44471,-0.20574,85.818,0.40155,0.40772,0.82007,-105.35,-0.28081,-0.79749,0.534,247.44
> view matrix models
> #5,0.88273,-0.43369,-0.18085,79.144,0.37202,0.40992,0.8328,-102.86,-0.28704,-0.80242,0.52319,250.58
> view matrix models
> #5,0.9163,-0.36038,-0.17473,62.091,0.3493,0.50564,0.78887,-107.99,-0.19594,-0.78387,0.58919,225
> view matrix models
> #5,0.91779,-0.35551,-0.17683,61.406,0.34969,0.51277,0.78408,-108.49,-0.18807,-0.78146,0.59494,222.67
> view matrix models
> #5,0.91962,-0.3442,-0.18926,61.073,0.35101,0.50381,0.78928,-108.03,-0.17632,-0.79227,0.58414,223.94
> view matrix models
> #5,0.95589,-0.26897,-0.11801,34.628,0.25336,0.55177,0.79458,-101.03,-0.1486,-0.78943,0.59558,217.74
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.95589,-0.26897,-0.11801,33.664,0.25336,0.55177,0.79458,-99.245,-0.1486,-0.78943,0.59558,216.11
> view matrix models
> #5,0.95589,-0.26897,-0.11801,36.357,0.25336,0.55177,0.79458,-99.077,-0.1486,-0.78943,0.59558,217.89
> view matrix models
> #5,0.95589,-0.26897,-0.11801,35.92,0.25336,0.55177,0.79458,-98.663,-0.1486,-0.78943,0.59558,217.3
> view matrix models
> #5,0.95589,-0.26897,-0.11801,36.01,0.25336,0.55177,0.79458,-98.452,-0.1486,-0.78943,0.59558,217.5
> fitmap #5 inMap #17
Fit molecule nipah-inzmap-coot-6.pdb (#5) to map
cryosparc_P22_J263_011_volume_map_sharp.mrc z flip (#17) using 3584 atoms
average map value = 0.372, steps = 84
shifted from previous position = 4.27
rotated from previous position = 13.8 degrees
atoms outside contour = 1497, contour level = 0.29427
Position of nipah-inzmap-coot-6.pdb (#5) relative to
cryosparc_P22_J263_011_volume_map_sharp.mrc z flip (#17) coordinates:
Matrix rotation and translation
0.99144703 -0.12635800 -0.03265620 1.03431449
0.08541180 0.43901641 0.89441009 -68.45460983
-0.09867926 -0.88954946 0.44605398 242.16583227
Axis -0.99235790 0.03672645 0.11780056
Axis point 0.00000000 158.65700839 177.07342981
Rotation angle (degrees) 64.00716689
Shift along axis 24.98676513
> select subtract #5
1 model selected
> transparency #5.1#17.1 50
> open /Users/hmed/Downloads/model2.pdb
Chain information for model2.pdb #18
---
Chain | Description
A | No description available
B | No description available
> select add #18
1833 atoms, 1882 bonds, 235 residues, 1 model selected
> view matrix models #18,1,0,0,2.4487,0,1,0,-8.1392,0,0,1,-27.048
> view matrix models #18,1,0,0,-53.622,0,1,0,-7.3341,0,0,1,-30.863
> ui mousemode right "rotate selected models"
> view matrix models
> #18,0.56827,-0.16668,0.80578,-56.745,0.38702,0.91833,-0.08299,-60.189,-0.72614,0.35902,0.58637,117.86
> view matrix models
> #18,0.53499,-0.034069,0.84417,-74.138,0.36294,0.91156,-0.19322,-39.335,-0.76293,0.40975,0.50004,129.84
> ui mousemode right "translate selected models"
> view matrix models
> #18,0.53499,-0.034069,0.84417,-80.403,0.36294,0.91156,-0.19322,-49.876,-0.76293,0.40975,0.50004,140.2
> view matrix models
> #18,0.53499,-0.034069,0.84417,-80.67,0.36294,0.91156,-0.19322,-48.239,-0.76293,0.40975,0.50004,140.3
> view matrix models
> #18,0.53499,-0.034069,0.84417,-85.043,0.36294,0.91156,-0.19322,-46.24,-0.76293,0.40975,0.50004,141.5
> fitmap #5 inMap #17
Fit molecule nipah-inzmap-coot-6.pdb (#5) to map
cryosparc_P22_J263_011_volume_map_sharp.mrc z flip (#17) using 3584 atoms
average map value = 0.372, steps = 44
shifted from previous position = 0.00585
rotated from previous position = 0.0249 degrees
atoms outside contour = 1494, contour level = 0.29427
Position of nipah-inzmap-coot-6.pdb (#5) relative to
cryosparc_P22_J263_011_volume_map_sharp.mrc z flip (#17) coordinates:
Matrix rotation and translation
0.99141463 -0.12651339 -0.03303611 1.11783968
0.08583265 0.43908699 0.89433515 -68.52483168
-0.09863964 -0.88949254 0.44617625 242.13569957
Axis -0.99232773 0.03649467 0.11812624
Axis point 0.00000000 158.61692039 177.12288156
Rotation angle (degrees) 64.00205337
Shift along axis 24.99252667
> fitmap #18 inMap #17
Fit molecule model2.pdb (#18) to map
cryosparc_P22_J263_011_volume_map_sharp.mrc z flip (#17) using 1833 atoms
average map value = 0.3677, steps = 140
shifted from previous position = 2.56
rotated from previous position = 27.2 degrees
atoms outside contour = 732, contour level = 0.29427
Position of model2.pdb (#18) relative to
cryosparc_P22_J263_011_volume_map_sharp.mrc z flip (#17) coordinates:
Matrix rotation and translation
0.26987021 0.34993679 0.89705870 -92.77685153
0.27818059 0.86356571 -0.42055895 6.68831907
-0.92183818 0.36304065 0.13570504 229.55053088
Axis 0.39539632 0.91779669 -0.03620744
Axis point 94.47967612 0.00000000 163.19505320
Rotation angle (degrees) 82.26621655
Shift along axis -38.85654552
> select subtract #18
Nothing selected
> open
> /Users/hmed/Downloads/fold_2024_11_19_11_37/fold_2024_11_19_11_37_model_4.cif
> /Users/hmed/Downloads/fold_2024_11_19_11_37/fold_2024_11_19_11_37_model_3.cif
> /Users/hmed/Downloads/fold_2024_11_19_11_37/fold_2024_11_19_11_37_model_1.cif
Chain information for fold_2024_11_19_11_37_model_4.cif #19
---
Chain | Description
A | .
B | .
Chain information for fold_2024_11_19_11_37_model_3.cif #20
---
Chain | Description
A | .
B | .
Chain information for fold_2024_11_19_11_37_model_1.cif #21
---
Chain | Description
A | .
B | .
> mmaker #19-21 to #18
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker model2.pdb, chain A (#18) with fold_2024_11_19_11_37_model_4.cif,
chain A (#19), sequence alignment score = 680.8
RMSD between 123 pruned atom pairs is 0.414 angstroms; (across all 128 pairs:
0.746)
Matchmaker model2.pdb, chain A (#18) with fold_2024_11_19_11_37_model_3.cif,
chain A (#20), sequence alignment score = 673.6
RMSD between 117 pruned atom pairs is 0.233 angstroms; (across all 128 pairs:
1.819)
Matchmaker model2.pdb, chain A (#18) with fold_2024_11_19_11_37_model_1.cif,
chain A (#21), sequence alignment score = 673.6
RMSD between 116 pruned atom pairs is 0.185 angstroms; (across all 128 pairs:
1.765)
> open /Users/hmed/Downloads/cryosparc_P844_J98__localfilter.mrc
Opened cryosparc_P844_J98__localfilter.mrc as #22, grid size 360,360,360,
pixel 0.829, shown at level 0.0351, step 2, values float32
> hide #18 models
> hide #19 models
> hide #20 models
> hide #21 models
> volume #22 level 0.2731
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #22 step 1
> hide #!22 models
> show #!22 models
> hide #!5 models
> open /Users/hmed/Downloads/cryosparc_P844_J93__localfilter.mrc
Opened cryosparc_P844_J93__localfilter.mrc as #23, grid size 360,360,360,
pixel 0.829, shown at level 0.039, step 2, values float32
> volume #23 level 0.09806
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #23 step 1
> volume #23 level 0.09045
> open /Users/hmed/Downloads/5toj.pdb
5toj.pdb title:
Crystal structure of the RSV F glycoprotein In complex with the neutralizing
single-domain antibody F-VHH-4 [more info...]
