![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 hours ago
Closed 82 minutes ago
#19766 closed defect (can't reproduce)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.7.3-arm64-arm-64bit
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001f302e240 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 56 in display
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 144 in show_save_file_dialog
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 133 in
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, PIL._imaging, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath (total: 59)
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"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 4369727464
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 10474c000-104750000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":1730},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 4369727464
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
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===== Log before crash start =====
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/shamiul/projects/fks1/apo_drug_sac_model44.cxs
Opened cryosparc_P1078_J1017_002_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.3, shown at level 0.495, step 1, values float32
Opened cryosparc_P23_J469_003_volume_map_sharp.mrc as #3, grid size
512,512,512, pixel 0.734, shown at level 0.0298, step 2, values float32
Opened emdb 33154 as #4, grid size 224,224,224, pixel 0.92, shown at level
0.00808, step 1, values float32
Log from Tue Jan 20 09:48:17 2026UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/shamiul/Downloads/cryosparc_P1078_J1017_002_volume_map_sharp.mrc
Opened cryosparc_P1078_J1017_002_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.3, shown at level 0.239, step 1, values float32
> open "/Users/shamiul/projects/fks1/Model
> Building/Coot/round19_real_space_refined_001-coot-44.pdb"
Summary of feedback from opening /Users/shamiul/projects/fks1/Model
Building/Coot/round19_real_space_refined_001-coot-44.pdb
---
warnings | Start residue of secondary structure not found: HELIX 9 9 ALA A 236 LYS A 242 1 7
Start residue of secondary structure not found: HELIX 10 10 LYS A 244 MET A
247 1 4
Start residue of secondary structure not found: HELIX 11 11 ALA A 255 ASP A
257 1 3
Start residue of secondary structure not found: HELIX 12 12 ILE A 258 ASN A
260 1 3
End residue of secondary structure not found: HELIX 64 64 ASN A 788 THR A 792
1 5
End residue of secondary structure not found: HELIX 69 69 PRO A 867 GLU A 888
1 22
Start residue of secondary structure not found: HELIX 70 70 ALA A 900 ASP A
906 1 7
Start residue of secondary structure not found: HELIX 71 71 PHE A 910 ILE A
913 1 4
Start residue of secondary structure not found: HELIX 96 96 PHE A 1239 ILE A
1242 1 4
Start residue of secondary structure not found: HELIX 97 97 LEU A 1243 PHE A
1245 1 3
Start residue of secondary structure not found: HELIX 98 98 THR A 1246 GLN A
1256 1 11
End residue of secondary structure not found: HELIX 108 108 SER A 1385 ASP A
1403 1 19
Chain information for round19_real_space_refined_001-coot-44.pdb #2
---
Chain | Description
A | No description available
> volume #1 level 0.5677
> select add #2
26286 atoms, 26649 bonds, 8 pseudobonds, 1636 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-40.366,0,1,0,75.715,0,0,1,45.059
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.23585,-0.8656,-0.44171,370.28,0.9416,-0.091141,-0.32417,159.44,0.24034,-0.49237,0.83655,114.88
> view matrix models
> #2,-0.87113,-0.1611,-0.46386,357.53,0.42268,-0.72682,-0.54136,382.19,-0.24993,-0.66766,0.70126,243.46
> view matrix models
> #2,-0.7965,0.49136,0.35236,106.84,-0.5959,-0.73666,-0.31974,510.13,0.10246,-0.46464,0.87955,125.29
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.7965,0.49136,0.35236,147.44,-0.5959,-0.73666,-0.31974,434.86,0.10246,-0.46464,0.87955,75.24
> view matrix models
> #2,-0.7965,0.49136,0.35236,156.43,-0.5959,-0.73666,-0.31974,440.13,0.10246,-0.46464,0.87955,75.704
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule round19_real_space_refined_001-coot-44.pdb (#2) to map
cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) using 26286 atoms
average map value = 0.505, steps = 112
shifted from previous position = 2.31
rotated from previous position = 14.5 degrees
atoms outside contour = 16699, contour level = 0.56771
Position of round19_real_space_refined_001-coot-44.pdb (#2) relative to
cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.66534498 0.63156314 0.39805034 104.96048430
-0.71667873 -0.68964915 -0.10370951 419.37917810
0.20901597 -0.35427681 0.91148246 37.72015838
Axis -0.18100709 0.13655637 -0.97395523
Axis point 135.48156726 190.61539580 0.00000000
Rotation angle (degrees) 136.19963585
Shift along axis 1.53255925
> select clear
> volume #1 level 0.4976
> select clear
> molmap #2 16 onGrid #1
Opened round19_real_space_refined_001-coot-44.pdb map 16 as #3, grid size