Chain information for 5toj.pdb #24
---
Chain | Description | UniProt
A B C | protein F | FUS_HRSVA 1-513
D E F | single-domain antibody F-VHH-4 |
Non-standard residues in 5toj.pdb #24
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
> select add #24
14124 atoms, 14399 bonds, 3 pseudobonds, 1826 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> ui mousemode right "translate selected models"
> view matrix models #24,1,0,0,165.03,0,1,0,171.74,0,0,1,-16.092
> view matrix models #24,1,0,0,149.04,0,1,0,203.97,0,0,1,-31.202
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.72767,-0.58504,0.35807,116.23,-0.17791,0.66515,0.7252,67.327,-0.66245,0.46401,-0.5881,290.25
> view matrix models
> #24,-0.65892,-0.75221,0.0030998,164.52,-0.52964,0.46687,0.70818,71.365,-0.53414,0.46499,-0.70603,305.79
> view matrix models
> #24,0.14062,-0.81189,0.56662,36.228,-0.78647,0.25604,0.56205,93.255,-0.6014,-0.52467,-0.60253,233.02
> view matrix models
> #24,0.040829,-0.94366,0.32838,72.756,-0.70714,0.20489,0.67673,67.882,-0.70589,-0.25984,-0.65894,261.8
> view matrix models
> #24,0.92532,0.30719,-0.2223,207.48,-0.13171,0.81013,0.57126,100.32,0.35558,-0.49932,0.79009,-37.276
> view matrix models
> #24,0.13032,0.91735,0.37613,169.62,-0.48382,-0.27229,0.83173,5.6781,0.86541,-0.29037,0.40835,21.561
> view matrix models
> #24,-0.55348,0.028906,0.83236,64.837,0.26879,-0.93972,0.21137,45.47,0.7883,0.34072,0.51234,43.317
> view matrix models
> #24,-0.41231,0.36612,0.83424,79.043,0.20371,-0.85546,0.47611,7.6006,0.88797,0.36625,0.27814,81.122
> view matrix models
> #24,-0.32489,0.018787,0.94556,36.727,0.21939,-0.97103,0.094676,65.313,0.91995,0.23821,0.31136,66.863
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.32489,0.018787,0.94556,0.20919,0.21939,-0.97103,0.094676,75.563,0.91995,0.23821,0.31136,108.68
> ui mousemode right "rotate selected models"
> view matrix models
> #24,0.063236,-0.76535,0.6405,-7.3852,0.51985,-0.52258,-0.67577,222.11,0.85191,0.3757,0.36482,110.01
> view matrix models
> #24,0.21637,-0.73419,0.64354,-11.607,0.63471,-0.39507,-0.66413,223.4,0.74184,0.55216,0.38052,121.56
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.21637,-0.73419,0.64354,-3.6322,0.63471,-0.39507,-0.66413,225.46,0.74184,0.55216,0.38052,121.22
> view matrix models
> #24,0.21637,-0.73419,0.64354,0.42671,0.63471,-0.39507,-0.66413,223.22,0.74184,0.55216,0.38052,115.45
> view matrix models
> #24,0.21637,-0.73419,0.64354,-1.5294,0.63471,-0.39507,-0.66413,221.48,0.74184,0.55216,0.38052,115.26
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.43758,-0.53641,0.72166,20.213,0.04201,0.7895,0.61231,94.199,-0.8982,0.29825,-0.32293,279.43
> view matrix models
> #24,-0.53931,0.76655,0.34864,163.21,0.44548,0.61103,-0.65437,285.13,-0.71463,-0.19759,-0.67101,303.3
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.53931,0.76655,0.34864,149.77,0.44548,0.61103,-0.65437,295.28,-0.71463,-0.19759,-0.67101,275.19
> view matrix models
> #24,-0.53931,0.76655,0.34864,147.57,0.44548,0.61103,-0.65437,284.35,-0.71463,-0.19759,-0.67101,271.96
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.57114,0.63241,0.5233,111.15,0.37718,0.76842,-0.51698,272.55,-0.72906,-0.097892,-0.67741,279.36
> view matrix models
> #24,-0.56822,0.60113,0.56193,102.65,0.23807,0.77378,-0.58702,289.81,-0.78769,-0.19977,-0.58279,259.43
> view matrix models
> #24,-0.57075,0.59451,0.56639,101.59,0.32461,0.79695,-0.50941,274.82,-0.75423,-0.10689,-0.64785,274.71
> view matrix models
> #24,-0.43389,0.78293,0.44582,128.17,0.32666,0.59786,-0.73202,301.1,-0.83966,-0.17199,-0.51516,251.39
> view matrix models
> #24,0.24283,0.052711,-0.96863,302.35,-0.35725,0.9332,-0.038778,227.1,0.90189,0.35546,0.24544,89.73
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.24283,0.052711,-0.96863,295.11,-0.35725,0.9332,-0.038778,222.4,0.90189,0.35546,0.24544,121.33
> view matrix models
> #24,0.24283,0.052711,-0.96863,304.72,-0.35725,0.9332,-0.038778,216.04,0.90189,0.35546,0.24544,121.75
> view matrix models
> #24,0.24283,0.052711,-0.96863,303.74,-0.35725,0.9332,-0.038778,215.17,0.90189,0.35546,0.24544,124.87
> view matrix models
> #24,0.24283,0.052711,-0.96863,304.61,-0.35725,0.9332,-0.038778,212.23,0.90189,0.35546,0.24544,126.91
> view matrix models
> #24,0.24283,0.052711,-0.96863,303.94,-0.35725,0.9332,-0.038778,212.36,0.90189,0.35546,0.24544,128.52
> view matrix models
> #24,0.24283,0.052711,-0.96863,304.12,-0.35725,0.9332,-0.038778,210.71,0.90189,0.35546,0.24544,118.21
> view matrix models
> #24,0.24283,0.052711,-0.96863,304.32,-0.35725,0.9332,-0.038778,216.21,0.90189,0.35546,0.24544,130.37
> view matrix models
> #24,0.24283,0.052711,-0.96863,306.37,-0.35725,0.9332,-0.038778,216.64,0.90189,0.35546,0.24544,130.06
> ui tool show "Fit in Map"
> fitmap #24 inMap #22
Fit molecule 5toj.pdb (#24) to map cryosparc_P844_J98__localfilter.mrc (#22)
using 14124 atoms
average map value = 0.06074, steps = 132
shifted from previous position = 3.56
rotated from previous position = 5.82 degrees
atoms outside contour = 12772, contour level = 0.27307
Position of 5toj.pdb (#24) relative to cryosparc_P844_J98__localfilter.mrc
(#22) coordinates:
Matrix rotation and translation
0.31506627 -0.01363833 -0.94897168 296.04815580
-0.34792317 0.92862520 -0.12885923 234.18851599
0.88299644 0.37076843 0.28783339 123.67669304
Axis 0.25913261 -0.95015293 -0.17337732
Axis point 114.54107458 0.00000000 274.96388960
Rotation angle (degrees) 74.58773835
Shift along axis -167.24190688
> view matrix models
> #24,0.31507,-0.013638,-0.94897,295.13,-0.34792,0.92863,-0.12886,232.24,0.883,0.37077,0.28783,123.22
> view matrix models
> #24,0.31507,-0.013638,-0.94897,294.24,-0.34792,0.92863,-0.12886,231.1,0.883,0.37077,0.28783,123.16
> view matrix models
> #24,0.31507,-0.013638,-0.94897,198.44,-0.34792,0.92863,-0.12886,193.27,0.883,0.37077,0.28783,117.53
> view matrix models
> #24,0.31507,-0.013638,-0.94897,300.64,-0.34792,0.92863,-0.12886,214.71,0.883,0.37077,0.28783,112.63
> view matrix models
> #24,0.31507,-0.013638,-0.94897,295.39,-0.34792,0.92863,-0.12886,231.84,0.883,0.37077,0.28783,117.18
> view matrix models
> #24,0.31507,-0.013638,-0.94897,294.67,-0.34792,0.92863,-0.12886,229.01,0.883,0.37077,0.28783,122.92
> view matrix models
> #24,0.31507,-0.013638,-0.94897,295.98,-0.34792,0.92863,-0.12886,230.72,0.883,0.37077,0.28783,123.12
> volume flip #22
Opened cryosparc_P844_J98__localfilter.mrc z flip as #25, grid size
360,360,360, pixel 0.829, shown at step 1, values float32
> ui mousemode right "rotate selected models"
> view matrix models
> #24,0.44342,0.4042,-0.8,290.27,0.84101,-0.49629,0.2154,46.371,-0.30997,-0.76832,-0.56,244.32
> view matrix models
> #24,0.42595,0.45145,-0.78406,290.93,0.64604,-0.75847,-0.085753,89.464,-0.63341,-0.47001,-0.61473,282.64
> view matrix models
> #24,-0.21492,0.82077,-0.52929,292.07,0.18721,-0.49728,-0.84715,250.92,-0.95852,-0.28116,-0.046783,208.55
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.21492,0.82077,-0.52929,285.56,0.18721,-0.49728,-0.84715,242.34,-0.95852,-0.28116,-0.046783,149.64
> view matrix models
> #24,-0.21492,0.82077,-0.52929,282.59,0.18721,-0.49728,-0.84715,255.86,-0.95852,-0.28116,-0.046783,145.55
> ui mousemode right "rotate selected models"
> view matrix models
> #24,0.46657,0.20668,-0.86,278.69,0.18781,-0.97329,-0.13201,106.3,-0.86432,-0.099923,-0.49292,228.72
> view matrix models
> #24,0.41134,0.32331,-0.85221,286.14,0.22572,-0.94199,-0.24842,126.59,-0.88309,-0.090182,-0.46046,224.43
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.41134,0.32331,-0.85221,301.32,0.22572,-0.94199,-0.24842,131.67,-0.88309,-0.090182,-0.46046,225.42
> view matrix models
> #24,0.41134,0.32331,-0.85221,303.29,0.22572,-0.94199,-0.24842,130.34,-0.88309,-0.090182,-0.46046,222.96
> view matrix models
> #24,0.41134,0.32331,-0.85221,301.66,0.22572,-0.94199,-0.24842,132.21,-0.88309,-0.090182,-0.46046,225.02
> fitmap #24 inMap #25
Fit molecule 5toj.pdb (#24) to map cryosparc_P844_J98__localfilter.mrc z flip
(#25) using 14124 atoms
average map value = 0.06259, steps = 276
shifted from previous position = 3.49
rotated from previous position = 5.57 degrees
atoms outside contour = 12638, contour level = 0.27307
Position of 5toj.pdb (#24) relative to cryosparc_P844_J98__localfilter.mrc z
flip (#25) coordinates:
Matrix rotation and translation
0.34375823 0.31012481 -0.88637062 304.93381541
0.27755267 -0.93527698 -0.21959390 125.12350606
-0.89710356 -0.17052732 -0.40758513 212.26952115
Axis 0.81963749 0.17928938 -0.54410450
Axis point 0.00000000 26.49299204 208.23346759
Rotation angle (degrees) 178.28477349
Shift along axis 156.87169891
> view matrix models
> #24,0.34376,0.31012,-0.88637,340.94,0.27755,-0.93528,-0.21959,161.21,-0.8971,-0.17053,-0.40759,168.11
> volume #22 level 0.253
> volume #25 level 0.09891
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.66912,0.2887,0.68479,108.44,-0.17771,-0.95688,0.22976,99.779,0.7216,0.032041,0.69157,-65.708
> view matrix models
> #24,-0.5595,-0.26799,0.78431,55.163,0.32325,-0.9419,-0.091245,137.31,0.7632,0.20247,0.61363,-44.013
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.5595,-0.26799,0.78431,45.759,0.32325,-0.9419,-0.091245,115.12,0.7632,0.20247,0.61363,42.108
> view matrix models
> #24,-0.5595,-0.26799,0.78431,5.2269,0.32325,-0.9419,-0.091245,112.37,0.7632,0.20247,0.61363,40.599
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.10302,-0.84848,0.51911,0.22027,0.67521,-0.44287,-0.58988,213.69,0.7304,0.28974,0.61852,46.02
> view matrix models
> #24,-0.18125,-0.81392,0.55198,-0.55398,0.61786,-0.53092,-0.57998,208.94,0.76512,0.23592,0.59912,44.947
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.18125,-0.81392,0.55198,14.437,0.61786,-0.53092,-0.57998,203.86,0.76512,0.23592,0.59912,48.727
> view matrix models
> #24,-0.18125,-0.81392,0.55198,15.936,0.61786,-0.53092,-0.57998,203.53,0.76512,0.23592,0.59912,48.006
> ui mousemode right "rotate selected models"
> view matrix models
> #24,-0.10292,-0.8131,0.57295,9.589,0.70508,-0.46593,-0.53458,196.43,0.70162,0.34896,0.62125,53.094
> view matrix models
> #24,-0.086073,-0.755,0.65006,-0.77766,0.60239,-0.55914,-0.56964,200.68,0.79355,0.34256,0.50293,69.573
> ui mousemode right "translate selected models"
> view matrix models
> #24,-0.086073,-0.755,0.65006,1.884,0.60239,-0.55914,-0.56964,200.75,0.79355,0.34256,0.50293,71.32
> view matrix models
> #24,-0.086073,-0.755,0.65006,-0.76548,0.60239,-0.55914,-0.56964,196.84,0.79355,0.34256,0.50293,84.18
> view matrix models
> #24,-0.086073,-0.755,0.65006,4.061,0.60239,-0.55914,-0.56964,195.21,0.79355,0.34256,0.50293,83.592
> ui mousemode right "rotate selected models"
> view matrix models
> #24,0.24419,-0.86749,0.43338,22.545,0.63947,-0.19192,-0.74448,245.03,0.72901,0.45893,0.50787,91.842
> view matrix models
> #24,0.099889,-0.89039,0.44409,24.586,0.44618,-0.35885,-0.81985,255.12,0.88935,0.28004,0.36143,100.62
> volume #22 level 0.06542
> view matrix models
> #24,0.46078,-0.496,-0.73598,235.61,-0.26961,-0.8683,0.41637,40.624,-0.84557,0.0065789,-0.53382,299.75
> view matrix models
> #24,0.3448,0.48637,-0.80285,308.31,0.26537,-0.87091,-0.41363,162.64,-0.90039,-0.070429,-0.42936,279.45
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.3448,0.48637,-0.80285,304.35,0.26537,-0.87091,-0.41363,156.6,-0.90039,-0.070429,-0.42936,243.77
> view matrix models
> #24,0.3448,0.48637,-0.80285,306.05,0.26537,-0.87091,-0.41363,155.93,-0.90039,-0.070429,-0.42936,243.25
> view matrix models
> #24,0.3448,0.48637,-0.80285,306.68,0.26537,-0.87091,-0.41363,160.74,-0.90039,-0.070429,-0.42936,238.83
> ui mousemode right "rotate selected models"
> view matrix models
> #24,0.27863,0.48489,-0.829,313.43,0.64945,-0.73103,-0.20931,120.22,-0.70752,-0.48007,-0.5186,223.27
> view matrix models
> #24,0.37302,0.49804,-0.78283,302.93,0.59101,-0.77795,-0.21331,120.28,-0.71524,-0.38309,-0.58453,240.43
> view matrix models
> #24,0.31389,0.49111,-0.81258,309.73,0.62821,-0.74914,-0.21009,120.07,-0.71191,-0.44452,-0.54367,229.77
> ui mousemode right "translate selected models"
> view matrix models
> #24,0.31389,0.49111,-0.81258,305.22,0.62821,-0.74914,-0.21009,124.37,-0.71191,-0.44452,-0.54367,226.32
> view matrix models
> #24,0.31389,0.49111,-0.81258,306.34,0.62821,-0.74914,-0.21009,128.53,-0.71191,-0.44452,-0.54367,225.1
> ui mousemode right "rotate selected models"
> view matrix models
> #24,0.34555,0.53409,-0.77158,300.71,0.59615,-0.75993,-0.25904,137.4,-0.7247,-0.37047,-0.581,236.23
> view matrix models
> #24,0.4711,0.4027,-0.78479,290.8,0.48753,-0.86033,-0.1488,116.69,-0.7351,-0.31251,-0.60163,243.49
> view matrix models
> #24,0.36617,0.29571,-0.88231,304.98,0.49378,-0.86541,-0.085121,105.32,-0.78873,-0.4045,-0.46291,216.43
> view matrix models
> #24,0.39921,0.31046,-0.8627,301.3,0.492,-0.86652,-0.084158,105.15,-0.77367,-0.39085,-0.49867,222.78
> view matrix models
> #24,0.45276,0.2062,-0.86746,294.12,0.44783,-0.89387,0.021263,87.189,-0.77101,-0.3981,-0.49705,221.98
> view matrix models
> #24,0.46053,0.18989,-0.8671,292.83,0.44048,-0.89698,0.037507,84.505,-0.77064,-0.39921,-0.49673,221.85
> view matrix models
> #24,0.42702,0.17731,-0.88669,296.65,0.48309,-0.87365,0.057944,80.844,-0.76438,-0.45309,-0.45872,212.01
> close #23
> fitmap #24 inMap #22
Fit molecule 5toj.pdb (#24) to map cryosparc_P844_J98__localfilter.mrc (#22)
using 14124 atoms
average map value = 0.06401, steps = 80
shifted from previous position = 1.48
rotated from previous position = 2.56 degrees
atoms outside contour = 9146, contour level = 0.065418
Position of 5toj.pdb (#24) relative to cryosparc_P844_J98__localfilter.mrc
(#22) coordinates:
Matrix rotation and translation
0.44516007 0.15489284 -0.88195279 293.44939612
0.44463257 -0.89316121 0.06756415 80.24675256
-0.77726082 -0.42222180 -0.46647011 215.28181104
Axis -0.84647421 -0.18093424 0.50074367
Axis point 0.00000000 34.33950373 189.88190728
Rotation angle (degrees) 163.18338234
Shift along axis -155.11572663
> volume #22 level 0.3066
> view matrix models
> #24,0.42031,0.1669,-0.8919,296.74,0.48099,-0.87445,0.063034,80.797,-0.76941,-0.45549,-0.44782,209.89
> open /Users/hmed/Downloads/7lue.pdb
7lue.pdb title:
Prefusion RSV F glycoprotein bound by neutralizing site V-directed antibody
adi-14442 [more info...]