256,256,256, pixel 1.3, shown at level 0.0587, step 1, values float32
> \
Unknown command: \
> molmap #2 16 onGrid #1
Opened round19_real_space_refined_001-coot-44.pdb map 16 as #3, grid size
256,256,256, pixel 1.3, shown at level 0.0587, step 1, values float32
> volume #3 level 0.1386
> volume #3 level 0.1278
> volume #3 level 0.1516
> save /Users/shamiul/Desktop/protein1072.mrc models #3
> close #3
> open /Users/shamiul/Downloads/cryosparc_P23_J469_003_volume_map_sharp.mrc
Opened cryosparc_P23_J469_003_volume_map_sharp.mrc as #3, grid size
512,512,512, pixel 0.734, shown at level 0.0147, step 2, values float32
> select add #3
2 models selected
> ui mousemode right "rotate selected models"
> volume #3 level 0.04773
> view matrix models
> #3,-0.079636,0.51981,-0.85056,277.07,-0.97778,-0.20673,-0.03479,415.67,-0.19392,0.82889,0.52472,-22.468
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.079636,0.51981,-0.85056,291.89,-0.97778,-0.20673,-0.03479,408.22,-0.19392,0.82889,0.52472,18.485
> view matrix models
> #3,-0.079636,0.51981,-0.85056,307.4,-0.97778,-0.20673,-0.03479,392.49,-0.19392,0.82889,0.52472,9.5176
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.74236,0.66559,-0.076754,248.06,-0.41506,-0.54679,-0.72715,490.4,-0.52595,-0.50796,0.68217,289.63
> view matrix models
> #3,0.99436,0.013795,0.10513,7.5729,-0.1047,-0.029291,0.99407,-12.114,0.016792,-0.99948,-0.027681,423.11
> view matrix models
> #3,0.98972,0.10493,0.097203,-6.9775,-0.085366,-0.11195,0.99004,0.51616,0.11477,-0.98816,-0.10184,417.62
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.98972,0.10493,0.097203,-72.684,-0.085366,-0.11195,0.99004,-8.2105,0.11477,-0.98816,-0.10184,383.63
> view matrix models
> #3,0.98972,0.10493,0.097203,-74.736,-0.085366,-0.11195,0.99004,-5.7417,0.11477,-0.98816,-0.10184,346.72
> view matrix models
> #3,0.98972,0.10493,0.097203,-68.072,-0.085366,-0.11195,0.99004,18.491,0.11477,-0.98816,-0.10184,353.16
> view matrix models
> #3,0.98972,0.10493,0.097203,-64.416,-0.085366,-0.11195,0.99004,14.455,0.11477,-0.98816,-0.10184,346.38
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.92649,0.020919,0.37573,-93.139,-0.34112,-0.37493,0.86201,137.37,0.15891,-0.92682,-0.34024,374.81
> view matrix models
> #3,0.90761,-0.1023,0.40715,-72.932,-0.40588,-0.46162,0.78878,180.49,0.10725,-0.88116,-0.46049,400.25
> view matrix models
> #3,0.92552,-0.24841,0.28584,-24.494,-0.37746,-0.54398,0.74941,198.5,-0.030665,-0.80149,-0.59723,438.84
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.92552,-0.24841,0.28584,-19.878,-0.37746,-0.54398,0.74941,201.85,-0.030665,-0.80149,-0.59723,439.42
> view matrix models
> #3,0.92552,-0.24841,0.28584,-23.844,-0.37746,-0.54398,0.74941,197.75,-0.030665,-0.80149,-0.59723,433.55
> fitmap #3 inMap #1
Fit map cryosparc_P23_J469_003_volume_map_sharp.mrc in map
cryosparc_P1078_J1017_002_volume_map_sharp.mrc using 20242 points
correlation = 0.8993, correlation about mean = 0.6277, overlap = 1661
steps = 188, shift = 6.85, angle = 20.8 degrees
Position of cryosparc_P23_J469_003_volume_map_sharp.mrc (#3) relative to
cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99518294 0.04427809 0.08746640 -46.83296081
-0.04864464 -0.55158245 0.83270073 121.26914196
0.08511534 -0.83294433 -0.54677156 406.40704997
Axis -0.99844649 0.00140931 -0.05570117
Axis point 0.00000000 170.37616190 171.87178256
Rotation angle (degrees) 123.47585517
Shift along axis 24.29376271
> select clear
> volume #3 level 0.04242
> volume #1 level 0.5381
> hide #!2 models
> show #!2 models
> hide #!3 models
> color #1 #b2b2b259 models
> set bgColor white
> color #1 #b2b2b285 models
> color #1 #b2b2b2b1 models
> volume #1 level 0.4841
> volume #1 level 0.4706
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> volume #3 level 0.03357
> hide #!2 models
> volume #3 level 0.03003
[Repeated 1 time(s)]
> surface dust #3 size 7.34
> volume #3 level 0.02472
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #3 level 0.02915
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!2 models
> surface dust #1 size 13
> surface dust #3 size 7.34
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> volume #3 level 0.03092
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> volume #3 level 0.0495
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.04419
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> volume #1 level 0.4031
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!2 models
> color #2 black
> color #2 #941100ff
> color #3 #b2b2ff9d models
> color #3 #b2b2ffea models
> color #3 #b2b2ffe2 models
> color #3 #b2b2ffdc models
> color #3 #b2b2ffdb models
> volume #3 level 0.03799
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> volume #1 level 0.4638
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!3 models
> volume #3 level 0.02915
> hide #!1 models
> volume #3 level 0.02472
> volume #3 level 0.03534
> show #!1 models
> volume #3 level 0.04242
> volume #1 level 0.4706
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.4368