Chain information for 7lue.pdb #23
---
Chain | Description | UniProt
A B C | fusion glycoprotein F0 | W8RJF9_HRSV 26-513
H I J | heavy chain of human antibody fab adi-14442 |
L M N | light chain of human antibody fab adi-14442 |
> show sel cartoons
> hide sel atoms
> show sel cartoons
> select subtract #24
Nothing selected
> select add #23
15018 atoms, 15303 bonds, 9 pseudobonds, 1947 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> hide #!24 models
> ui mousemode right "rotate selected models"
> view matrix models
> #23,-0.058109,0.18108,0.98175,-24.421,0.15419,0.97324,-0.17038,8.2518,-0.98633,0.14147,-0.084474,320.75
> view matrix models
> #23,-0.81662,0.56398,-0.12272,226.46,0.57432,0.81513,-0.075668,-51.167,0.05736,-0.13227,-0.98955,348.57
> view matrix models
> #23,-0.4192,0.83708,-0.35153,160,0.88644,0.46105,0.040784,-67.143,0.19621,-0.29451,-0.93529,341.76
> view matrix models
> #23,-0.41296,0.81711,-0.40222,170.64,0.88216,0.46866,0.046353,-68.56,0.22638,-0.33569,-0.91437,339.63
> view matrix models
> #23,-0.37258,0.85652,-0.35715,150.52,0.90388,0.42211,0.069384,-68.874,0.21019,-0.29697,-0.93147,339.24
> view matrix models
> #23,-0.43873,0.85053,-0.29002,150.64,0.88172,0.46973,0.043755,-68.213,0.17345,-0.23652,-0.95602,340.11
> ui mousemode right "translate selected models"
> view matrix models
> #23,-0.43873,0.85053,-0.29002,127.46,0.88172,0.46973,0.043755,-76.406,0.17345,-0.23652,-0.95602,326.68
> view matrix models
> #23,-0.43873,0.85053,-0.29002,127.46,0.88172,0.46973,0.043755,-72.224,0.17345,-0.23652,-0.95602,325.6
> view matrix models
> #23,-0.43873,0.85053,-0.29002,128.57,0.88172,0.46973,0.043755,-73.78,0.17345,-0.23652,-0.95602,326.14
> ui mousemode right "rotate selected models"
> view matrix models
> #23,-0.5016,0.86498,-0.014183,89.647,0.8648,0.50179,0.017848,-71.545,0.022555,-0.0033128,-0.99974,322.29
> view matrix models
> #23,-0.12566,0.99004,0.063463,-2.8586,0.97099,0.10961,0.21251,-61.966,0.20344,0.088325,-0.9751,275.15
> view matrix models
> #23,0.062923,0.99454,0.08323,-37.148,0.97032,-0.080475,0.22806,-35.583,0.23351,0.06641,-0.97008,272.81
> view matrix models
> #23,0.085084,0.98626,0.14159,-49.348,0.94574,-0.12467,0.30006,-37.139,0.31359,0.10838,-0.94335,249.05
> view matrix models
> #23,0.082973,0.97398,0.21092,-58.906,0.92297,-0.15492,0.35231,-37.752,0.37582,0.16544,-0.91181,225.03
> view matrix models
> #23,-0.44275,0.89663,-0.0042584,73.708,0.79914,0.39675,0.45162,-118.65,0.40663,0.19655,-0.8922,212.03
> ui mousemode right "translate selected models"
> view matrix models
> #23,-0.44275,0.89663,-0.0042584,77.712,0.79914,0.39675,0.45162,-106.14,0.40663,0.19655,-0.8922,192.8
> view matrix models
> #23,-0.44275,0.89663,-0.0042584,79.022,0.79914,0.39675,0.45162,-102.57,0.40663,0.19655,-0.8922,191.69
> view matrix models
> #23,-0.44275,0.89663,-0.0042584,79.215,0.79914,0.39675,0.45162,-102.96,0.40663,0.19655,-0.8922,192.81
> view matrix models
> #23,-0.44275,0.89663,-0.0042584,76.021,0.79914,0.39675,0.45162,-107.05,0.40663,0.19655,-0.8922,192.93
> view matrix models
> #23,-0.44275,0.89663,-0.0042584,76.815,0.79914,0.39675,0.45162,-106.61,0.40663,0.19655,-0.8922,192.16
> view matrix models
> #23,-0.44275,0.89663,-0.0042584,77.743,0.79914,0.39675,0.45162,-107.73,0.40663,0.19655,-0.8922,192.36
> view matrix models
> #23,-0.44275,0.89663,-0.0042584,80.02,0.79914,0.39675,0.45162,-107.1,0.40663,0.19655,-0.8922,192.52
> view matrix models
> #23,-0.44275,0.89663,-0.0042584,81.456,0.79914,0.39675,0.45162,-107.4,0.40663,0.19655,-0.8922,194.13
> fitmap #23 inMap #22
Fit molecule 7lue.pdb (#23) to map cryosparc_P844_J98__localfilter.mrc (#22)
using 15018 atoms
average map value = 0.05889, steps = 120
shifted from previous position = 1.84
rotated from previous position = 3.81 degrees
atoms outside contour = 13876, contour level = 0.30656
Position of 7lue.pdb (#23) relative to cryosparc_P844_J98__localfilter.mrc
(#22) coordinates:
Matrix rotation and translation
-0.48219330 0.87543428 0.03323307 86.41164844
0.77596682 0.40918271 0.48004689 -108.93895351
0.40665111 0.25726315 -0.87661311 181.67364929
Axis -0.49945058 -0.83715202 -0.22299242
Axis point 63.33502457 0.00000000 111.42821778
Rotation angle (degrees) 167.11300788
Shift along axis 7.52827052
> show #!25 models
> hide #!22 models
> view matrix models
> #23,-0.48219,0.87543,0.033233,84.762,0.77597,0.40918,0.48005,-115.37,0.40665,0.25726,-0.87661,179.75
> ui mousemode right "rotate selected models"
> view matrix models
> #23,-0.38594,0.092133,0.91791,38.32,0.50661,-0.81038,0.29434,144.85,0.77097,0.57862,0.26608,-121.49
> view matrix models
> #23,-0.94275,0.14798,-0.29889,325.65,-0.15536,-0.98786,0.00091976,327.83,-0.29512,0.047301,0.95429,13.539
> view matrix models
> #23,-0.68181,-0.70605,-0.1914,395.45,0.72954,-0.67555,-0.1068,156.66,-0.053897,-0.21245,0.97568,10.72
> view matrix models
> #23,-0.62782,-0.77764,-0.033518,370.88,0.77579,-0.62167,-0.10804,141.25,0.063177,-0.093831,0.99358,-29.139
> view matrix models
> #23,-0.89249,-0.43274,-0.12725,376.79,0.44088,-0.89652,-0.043434,225.82,-0.095284,-0.094866,0.99092,-3.1108
> ui mousemode right "translate selected models"
> view matrix models
> #23,-0.89249,-0.43274,-0.12725,386.7,0.44088,-0.89652,-0.043434,233.29,-0.095284,-0.094866,0.99092,23.213
> view matrix models
> #23,-0.89249,-0.43274,-0.12725,391.91,0.44088,-0.89652,-0.043434,229.72,-0.095284,-0.094866,0.99092,23.793
> view matrix models
> #23,-0.89249,-0.43274,-0.12725,389.31,0.44088,-0.89652,-0.043434,233.46,-0.095284,-0.094866,0.99092,29.147
> view matrix models
> #23,-0.89249,-0.43274,-0.12725,387.85,0.44088,-0.89652,-0.043434,232.31,-0.095284,-0.094866,0.99092,29.106
> view matrix models
> #23,-0.89249,-0.43274,-0.12725,386.9,0.44088,-0.89652,-0.043434,231.6,-0.095284,-0.094866,0.99092,27.27
> view matrix models
> #23,-0.89249,-0.43274,-0.12725,387.54,0.44088,-0.89652,-0.043434,230.26,-0.095284,-0.094866,0.99092,25.461
> view matrix models
> #23,-0.89249,-0.43274,-0.12725,387.53,0.44088,-0.89652,-0.043434,229.55,-0.095284,-0.094866,0.99092,25.794
> view matrix models
> #23,-0.89249,-0.43274,-0.12725,388.29,0.44088,-0.89652,-0.043434,230.78,-0.095284,-0.094866,0.99092,25.858
> volume #25 level 0.3401
> view matrix models
> #23,-0.89249,-0.43274,-0.12725,388.32,0.44088,-0.89652,-0.043434,230.57,-0.095284,-0.094866,0.99092,25.962
> fitmap #23 inMap #25
Fit molecule 7lue.pdb (#23) to map cryosparc_P844_J98__localfilter.mrc z flip
(#25) using 15018 atoms
average map value = 0.06772, steps = 60
shifted from previous position = 1.58
rotated from previous position = 2.62 degrees
atoms outside contour = 13978, contour level = 0.34005
Position of 7lue.pdb (#23) relative to cryosparc_P844_J98__localfilter.mrc z
flip (#25) coordinates:
Matrix rotation and translation
-0.87184845 -0.47312012 -0.12663974 391.27512350
0.48035838 -0.87646711 -0.03257658 219.36184765
-0.09558293 -0.08923430 0.99141371 23.45870689
Axis -0.05928616 -0.03249758 0.99771191
Axis point 168.39905238 159.89026979 0.00000000
Rotation angle (degrees) 151.45606036
Shift along axis -6.92089965
> view matrix models
> #23,-0.87185,-0.47312,-0.12664,391,0.48036,-0.87647,-0.032577,219.27,-0.095583,-0.089234,0.99141,23.387
> volume #25 level 0.1592
> open /Users/hmed/Downloads/cryosparc_P844_J89_003_volume_map_sharp.mrc
Opened cryosparc_P844_J89_003_volume_map_sharp.mrc as #26, grid size
360,360,360, pixel 0.829, shown at level 0.0489, step 2, values float32
> volume #26 level 0.1322
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #26 step 1
> view matrix models
> #23,-0.87185,-0.47312,-0.12664,441.18,0.48036,-0.87647,-0.032577,188.24,-0.095583,-0.089234,0.99141,14.636
> ui mousemode right "rotate selected models"
> view matrix models
> #23,-0.25443,0.95263,0.16661,75.518,0.9146,0.18104,0.36156,-109.16,0.31427,0.24437,-0.91734,222.08
> view matrix models
> #23,-0.5685,0.81909,0.076756,161.46,0.77231,0.49922,0.39283,-140.03,0.28345,0.2826,-0.9164,221.06
> view matrix models
> #23,-0.010629,0.92597,0.37745,4.6824,0.95273,-0.10524,0.28501,-58.738,0.30364,0.36263,-0.88108,199.65
> ui mousemode right "translate selected models"
> view matrix models
> #23,-0.010629,0.92597,0.37745,-49.842,0.95273,-0.10524,0.28501,-33.943,0.30364,0.36263,-0.88108,200.85
> view matrix models
> #23,-0.010629,0.92597,0.37745,-49.006,0.95273,-0.10524,0.28501,-39.119,0.30364,0.36263,-0.88108,188.4
> ui mousemode right "rotate selected models"
> view matrix models
> #23,-0.38673,0.92062,0.053769,67.071,0.91327,0.37425,0.16086,-84.649,0.12796,0.11131,-0.98551,272.53
> view matrix models
> #23,-0.37294,0.87848,0.29866,29.708,0.92785,0.35386,0.11778,-76.577,-0.0022175,0.32103,-0.94707,254.99
> view matrix models
> #23,-0.35092,0.8946,0.27667,27.455,0.93564,0.32302,0.14227,-77.291,0.037903,0.30879,-0.95037,250.98
> view matrix models
> #23,-0.26003,0.92456,0.27852,8.0055,0.96403,0.23212,0.12951,-65.854,0.055087,0.30218,-0.95166,249.45
> view matrix models
> #23,-0.2669,0.94569,0.18554,21.673,0.95697,0.23733,0.16695,-71.87,0.11385,0.22212,-0.96835,255.03
> ui mousemode right "translate selected models"
> view matrix models
> #23,-0.2669,0.94569,0.18554,15.937,0.95697,0.23733,0.16695,-62.079,0.11385,0.22212,-0.96835,255.37
> view matrix models
> #23,-0.2669,0.94569,0.18554,16.559,0.95697,0.23733,0.16695,-63.706,0.11385,0.22212,-0.96835,254.68
> ui mousemode right "rotate selected models"
> view matrix models
> #23,-0.61768,0.69862,0.36111,80.61,0.64761,0.71237,-0.27044,-12.101,-0.44618,0.066814,-0.89245,355.25
> ui mousemode right "translate selected models"
> view matrix models
> #23,-0.61768,0.69862,0.36111,82.691,0.64761,0.71237,-0.27044,-27.146,-0.44618,0.066814,-0.89245,352.42
> view matrix models
> #23,-0.61768,0.69862,0.36111,86.021,0.64761,0.71237,-0.27044,-31.42,-0.44618,0.066814,-0.89245,354.8
> ui mousemode right "rotate selected models"
> view matrix models
> #23,-0.35403,0.88521,0.30177,25.419,0.88952,0.41836,-0.18364,-40.238,-0.28881,0.20342,-0.93553,316.09
> view matrix models
> #23,-0.33892,0.89184,0.2996,22.355,0.89833,0.40138,-0.17858,-39.929,-0.27952,0.20862,-0.9372,314.1
> view matrix models
> #23,-0.36822,0.82682,0.42519,15.632,0.89978,0.43207,-0.060959,-64.79,-0.23411,0.36013,-0.90305,277.97
> ui mousemode right "translate selected models"
> view matrix models
> #23,-0.36822,0.82682,0.42519,17.105,0.89978,0.43207,-0.060959,-59.623,-0.23411,0.36013,-0.90305,278.64
> view matrix models
> #23,-0.36822,0.82682,0.42519,17.82,0.89978,0.43207,-0.060959,-55.938,-0.23411,0.36013,-0.90305,278.06
> view matrix models
> #23,-0.36822,0.82682,0.42519,18.464,0.89978,0.43207,-0.060959,-55.945,-0.23411,0.36013,-0.90305,274.65
> view matrix models
> #23,-0.36822,0.82682,0.42519,18.733,0.89978,0.43207,-0.060959,-59.948,-0.23411,0.36013,-0.90305,275.15
> view matrix models
> #23,-0.36822,0.82682,0.42519,17.065,0.89978,0.43207,-0.060959,-57.145,-0.23411,0.36013,-0.90305,275.71
> ui mousemode right "rotate selected models"
> view matrix models
> #23,-0.4082,0.80148,0.43703,25.321,0.88087,0.47149,-0.041926,-63.339,-0.23966,0.36786,-0.89847,274.65
> view matrix models
> #23,-0.37624,0.84299,0.38447,22.802,0.87933,0.45563,-0.13852,-44.284,-0.29195,0.28596,-0.91269,297.9
> view matrix models
> #23,-0.27216,0.91689,0.29197,10.564,0.92133,0.33584,-0.19584,-23.076,-0.27762,0.2157,-0.93616,310.28
> view matrix models
> #23,-0.2881,0.91057,0.2964,13.33,0.93175,0.33799,-0.13267,-35.794,-0.22098,0.23795,-0.9458,299.44
> view matrix models
> #23,-0.58694,0.80263,-0.10625,146.02,0.80924,0.58565,-0.046238,-68.48,0.025112,-0.11312,-0.99326,321.42
> ui mousemode right "translate selected models"
> view matrix models
> #23,-0.58694,0.80263,-0.10625,141.18,0.80924,0.58565,-0.046238,-73.034,0.025112,-0.11312,-0.99326,322.73
> view matrix models
> #23,-0.58694,0.80263,-0.10625,148.8,0.80924,0.58565,-0.046238,-71.214,0.025112,-0.11312,-0.99326,315.23
> view matrix models
> #23,-0.58694,0.80263,-0.10625,139.02,0.80924,0.58565,-0.046238,-66.06,0.025112,-0.11312,-0.99326,313.75
> view matrix models
> #23,-0.58694,0.80263,-0.10625,135.19,0.80924,0.58565,-0.046238,-65.768,0.025112,-0.11312,-0.99326,313.68
> hide #!26 models
> show #!26 models
> select subtract #23
Nothing selected
> hide #!23 models
> volume #25 level 0.2597
> open /Users/hmed/Documents/nipah/nipah1/output_ca_points_before_pruning.cif
> /Users/hmed/Documents/nipah/nipah1/see_alpha_output_p.cif
> /Users/hmed/Documents/nipah/nipah1/see_alpha_output_ca.cif
> /Users/hmed/Documents/nipah/nipah1/see_alpha_merged_output.cif
> /Users/hmed/Documents/nipah/nipah1/output_p_points_before_pruning.cif
Summary of feedback from opening
/Users/hmed/Documents/nipah/nipah1/output_ca_points_before_pruning.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Summary of feedback from opening
/Users/hmed/Documents/nipah/nipah1/see_alpha_output_p.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Summary of feedback from opening
/Users/hmed/Documents/nipah/nipah1/see_alpha_output_ca.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Summary of feedback from opening
/Users/hmed/Documents/nipah/nipah1/see_alpha_merged_output.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Summary of feedback from opening
/Users/hmed/Documents/nipah/nipah1/output_p_points_before_pruning.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for output_ca_points_before_pruning.cif #27
---
Chain | Description
1 | No description available
Chain information for see_alpha_output_p.cif #28
---
Chain | Description
1 | No description available
Chain information for see_alpha_output_ca.cif #29
---
Chain | Description
1 | No description available
Chain information for see_alpha_merged_output.cif #30
---
Chain | Description
1 | No description available
2 | No description available
Chain information for output_p_points_before_pruning.cif #31
---
Chain | Description
1 | No description available
> hide #!31 models
> hide #!30 models
> hide #!29 models
> hide #!28 models
> hide #!27 models
> show #!28 models
> hide #!28 models
> show #!29 models
> show #!30 models
> hide #!29 models