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #3 level 0.03711
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #3 level 0.03357
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.04507
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!2 models
> color #2 forest green
> select #2:1344
24 atoms, 23 bonds, 1 residue, 1 model selected
> color sel red
> show #!1 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select /A:625
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:624
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:625
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> select /A:624
21 atoms, 21 bonds, 1 residue, 1 model selected
> color sel red
> show sel atoms
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> select /A:623
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> show #!1 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select /A:629
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> show #!1 models
> hide #!1 models
> select /A:1344
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> volume #3 level 0.05392
> volume #3 level 0.0495
> select /A:628
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.4031
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #3 level 0.04065
> volume #3 level 0.0318
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select /A:604
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> show #!1 models
> hide #!1 models
> select /A:231
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.04861
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> volume #1 level 0.4571
> hide #!1 models
> select /A:603
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> show #!1 models
> hide #!1 models
> select /A:605
24 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> volume #1 level 0.5381
> volume #1 level 0.7948
> volume #1 level 0.4436
> volume #1 level 0.4706
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.8353
> volume #1 level 0.4706
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!1 models
> volume #3 level 0.03357
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #3 level 0.02826
> volume #3 level 0.03357
> volume #3 level 0.04065
> show #!1 models
> volume #1 level 0.3828
> hide #!1 models
> volume #3 level 0.03622
> volume #3 level 0.03357
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> volume #1 level 0.4301
> volume #1 level 0.4503
> volume #1 level 0.4436
> show #!3 models
> volume #3 level 0.05127
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> volume #3 level 0.04596
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #1 level 0.4031
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> open 33154 fromDatabase emdb_fits format ccp4
Summary of feedback from opening 33154 fetched from emdb_fits
---
notes | Fetching compressed map 33154 from https://files.wwpdb.org/pub/emdb/structures/EMD-33154/map/emd_33154.map.gz
Fetching map header 33154 from
https://files.wwpdb.org/pub/emdb/structures/EMD-33154/header/emd-33154.xml
Fetching compressed mmCIF 7xe4 from http://files.rcsb.org/download/7xe4.cif
Fetching CCD C14 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/C14/C14.cif
Fetching CCD D10 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/0/D10/D10.cif
Fetching CCD D12 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/2/D12/D12.cif
Fetching CCD DD9 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/9/DD9/DD9.cif
Fetching CCD HP6 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/6/HP6/HP6.cif
Fetching CCD NAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif
Fetching CCD XKP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/XKP/XKP.cif
Opened emdb 33154 as #4, grid size 224,224,224, pixel 0.92, shown at level
0.01, step 1, values float32, fit PDB 7xe4
7xe4 title:
structure of a membrane-bound glycosyltransferase [more info...]
Chain information for 7xe4 #5
---
Chain | Description | UniProt
F | 1,3-beta-glucan synthase component FKS1 | FKS1_YEAST 1-1876
Non-standard residues in 7xe4 #5
---
C14 — tetradecane
D10 — decane
D12 — dodecane
DD9 — nonane
HP6 — heptane
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
XKP —
(11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl
decanoate
> select add #5
12529 atoms, 12835 bonds, 10 pseudobonds, 1530 residues, 3 models selected
> select add #4
12529 atoms, 12835 bonds, 10 pseudobonds, 1530 residues, 5 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.86725,0.45253,-0.2076,173.55,-0.088087,0.27094,0.95856,-21.349,0.49002,0.8496,-0.19511,-7.4292,#5,-0.86725,0.45253,-0.2076,173.55,-0.088087,0.27094,0.95856,-21.349,0.49002,0.8496,-0.19511,-7.4292
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.71393,0.63567,-0.29366,148.63,-0.01025,0.40985,0.91209,-38.223,0.70015,0.65418,-0.28609,-0.53684,#5,-0.71393,0.63567,-0.29366,148.63,-0.01025,0.40985,0.91209,-38.223,0.70015,0.65418,-0.28609,-0.53684
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.71393,0.63567,-0.29366,196.82,-0.01025,0.40985,0.91209,41.09,0.70015,0.65418,-0.28609,59.182,#5,-0.71393,0.63567,-0.29366,196.82,-0.01025,0.40985,0.91209,41.09,0.70015,0.65418,-0.28609,59.182
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.86827,0.12771,-0.47937,282.81,-0.36197,0.49769,0.78821,82.573,0.33925,0.8579,-0.3859,87.659,#5,-0.86827,0.12771,-0.47937,282.81,-0.36197,0.49769,0.78821,82.573,0.33925,0.8579,-0.3859,87.659
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.86827,0.12771,-0.47937,285.04,-0.36197,0.49769,0.78821,76.609,0.33925,0.8579,-0.3859,84.03,#5,-0.86827,0.12771,-0.47937,285.04,-0.36197,0.49769,0.78821,76.609,0.33925,0.8579,-0.3859,84.03
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.82789,0.45334,-0.33028,232.85,-0.02596,0.55725,0.82994,31.043,0.56029,0.69567,-0.44957,83.596,#5,-0.82789,0.45334,-0.33028,232.85,-0.02596,0.55725,0.82994,31.043,0.56029,0.69567,-0.44957,83.596
> fitmap #4 inMap #1
Fit map emdb 33154 in map cryosparc_P1078_J1017_002_volume_map_sharp.mrc using
104898 points
correlation = 0.8147, correlation about mean = 0.471, overlap = 1137
steps = 108, shift = 4.72, angle = 10.5 degrees
Position of emdb 33154 (#4) relative to
cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.77559150 0.44110259 -0.45153775 245.46031073
-0.19104122 0.51774969 0.83392956 51.53255230
0.60163202 0.73305099 -0.31729348 58.39718054
Axis -0.08185163 -0.85452901 -0.51291372
Axis point 118.21635546 0.00000000 61.69084670
Rotation angle (degrees) 141.95878126
Shift along axis -94.08010205
> fitmap #5 inMap #1
Fit molecule 7xe4 (#5) to map cryosparc_P1078_J1017_002_volume_map_sharp.mrc
(#1) using 12529 atoms
average map value = 0.5176, steps = 108
shifted from previous position = 4.28
rotated from previous position = 10.4 degrees
atoms outside contour = 5925, contour level = 0.40307
Position of 7xe4 (#5) relative to
cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.77580956 0.44096383 -0.45129860 245.45501288
-0.19028465 0.51843695 0.83367553 51.42373913
0.60159063 0.73264864 -0.31829969 58.48259859
Axis -0.08201767 -0.85477760 -0.51247278
Axis point 118.18885277 0.00000000 61.73225462
Rotation angle (degrees) 141.98375373
Shift along axis -94.05824869
> volume #4 level 0.01035
> surface dust #4 size 9.2
> volume #4 level 0.008252
> volume #4 level 0.009126
> select clear
> hide #!2 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #4 level 0.007727
> show #!5 models
> hide #!3 models
> color #4 #ffb2ff7f models
> color #4 #ffb2ffa2 models
> color #4 #ffb2ffd0 models
> color #4 #ffb2ffd1 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> color #5 #941100ff
> color #4 #ffb2ffaa models
> color #4 #ffb2ffab models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> volume #4 level 0.00965
> volume #4 level 0.006328
> volume #4 level 0.009126
> show #!1 models
> hide #!1 models
> show #!3 models
> volume #3 level 0.0285
> volume #4 level 0.009126
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!5 models
> hide #!3 models
> hide #!4 models
> show #!5 models
> color #5 #0433ffff
> select #5/F:1357
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/F:639
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> select #5/F:619
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #5/F:617
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/F:618
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> hide #!1 models
> show #!4 models
> volume #4 level 0.008601
> fitmap #5 inMap #4
Fit molecule 7xe4 (#5) to map emdb 33154 (#4) using 12529 atoms
average map value = 0.0173, steps = 56
shifted from previous position = 0.0796
rotated from previous position = 0.0627 degrees
atoms outside contour = 2448, contour level = 0.0086013
Position of 7xe4 (#5) relative to emdb 33154 (#4) coordinates:
Matrix rotation and translation
1.00000000 0.00005862 0.00004014 -0.00661266
-0.00005862 1.00000000 -0.00007132 0.02208420
-0.00004015 0.00007131 1.00000000 -0.00293560
Axis 0.70843877 0.39881019 -0.58229283
Axis point 0.00000000 -6.44294241 277.04962384
Rotation angle (degrees) 0.00576774
Shift along axis 0.00583212
> volume #4 level 0.008601
> show #!3 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!2 models
> show #!4 models
> volume #1 level 0.4236
> volume #4 level 0.009126
> volume #1 level 0.4133
> show #!2 models
> hide #!2 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> volume #4 level 0.008077
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> show #!1 models
> hide #!4 models
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> volume #1 level 0.4031
> volume #1 level 0.4133
> volume #1 level 0.4031
> surface dust #1 size 13
> ui tool show "Hide Dust"
> surface dust #1 size 1.3
> surface undust #1
> volume #1 level 0.4338
> volume #1 level 0.5363
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!2 models
> select #2:1248
Nothing selected
> select #2:1209
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide #!3 models
> show sel atoms
> color sel orange red
> show #!4 models
> hide #!4 models
> show #!1 models
> volume #1 level 0.3826