> show #!28 models
> hide #!30 models
> hide #!28 models
> show #!29 models
> hide #!29 models
> show #!30 models
> hide #!30 models
> show #!31 models
> hide #!31 models
> show #!27 models
> hide #!27 models
> show #!23 models
> hide #!23 models
> show #!31 models
> hide #!31 models
> show #!27 models
> hide #!27 models
> open /Users/hmed/Documents/nipah/nipah1/job005.cif
Summary of feedback from opening /Users/hmed/Documents/nipah/nipah1/job005.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for job005.cif #32
---
Chain | Description
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Af | No description available
Ag | No description available
Ah | No description available
Ba | No description available
Bb | No description available
Ca | No description available
Cb | No description available
Cc | No description available
> open /Users/hmed/Documents/nipah/nipah1/job005_raw.cif
Summary of feedback from opening
/Users/hmed/Documents/nipah/nipah1/job005_raw.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for job005_raw.cif #33
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
8 | No description available
9 | No description available
A | No description available
AA | No description available
AB | No description available
AC | No description available
AD | No description available
AE | No description available
AF | No description available
AG | No description available
AH | No description available
AI | No description available
AJ | No description available
AK | No description available
AL | No description available
AM | No description available
AN | No description available
AO | No description available
AP | No description available
AQ | No description available
AR | No description available
AS | No description available
AT | No description available
AU | No description available
AV AW | No description available
AX | No description available
AY | No description available
AZ | No description available
Aa | No description available
Ab | No description available
Ac | No description available
Ad | No description available
Ae | No description available
Af | No description available
Ag | No description available
Ah | No description available
Ai | No description available
Aj | No description available
Ak | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h l | No description available
i | No description available
j | No description available
k | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> hide #!32 models
> show #33 cartoons
> hide #33 atoms
> show #!32 models
> hide #33 models
> show #!32 cartoons
> hide #!32 atoms
> show #!25 models
> hide #!25 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!1 models
> hide #!1 models
> select #32/Ba /Ca
1745 atoms, 1793 bonds, 1 pseudobond, 224 residues, 2 models selected
> select ~sel & ##selected
5383 atoms, 5492 bonds, 20 pseudobonds, 686 residues, 2 models selected
> delete sel
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/hmed/Documents/nipah/nipah1/ModelAngelo3_fabonly.pdb models #32
> relModel #1
> open /Users/hmed/Downloads/cryosparc_P1301_J47_007_volume_map_sharp.mrc
Opened cryosparc_P1301_J47_007_volume_map_sharp.mrc as #34, grid size
352,352,352, pixel 0.96, shown at level 1.1, step 2, values float32
> volume #34 level 0.4837
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #34 step 1
> open "/Users/hmed/Downloads/2ws9 (1).pdb"
2ws9 (1).pdb title:
Equine rhinitis A virus At low pH [more info...]
Chain information for 2ws9 (1).pdb #35
---
Chain | Description | UniProt
1 | P1 | B9VV85_9PICO 1-246
2 | P1 | B9VV85_9PICO 1-230
3 | P1 | B9VV85_9PICO 1-226
4 | P1 | B9VV85_9PICO 1-80
> select add #35
5364 atoms, 5534 bonds, 693 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #35,1,0,0,291.22,0,1,0,-132.27,0,0,1,-87.441
> view matrix models #35,1,0,0,327.34,0,1,0,-129.32,0,0,1,-64.612
> view matrix models #35,1,0,0,360.84,0,1,0,-129.46,0,0,1,-41.425
> ui mousemode right "rotate selected models"
> view matrix models
> #35,0.51908,-0.33218,-0.78754,598.33,0.34963,0.9233,-0.15899,-73.989,0.77995,-0.19281,0.5954,97.896
> view matrix models
> #35,0.76214,-0.46532,-0.45014,558.33,0.43495,0.88301,-0.17636,-60.259,0.47954,-0.061376,0.87537,4.8157
> view matrix models
> #35,0.76073,-0.45562,-0.46227,558.77,0.4231,0.8882,-0.17913,-60.96,0.49221,-0.059315,0.86846,5.9968
> ui mousemode right "translate selected models"
> view matrix models
> #35,0.76073,-0.45562,-0.46227,483.96,0.4231,0.8882,-0.17913,-47.31,0.49221,-0.059315,0.86846,19.088
> view matrix models
> #35,0.76073,-0.45562,-0.46227,469.62,0.4231,0.8882,-0.17913,-65.677,0.49221,-0.059315,0.86846,7.8672
> view matrix models
> #35,0.76073,-0.45562,-0.46227,431.66,0.4231,0.8882,-0.17913,-77.037,0.49221,-0.059315,0.86846,-17.413
> view matrix models
> #35,0.76073,-0.45562,-0.46227,442.63,0.4231,0.8882,-0.17913,-95.981,0.49221,-0.059315,0.86846,-20.118
> view matrix models
> #35,0.76073,-0.45562,-0.46227,443.52,0.4231,0.8882,-0.17913,-92.066,0.49221,-0.059315,0.86846,-27.933
> ui mousemode right "rotate selected models"
> view matrix models
> #35,0.96596,-0.081199,-0.24563,316.07,0.1779,0.89783,0.40281,-222.31,0.18783,-0.4328,0.88171,48.67
> ui mousemode right "translate selected models"
> view matrix models
> #35,0.96596,-0.081199,-0.24563,313.02,0.1779,0.89783,0.40281,-222.21,0.18783,-0.4328,0.88171,43.313
> ui mousemode right "rotate selected models"
> view matrix models
> #35,0.95788,-0.040004,-0.28438,312.08,0.14952,0.91492,0.37492,-220.36,0.24518,-0.40165,0.88236,36.929
> view matrix models
> #35,0.93117,0.010858,-0.36444,317.66,0.18362,0.84958,0.49447,-231.12,0.31499,-0.52735,0.78911,85.802
> view matrix models
> #35,0.91735,0.033295,-0.39669,319.44,0.19992,0.82319,0.53141,-232.99,0.34424,-0.56679,0.7485,103.67
> view matrix models
> #35,0.98423,0.089007,-0.15289,255.41,0.0013904,0.86031,0.50978,-238.99,0.17691,-0.50195,0.84661,66.118
> view matrix models
> #35,0.95799,0.065121,-0.2793,287.6,0.092242,0.85216,0.51509,-237.23,0.27155,-0.51921,0.81036,78.897
> view matrix models
> #35,0.90447,-0.11964,-0.4094,356.05,0.23749,0.93857,0.25039,-197.78,0.3543,-0.3237,0.87732,21.98
> ui mousemode right "translate selected models"
> view matrix models
> #35,0.90447,-0.11964,-0.4094,345.87,0.23749,0.93857,0.25039,-202.07,0.3543,-0.3237,0.87732,22.616
> view matrix models
> #35,0.90447,-0.11964,-0.4094,348.91,0.23749,0.93857,0.25039,-203.7,0.3543,-0.3237,0.87732,19.067
> view matrix models
> #35,0.90447,-0.11964,-0.4094,344.4,0.23749,0.93857,0.25039,-206.93,0.3543,-0.3237,0.87732,18.124
> ui mousemode right "rotate selected models"
> view matrix models
> #35,0.85072,0.064644,-0.52162,326.87,0.069158,0.97001,0.233,-212.22,0.52104,-0.2343,0.82074,12.405
> view matrix models
> #35,0.89865,0.13735,-0.4166,288.68,-0.033702,0.96853,0.24661,-216.06,0.43736,-0.20758,0.875,-6.2186
> ui mousemode right "translate selected models"
> view matrix models
> #35,0.89865,0.13735,-0.4166,283.51,-0.033702,0.96853,0.24661,-215.3,0.43736,-0.20758,0.875,-10.201
> view matrix models