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #3 level 0.02985
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.4338
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
Desktop color scheme is light
> view matrix models
> #2,-0.66534,0.63156,0.39805,104.96,-0.71668,-0.68965,-0.10371,419.38,0.20902,-0.35428,0.91148,37.72
[Repeated 2 time(s)]
> show #!1 models
> volume #1 level 0.4953
> show #!4 models
> show #!2 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> save /Users/shamiul/projects/fks1/apo_drug_sac_model44.cxs includeMaps true
——— End of log from Tue Jan 20 09:48:17 2026 ———
> view name session-start
opened ChimeraX session
> open /Users/shamiul/Downloads/cryosparc_P1078_J1041_002_volume_map_sharp.mrc
Opened cryosparc_P1078_J1041_002_volume_map_sharp.mrc as #6, grid size
256,256,256, pixel 1.3, shown at level 0.232, step 1, values float32
> volume #6 level 0.5479
> close #1
> hide #!2 models
> show #!2 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> volume #6 level 0.4522
> surface dust #6 size 13
> volume #6 level 0.3949
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> color #6 #b2b2b2e6 models
> color #6 #b2b2b2d8 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> volume #3 level 0.0285
> volume #3 level 0.03387
> volume #3 level 0.03924
> volume #3 level 0.05536
> hide #!2 models
> volume #3 level 0.0379
> select #2: 625-633, 676-686, 1341-1344
440 atoms, 445 bonds, 24 residues, 1 model selected
> show #!2 models
> select #2: 625-633, 676-686, 1341-1344 col yellow target C
Expected a keyword
> select #2: 625-633, 676-686, 1341-1344 col yellow target c
Expected a keyword
> color sel light sea green
> color sel hot pink
> color #3 #b2b2ffc2 models
> select #3
2 models selected
> select #2: 625-633, 676-686, 1341-1344 col yellow target c
Expected a keyword
> select #2: 625-633, 676-686, 1341-1344
440 atoms, 445 bonds, 24 residues, 1 model selected
> color sel red
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> volume #6 level 0.4235
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!6 models
> volume #3 level 0.02985
> hide #!3 models
> show #!6 models
> volume #6 level 0.3949
> show #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> volume #3 level 0.02716
> surface dust #3 size 7.34
> volume #3 level 0.0285
> volume #3 level 0.03119
> show #!6 models
> volume #6 level 0.3757
> volume #6 level 0.4044
> volume #3 level 0.03656
> volume #6 level 0.4235
> volume #3 level 0.04864
> volume #6 level 0.5192
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #6 level 0.4427
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> volume #3 level 0.04327
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!2 models
> select clear
> volume #6 level 0.4427
> volume #3 level 0.02582
> volume #6 level 0.3757
> open /Users/shamiul/Downloads/cryosparc_P1078_J1017_002_volume_map_sharp.mrc
Opened cryosparc_P1078_J1017_002_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.3, shown at level 0.239, step 1, values float32
> volume #1 level 0.5467
> hide #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> volume #3 level 0.04059
> volume #3 level 0.02447
> volume #3 level 0.02985
> volume #3 level 0.02447
> volume #3 level 0.02716
> show #!6 models
> volume #6 level 0.3949
> hide #!2 models
> show #!1 models
> hide #!1 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> volume #1 level 0.4471
> surface dust #1 size 13
> volume #1 level 0.3775
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!6 models
> show #!2 models
> hide #!2 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!6 models
> show #!6 models
> volume #6 level 0.4413
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.0389
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> volume #6 level 0.4041
> hide #!3 models
> show #!3 models
> volume #6 level 0.3949
> show #!2 models
> hide #!2 models
> open /Users/shamiul/projects/fks1/round18_aligntocaspo-coot-8.pdb
Chain information for round18_aligntocaspo-coot-8.pdb #7
---
Chain | Description
A | No description available
> matchmaker #7 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker round19_real_space_refined_001-coot-44.pdb, chain A (#2) with
round18_aligntocaspo-coot-8.pdb, chain A (#7), sequence alignment score =
6930.2
RMSD between 1423 pruned atom pairs is 0.575 angstroms; (across all 1636
pairs: 4.230)
> molmap #7 16 onGrid 6
Invalid "onGrid" argument: invalid density map specifier
> hide #!3 models
> ui tool show "Fit in Map"
> fitmap #7 inMap #6
Fit molecule round18_aligntocaspo-coot-8.pdb (#7) to map
cryosparc_P1078_J1041_002_volume_map_sharp.mrc (#6) using 28257 atoms
average map value = 0.4365, steps = 60
shifted from previous position = 0.0995
rotated from previous position = 0.292 degrees
atoms outside contour = 15905, contour level = 0.39486
Position of round18_aligntocaspo-coot-8.pdb (#7) relative to
cryosparc_P1078_J1041_002_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.99974929 -0.01555337 -0.01610747 359.00321150
-0.02111031 0.41492603 0.90961021 -79.40764228
-0.00746409 0.90972220 -0.41515034 70.51887473
Axis 0.01089752 -0.84110706 -0.54075887
Axis point 178.85260398 0.00000000 61.33327506
Rotation angle (degrees) 179.70560747
Shift along axis 32.56886537
> molmap #7 16 onGrid #6
Opened round18_aligntocaspo-coot-8.pdb map 16 as #8, grid size 256,256,256,
pixel 1.3, shown at level 0.0593, step 1, values float32
> hide #7 models
> show #7 models
> hide #!6 models
> volume #8 level 0.06604
> save /Users/shamiul/Desktop/protein1041.mrc models #8
> volume #8 level 0.1571
> hide #7 models
> show #!6 models
> volume #8 level 0.1651
> hide #!8 models
> volume #6 level 0.3949
> show #!8 models
> volume #8 level 0.151
> open /Users/shamiul/Downloads/cryosparc_P1078_J1048_003_volume_map_sharp.mrc
Opened cryosparc_P1078_J1048_003_volume_map_sharp.mrc as #9, grid size
256,256,256, pixel 1.3, shown at level 0.236, step 1, values float32
> hide #!6 models
> show #!6 models
> hide #!8 models
> volume #9 level 0.5183
> hide #!6 models
> surface dust #9 size 13
> volume #9 level 0.3995
> show #!3 models
> hide #!3 models
> volume #9 level 0.4143
> show #!3 models
> hide #!3 models
> volume #9 level 0.3921
> color #9 silver models
> close #6
> volume #9 level 0.3728
> volume #9 level 0.4017
> show #!3 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> fitmap #9 inMap #3
Fit map cryosparc_P1078_J1048_003_volume_map_sharp.mrc in map
cryosparc_P23_J469_003_volume_map_sharp.mrc using 52265 points
correlation = 0.8411, correlation about mean = 0.7355, overlap = 2719
steps = 64, shift = 0.137, angle = 0.284 degrees
Position of cryosparc_P1078_J1048_003_volume_map_sharp.mrc (#9) relative to
cryosparc_P23_J469_003_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99562998 -0.04508186 0.08178364 17.79528418
0.04351058 -0.55095466 -0.83340013 407.68451908
0.08263030 0.83331661 -0.54658544 125.90881048
Axis 0.99859019 -0.00050727 0.05307893
Axis point 0.00000000 170.27130670 172.32267538
Rotation angle (degrees) 123.43255903
Shift along axis 24.24649662
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> volume #3 level 0.02904
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #4 level 0.00936
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> fitmap #4 inMap #3
Fit map emdb 33154 in map cryosparc_P23_J469_003_volume_map_sharp.mrc using
116253 points
correlation = 0.5847, correlation about mean = 0.3523, overlap = 99
steps = 72, shift = 0.181, angle = 0.177 degrees
Position of emdb 33154 (#4) relative to
cryosparc_P23_J469_003_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.71048798 0.47703780 -0.51734105 264.67558202
-0.43239360 -0.87595053 -0.21388416 341.14525553
-0.55519599 0.07173283 0.82862042 157.39209429
Axis 0.29939554 0.03968112 -0.95330358
Axis point 202.77925698 136.32398446 -0.00000000
Rotation angle (degrees) 151.51104117
Shift along axis -57.26273245
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!1 models
> volume #9 level 0.4111
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> volume #3 level 0.02644
> show #!9 models
> volume #9 level 0.4111
> hide #!3 models
> show #!3 models
> hide #!9 models
> volume #3 level 0.02644
> show #!2 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!3 models
> fitmap #2 inMap #9
Fit molecule round19_real_space_refined_001-coot-44.pdb (#2) to map
cryosparc_P1078_J1048_003_volume_map_sharp.mrc (#9) using 26286 atoms
average map value = 0.4951, steps = 28
shifted from previous position = 0.0281
rotated from previous position = 0.0329 degrees
atoms outside contour = 13242, contour level = 0.41108
Position of round19_real_space_refined_001-coot-44.pdb (#2) relative to
cryosparc_P1078_J1048_003_volume_map_sharp.mrc (#9) coordinates:
Matrix rotation and translation
-0.66233458 0.63252332 0.40153103 103.73969491
-0.71883862 -0.68755706 -0.10264664 419.32753451
0.21114910 -0.35662243 0.91007500 38.03008402
Axis -0.18296144 0.13714910 -0.97350667
Axis point 135.16573018 190.78373405 0.00000000
Rotation angle (degrees) 136.04691145
Shift along axis 1.50749046
> color #9 #c0c0c0ce models
> color #9 #c0c0c0cf models
> show #!3 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> volume #3 level 0.02644
> hide #!9 models
> volume #3 level 0.03109
> volume #3 level 0.04132
> show #!9 models
> hide #!9 models
> show #!9 models
> volume #9 level 0.4378
> hide #!9 models
> volume #3 level 0.03202
> volume #3 level 0.03109
> volume #3 level 0.02644
> volume #3 level 0.04039
> volume #3 level 0.02458
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.02551
> volume #3 level 0.02644
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.03481
> hide #!2 models
> hide #!3 models
> show #!3 models
QPainter::begin: Paint device returned engine == 0, type: 2
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/shamiul/projects/fks1/apo_drug_sac_model44.cxs
Opened cryosparc_P1078_J1017_002_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.3, shown at level 0.495, step 1, values float32