> #35,0.89865,0.13735,-0.4166,282.4,-0.033702,0.96853,0.24661,-214.2,0.43736,-0.20758,0.875,-11.85
> view matrix models
> #35,0.89865,0.13735,-0.4166,285.72,-0.033702,0.96853,0.24661,-213.62,0.43736,-0.20758,0.875,-12.142
> view matrix models
> #35,0.89865,0.13735,-0.4166,291.26,-0.033702,0.96853,0.24661,-211.83,0.43736,-0.20758,0.875,-9.281
> view matrix models
> #35,0.89865,0.13735,-0.4166,291.57,-0.033702,0.96853,0.24661,-215.33,0.43736,-0.20758,0.875,-9.2218
> view matrix models
> #35,0.89865,0.13735,-0.4166,293.61,-0.033702,0.96853,0.24661,-212.87,0.43736,-0.20758,0.875,-13.262
> view matrix models
> #35,0.89865,0.13735,-0.4166,293.72,-0.033702,0.96853,0.24661,-213.35,0.43736,-0.20758,0.875,-11.854
> view matrix models
> #35,0.89865,0.13735,-0.4166,289.17,-0.033702,0.96853,0.24661,-214.4,0.43736,-0.20758,0.875,-11.776
> view matrix models
> #35,0.89865,0.13735,-0.4166,285.07,-0.033702,0.96853,0.24661,-211.48,0.43736,-0.20758,0.875,-6.7416
> view matrix models
> #35,0.89865,0.13735,-0.4166,283.04,-0.033702,0.96853,0.24661,-213.5,0.43736,-0.20758,0.875,4.1314
> view matrix models
> #35,0.89865,0.13735,-0.4166,282.86,-0.033702,0.96853,0.24661,-215.02,0.43736,-0.20758,0.875,1.722
> view matrix models
> #35,0.89865,0.13735,-0.4166,282.92,-0.033702,0.96853,0.24661,-216.05,0.43736,-0.20758,0.875,3.7176
> view matrix models
> #35,0.89865,0.13735,-0.4166,287.23,-0.033702,0.96853,0.24661,-214.93,0.43736,-0.20758,0.875,2.6605
> view matrix models
> #35,0.89865,0.13735,-0.4166,287.33,-0.033702,0.96853,0.24661,-217.43,0.43736,-0.20758,0.875,7.6712
> view matrix models
> #35,0.89865,0.13735,-0.4166,287.09,-0.033702,0.96853,0.24661,-218.54,0.43736,-0.20758,0.875,7.8258
> view matrix models
> #35,0.89865,0.13735,-0.4166,289.33,-0.033702,0.96853,0.24661,-218.82,0.43736,-0.20758,0.875,10.624
> view matrix models
> #35,0.89865,0.13735,-0.4166,290.2,-0.033702,0.96853,0.24661,-218.02,0.43736,-0.20758,0.875,13.282
> color sel bychain
> view matrix models
> #35,0.89865,0.13735,-0.4166,289.38,-0.033702,0.96853,0.24661,-218.27,0.43736,-0.20758,0.875,13.384
> ui mousemode right "rotate selected models"
> view matrix models
> #35,0.34982,0.88777,0.29915,-38.165,-0.85104,0.43464,-0.29466,7.1052,-0.39161,-0.15151,0.90757,-16.091
> view matrix models
> #35,-0.51756,0.85563,0.0057505,21.631,-0.38093,-0.22439,-0.89696,288.97,-0.76617,-0.46643,0.44207,149.59
> view matrix models
> #35,-0.42598,-0.055543,0.90303,32.559,-0.51028,-0.80946,-0.2905,287.2,0.7471,-0.58454,0.31647,221.12
> ui mousemode right "translate selected models"
> view matrix models
> #35,-0.42598,-0.055543,0.90303,57.091,-0.51028,-0.80946,-0.2905,311.91,0.7471,-0.58454,0.31647,220.58
> view matrix models
> #35,-0.42598,-0.055543,0.90303,61.813,-0.51028,-0.80946,-0.2905,308.58,0.7471,-0.58454,0.31647,214.4
> view matrix models
> #35,-0.42598,-0.055543,0.90303,68.257,-0.51028,-0.80946,-0.2905,313.51,0.7471,-0.58454,0.31647,220.83
> view matrix models
> #35,-0.42598,-0.055543,0.90303,66.015,-0.51028,-0.80946,-0.2905,312.66,0.7471,-0.58454,0.31647,228.57
> view matrix models
> #35,-0.42598,-0.055543,0.90303,75.284,-0.51028,-0.80946,-0.2905,306.74,0.7471,-0.58454,0.31647,223.56
> ui mousemode right "rotate selected models"
> view matrix models
> #35,-0.42067,-0.22504,0.87886,118.27,0.11946,-0.97405,-0.19223,329.83,0.89931,0.024121,0.43664,64.097
> view matrix models
> #35,-0.085489,0.038536,0.99559,38.543,0.17164,-0.98374,0.052816,279.91,0.98144,0.1754,0.077484,108.65
> view matrix models
> #35,0.0017686,0.088627,0.99606,28.346,0.01134,-0.996,0.088601,273.01,0.99993,0.011139,-0.0027665,162.69
> view matrix models
> #35,0.01909,-0.12031,0.99255,75.811,0.048455,-0.99146,-0.12111,317.55,0.99864,0.050406,-0.013097,156.16
> view matrix models
> #35,-0.068663,-0.062774,0.99566,61.278,0.20604,-0.97739,-0.047413,300.47,0.97613,0.20189,0.080045,102.14
> view matrix models
> #35,-0.059322,-0.13618,0.98891,79.18,0.22051,-0.96797,-0.12007,314.17,0.97358,0.21094,0.08745,98.508
> view matrix models
> #35,-0.044082,-0.19998,0.97881,95.735,0.2296,-0.95556,-0.18489,325.46,0.97229,0.21658,0.088037,97.11
> view matrix models
> #35,-0.042575,-0.19323,0.98023,93.946,0.22409,-0.95797,-0.17911,324.69,0.97364,0.21203,0.084086,98.989
> view matrix models
> #35,-0.036963,-0.073152,0.99664,63.761,0.21393,-0.97477,-0.063613,303.47,0.97615,0.21086,0.05168,106.25
> view matrix models
> #35,0.22998,-0.22087,0.9478,110.36,-0.29907,-0.94282,-0.14714,308.13,0.9261,-0.24962,-0.28288,280.08
> view matrix models
> #35,0.34064,-0.24824,0.90683,126.59,-0.26526,-0.95071,-0.16061,313.19,0.902,-0.18584,-0.3897,288.56
> view matrix models
> #35,0.30907,-0.24288,0.9195,122.29,-0.1568,-0.96662,-0.20263,327.08,0.93802,-0.081552,-0.33684,254.42
> view matrix models
> #35,0.082558,0.24997,0.96473,0.15116,-0.08965,-0.96225,0.257,228.07,0.99255,-0.10771,-0.057031,200.72
> volume flip #34
Opened cryosparc_P1301_J47_007_volume_map_sharp.mrc z flip as #36, grid size
352,352,352, pixel 0.96, shown at step 1, values float32
> view matrix models
> #35,-0.00067091,0.023816,0.99972,41.955,-0.028759,-0.9993,0.023787,287.2,0.99959,-0.028735,0.0013554,170.68
> view matrix models
> #35,-0.0088848,0.091017,0.99581,27.74,-0.17167,-0.9812,0.08815,267.61,0.98511,-0.17017,0.024343,197.04
> view matrix models
> #35,-0.21102,0.036949,0.97678,41.429,0.25394,-0.9629,0.091283,268,0.94392,0.2673,0.19381,62.733
> view matrix models
> #35,-0.16544,0.03807,0.98548,39.857,0.2756,-0.95766,0.083263,268.81,0.94693,0.28538,0.14794,68.611
> view matrix models
> #35,-0.14526,-0.010914,0.98933,50.175,0.24042,-0.97036,0.024594,283.83,0.95974,0.24142,0.14357,79.487
> ui tool show "Fit in Map"
> fitmap #35 inMap #36
Fit molecule 2ws9 (1).pdb (#35) to map
cryosparc_P1301_J47_007_volume_map_sharp.mrc z flip (#36) using 5364 atoms
average map value = 0.7781, steps = 116
shifted from previous position = 5.52
rotated from previous position = 15.5 degrees
atoms outside contour = 1385, contour level = 0.48369
Position of 2ws9 (1).pdb (#35) relative to
cryosparc_P1301_J47_007_volume_map_sharp.mrc z flip (#36) coordinates:
Matrix rotation and translation
-0.03078576 0.02356208 0.99924825 41.92263837
-0.00007065 -0.99972216 0.02357107 291.20808902
0.99952601 0.00065505 0.03077887 163.05175872
Axis -0.69611220 -0.00843723 -0.71788343
Axis point -56.42996371 144.99890600 0.00000000
Rotation angle (degrees) 179.05686867
Shift along axis -148.69200656
> select subtract #35
Nothing selected
> transparency #36.1 50
> measure symmetry
Missing or invalid "volumes" argument: empty atom specifier
> measure symmetry #35
No volume specified
> measure symmetry #36
Symmetry cryosparc_P1301_J47_007_volume_map_sharp.mrc z flip: Icosahedral
222r, center 176 176 175
> sym #35 symmetry #36
Made 60 graphical clones for 2ws9 (1).pdb symmetry #36
> color #35#!32 bychain
> ui tool show "Side View"
> style #35#!32 stick
Changed 7109 atom styles
> show #35#!32 atoms
> color #35#!32 byhetero
> open "/Users/hmed/Downloads/2wff (1).pdb"
2wff (1).pdb title:
Equine rhinitis A virus [more info...]
Chain information for 2wff (1).pdb #37
---
Chain | Description | UniProt
1 | P1 | B9VV85_9PICO 1-246
2 | P1 | B9VV85_9PICO 1-230
3 | P1 | B9VV85_9PICO 1-226
4 | P1 | B9VV85_9PICO 1-80
> mmaker #37 to #35
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2ws9 (1).pdb, chain 1 (#35) with 2wff (1).pdb, chain 1 (#37),
sequence alignment score = 1196.8
RMSD between 221 pruned atom pairs is 0.599 angstroms; (across all 246 pairs:
4.654)
> fitmap #37 inMap #36
Fit molecule 2wff (1).pdb (#37) to map
cryosparc_P1301_J47_007_volume_map_sharp.mrc z flip (#36) using 5506 atoms
average map value = 0.7362, steps = 60
shifted from previous position = 0.215
rotated from previous position = 0.372 degrees
atoms outside contour = 1662, contour level = 0.48369
Position of 2wff (1).pdb (#37) relative to
cryosparc_P1301_J47_007_volume_map_sharp.mrc z flip (#36) coordinates:
Matrix rotation and translation
-0.53336579 -0.01351308 0.84577676 9.47543369
0.01340566 -0.99988185 -0.00752133 169.56462999
0.84577847 0.00732658 0.53348392 33.92218426
Axis 0.48298221 -0.00005561 0.87563016
Axis point -5.36192282 84.75233440 0.00000000
Rotation angle (degrees) 179.11926776
Shift along axis 34.27032484
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #37
5506 atoms, 5676 bonds, 713 residues, 1 model selected
> show sel atoms
> select subtract #37
Nothing selected
> ui tool show "Map Coordinates"
> hide #!36 models
> show #!36 models
> hide #35 models
Opened 2wff (1).pdb map 3 as #38, grid size 105,105,99, pixel 1, shown at
level 0.111, step 1, values float32
Opened 2wff (1).pdb map 3 as #39, grid size 105,105,99, pixel 1, shown at
level 0.111, step 1, values float32
> fitmap #37 inMap #36 resolution 3
Fit map 2wff (1).pdb map 3 in map cryosparc_P1301_J47_007_volume_map_sharp.mrc
z flip using 58352 points
correlation = 0.7942, correlation about mean = 0.5162, overlap = 1.983e+04
steps = 44, shift = 0.0079, angle = 0.0129 degrees
Position of 2wff (1).pdb map 3 (#39) relative to
cryosparc_P1301_J47_007_volume_map_sharp.mrc z flip (#36) coordinates:
Matrix rotation and translation
-0.53335577 -0.01331552 0.84578621 9.45041894
0.01338988 -0.99988372 -0.00729783 169.49789764
0.84578504 0.00743264 0.53347205 33.91981803
Axis 0.48298813 0.00003849 0.87562690
Axis point -5.36772928 84.71727810 0.00000000
Rotation angle (degrees) 179.12624528
Shift along axis 34.27206922
Average map value = 0.7362 for 5506 atoms, 1656 outside contour
> select add #37
5506 atoms, 5676 bonds, 713 residues, 1 model selected
> view matrix models
> #37,-0.53106,-0.01556,0.84719,9.3362,0.016148,-0.99984,-0.0082411,169.82,0.84718,0.0093036,0.53123,34.396
> ui mousemode right "translate selected models"
> view matrix models
> #37,-0.53106,-0.01556,0.84719,13.882,0.016148,-0.99984,-0.0082411,167.74,0.84718,0.0093036,0.53123,38.097
> view matrix models
> #37,-0.53106,-0.01556,0.84719,13.67,0.016148,-0.99984,-0.0082411,168.58,0.84718,0.0093036,0.53123,36.117
> view matrix models
> #37,-0.53106,-0.01556,0.84719,15.525,0.016148,-0.99984,-0.0082411,169.55,0.84718,0.0093036,0.53123,40.012
> select subtract #37
Nothing selected
> hide #37 models
> show #35 models
> show #37 models
> fitmap #37 inMap #36 resolution 3
Fit map 2wff (1).pdb map 3 in map cryosparc_P1301_J47_007_volume_map_sharp.mrc
z flip using 58352 points
correlation = 0.7942, correlation about mean = 0.5161, overlap = 1.983e+04
steps = 140, shift = 8.38, angle = 0.237 degrees
Position of 2wff (1).pdb map 3 (#38) relative to
cryosparc_P1301_J47_007_volume_map_sharp.mrc z flip (#36) coordinates:
Matrix rotation and translation
-0.53343864 -0.01326730 0.84573471 9.45729930
0.01318503 -0.99988592 -0.00736920 169.51126257
0.84573600 0.00722002 0.53355271 33.89940269
Axis 0.48294611 -0.00004259 0.87565007
Axis point -5.35063405 84.72591927 0.00000000
Rotation angle (degrees) 179.13454913
Shift along axis 34.24416042
Average map value = 0.7362 for 5506 atoms, 1659 outside contour
> hide #35 models
> show #35 models
> hide #35 models
> show #35 models
> hide #35 models
> show #35 models
> volume #36 level 0.3611
> ui tool show "Side View"
> volume #36 level 0.5888
> volume #36 level 0.3261
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/hmed/Downloads/cryosparc_P4_J52_004_volume_map_sharp (1).mrc"
Opened cryosparc_P4_J52_004_volume_map_sharp (1).mrc as #1, grid size
280,280,280, pixel 1.46, shown at level 0.121, step 2, values float32
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,9
Model Number: MPHF3B/A
Chip: Apple M2 Pro
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.121.1
OS Loader Version: 8422.141.2.700.1
Software:
System Software Overview:
System Version: macOS 13.6.7 (22G720)
Kernel Version: Darwin 22.6.0
Time since boot: 6 days, 8 hours, 2 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 19
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
annotated-types: 0.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-ArtiaX: 0.4.7
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
geomdl: 5.3.1
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
pandas: 2.2.3
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pyarrow: 17.0.0
pycollada: 0.8
pydantic: 2.9.2
pydantic-core: 2.23.4
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
starfile: 0.5.8
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 12 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 , 12 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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ChimeraX crashed in the Qt window toolkit. This is a bug in Qt which we seen cause crashes when plugging in or unplugging an external display or sometimes waking from sleep. The crash report says a display was being reconfigured and shows ChimeraX was in the background (not the active app). Unfortunately we don't have any way to fix this. The ChimeraX 1.9 release candidate and current daily build uses a newer Qt version (6.7 instead of 6.6) which we think crashes less often, but have still seen some crashes with it.
Were you using an external display during this ChimeraX session that crashed or did the computer just wake from sleep, or did it crash with neither of those conditions? I've been working on some fix for this crash for 5 months but have not been able to reproduce it on my own machine.