Opened cryosparc_P23_J469_003_volume_map_sharp.mrc as #3, grid size
512,512,512, pixel 0.734, shown at level 0.0298, step 2, values float32
Opened emdb 33154 as #4, grid size 224,224,224, pixel 0.92, shown at level
0.00808, step 1, values float32
Log from Tue Jan 20 09:48:17 2026UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/shamiul/Downloads/cryosparc_P1078_J1017_002_volume_map_sharp.mrc
Opened cryosparc_P1078_J1017_002_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.3, shown at level 0.239, step 1, values float32
> open "/Users/shamiul/projects/fks1/Model
> Building/Coot/round19_real_space_refined_001-coot-44.pdb"
Summary of feedback from opening /Users/shamiul/projects/fks1/Model
Building/Coot/round19_real_space_refined_001-coot-44.pdb
---
warnings | Start residue of secondary structure not found: HELIX 9 9 ALA A 236 LYS A 242 1 7
Start residue of secondary structure not found: HELIX 10 10 LYS A 244 MET A
247 1 4
Start residue of secondary structure not found: HELIX 11 11 ALA A 255 ASP A
257 1 3
Start residue of secondary structure not found: HELIX 12 12 ILE A 258 ASN A
260 1 3
End residue of secondary structure not found: HELIX 64 64 ASN A 788 THR A 792
1 5
End residue of secondary structure not found: HELIX 69 69 PRO A 867 GLU A 888
1 22
Start residue of secondary structure not found: HELIX 70 70 ALA A 900 ASP A
906 1 7
Start residue of secondary structure not found: HELIX 71 71 PHE A 910 ILE A
913 1 4
Start residue of secondary structure not found: HELIX 96 96 PHE A 1239 ILE A
1242 1 4
Start residue of secondary structure not found: HELIX 97 97 LEU A 1243 PHE A
1245 1 3
Start residue of secondary structure not found: HELIX 98 98 THR A 1246 GLN A
1256 1 11
End residue of secondary structure not found: HELIX 108 108 SER A 1385 ASP A
1403 1 19
Chain information for round19_real_space_refined_001-coot-44.pdb #2
---
Chain | Description
A | No description available
> volume #1 level 0.5677
> select add #2
26286 atoms, 26649 bonds, 8 pseudobonds, 1636 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-40.366,0,1,0,75.715,0,0,1,45.059
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.23585,-0.8656,-0.44171,370.28,0.9416,-0.091141,-0.32417,159.44,0.24034,-0.49237,0.83655,114.88
> view matrix models
> #2,-0.87113,-0.1611,-0.46386,357.53,0.42268,-0.72682,-0.54136,382.19,-0.24993,-0.66766,0.70126,243.46
> view matrix models
> #2,-0.7965,0.49136,0.35236,106.84,-0.5959,-0.73666,-0.31974,510.13,0.10246,-0.46464,0.87955,125.29
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.7965,0.49136,0.35236,147.44,-0.5959,-0.73666,-0.31974,434.86,0.10246,-0.46464,0.87955,75.24
> view matrix models
> #2,-0.7965,0.49136,0.35236,156.43,-0.5959,-0.73666,-0.31974,440.13,0.10246,-0.46464,0.87955,75.704
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule round19_real_space_refined_001-coot-44.pdb (#2) to map
cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) using 26286 atoms
average map value = 0.505, steps = 112
shifted from previous position = 2.31
rotated from previous position = 14.5 degrees
atoms outside contour = 16699, contour level = 0.56771
Position of round19_real_space_refined_001-coot-44.pdb (#2) relative to
cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.66534498 0.63156314 0.39805034 104.96048430
-0.71667873 -0.68964915 -0.10370951 419.37917810
0.20901597 -0.35427681 0.91148246 37.72015838
Axis -0.18100709 0.13655637 -0.97395523
Axis point 135.48156726 190.61539580 0.00000000
Rotation angle (degrees) 136.19963585
Shift along axis 1.53255925
> select clear
> volume #1 level 0.4976
> select clear
> molmap #2 16 onGrid #1
Opened round19_real_space_refined_001-coot-44.pdb map 16 as #3, grid size
256,256,256, pixel 1.3, shown at level 0.0587, step 1, values float32
> \
Unknown command: \
> molmap #2 16 onGrid #1
Opened round19_real_space_refined_001-coot-44.pdb map 16 as #3, grid size
256,256,256, pixel 1.3, shown at level 0.0587, step 1, values float32
> volume #3 level 0.1386
> volume #3 level 0.1278
> volume #3 level 0.1516
> save /Users/shamiul/Desktop/protein1072.mrc models #3
> close #3
> open /Users/shamiul/Downloads/cryosparc_P23_J469_003_volume_map_sharp.mrc
Opened cryosparc_P23_J469_003_volume_map_sharp.mrc as #3, grid size
512,512,512, pixel 0.734, shown at level 0.0147, step 2, values float32
> select add #3
2 models selected
> ui mousemode right "rotate selected models"
> volume #3 level 0.04773
> view matrix models
> #3,-0.079636,0.51981,-0.85056,277.07,-0.97778,-0.20673,-0.03479,415.67,-0.19392,0.82889,0.52472,-22.468
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.079636,0.51981,-0.85056,291.89,-0.97778,-0.20673,-0.03479,408.22,-0.19392,0.82889,0.52472,18.485
> view matrix models
> #3,-0.079636,0.51981,-0.85056,307.4,-0.97778,-0.20673,-0.03479,392.49,-0.19392,0.82889,0.52472,9.5176
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.74236,0.66559,-0.076754,248.06,-0.41506,-0.54679,-0.72715,490.4,-0.52595,-0.50796,0.68217,289.63
> view matrix models
> #3,0.99436,0.013795,0.10513,7.5729,-0.1047,-0.029291,0.99407,-12.114,0.016792,-0.99948,-0.027681,423.11
> view matrix models
> #3,0.98972,0.10493,0.097203,-6.9775,-0.085366,-0.11195,0.99004,0.51616,0.11477,-0.98816,-0.10184,417.62
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.98972,0.10493,0.097203,-72.684,-0.085366,-0.11195,0.99004,-8.2105,0.11477,-0.98816,-0.10184,383.63
> view matrix models
> #3,0.98972,0.10493,0.097203,-74.736,-0.085366,-0.11195,0.99004,-5.7417,0.11477,-0.98816,-0.10184,346.72
> view matrix models
> #3,0.98972,0.10493,0.097203,-68.072,-0.085366,-0.11195,0.99004,18.491,0.11477,-0.98816,-0.10184,353.16
> view matrix models
> #3,0.98972,0.10493,0.097203,-64.416,-0.085366,-0.11195,0.99004,14.455,0.11477,-0.98816,-0.10184,346.38
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.92649,0.020919,0.37573,-93.139,-0.34112,-0.37493,0.86201,137.37,0.15891,-0.92682,-0.34024,374.81
> view matrix models
> #3,0.90761,-0.1023,0.40715,-72.932,-0.40588,-0.46162,0.78878,180.49,0.10725,-0.88116,-0.46049,400.25
> view matrix models
> #3,0.92552,-0.24841,0.28584,-24.494,-0.37746,-0.54398,0.74941,198.5,-0.030665,-0.80149,-0.59723,438.84
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.92552,-0.24841,0.28584,-19.878,-0.37746,-0.54398,0.74941,201.85,-0.030665,-0.80149,-0.59723,439.42
> view matrix models
> #3,0.92552,-0.24841,0.28584,-23.844,-0.37746,-0.54398,0.74941,197.75,-0.030665,-0.80149,-0.59723,433.55
> fitmap #3 inMap #1
Fit map cryosparc_P23_J469_003_volume_map_sharp.mrc in map
cryosparc_P1078_J1017_002_volume_map_sharp.mrc using 20242 points
correlation = 0.8993, correlation about mean = 0.6277, overlap = 1661
steps = 188, shift = 6.85, angle = 20.8 degrees
Position of cryosparc_P23_J469_003_volume_map_sharp.mrc (#3) relative to
cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99518294 0.04427809 0.08746640 -46.83296081
-0.04864464 -0.55158245 0.83270073 121.26914196
0.08511534 -0.83294433 -0.54677156 406.40704997
Axis -0.99844649 0.00140931 -0.05570117
Axis point 0.00000000 170.37616190 171.87178256
Rotation angle (degrees) 123.47585517
Shift along axis 24.29376271
> select clear
> volume #3 level 0.04242
> volume #1 level 0.5381
> hide #!2 models
> show #!2 models
> hide #!3 models
> color #1 #b2b2b259 models
> set bgColor white
> color #1 #b2b2b285 models
> color #1 #b2b2b2b1 models
> volume #1 level 0.4841
> volume #1 level 0.4706
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> volume #3 level 0.03357
> hide #!2 models
> volume #3 level 0.03003
[Repeated 1 time(s)]
> surface dust #3 size 7.34
> volume #3 level 0.02472
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #3 level 0.02915
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!2 models
> show #!1 models
> hide #!2 models
> surface dust #1 size 13
> surface dust #3 size 7.34
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> volume #3 level 0.03092
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> volume #3 level 0.0495
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.04419
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> volume #1 level 0.4031
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!2 models
> color #2 black
> color #2 #941100ff
> color #3 #b2b2ff9d models
> color #3 #b2b2ffea models
> color #3 #b2b2ffe2 models
> color #3 #b2b2ffdc models
> color #3 #b2b2ffdb models
> volume #3 level 0.03799
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> volume #1 level 0.4638
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!3 models
> volume #3 level 0.02915
> hide #!1 models
> volume #3 level 0.02472
> volume #3 level 0.03534
> show #!1 models
> volume #3 level 0.04242
> volume #1 level 0.4706
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.4368
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #3 level 0.03711
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #3 level 0.03357
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.04507
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!2 models
> color #2 forest green
> select #2:1344
24 atoms, 23 bonds, 1 residue, 1 model selected
> color sel red
> show #!1 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select /A:625
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /A:624
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:625
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> select /A:624
21 atoms, 21 bonds, 1 residue, 1 model selected
> color sel red
> show sel atoms
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> select /A:623
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> show #!1 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select /A:629
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> show #!1 models
> hide #!1 models
> select /A:1344
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> volume #3 level 0.05392
> volume #3 level 0.0495
> select /A:628
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.4031
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #3 level 0.04065
> volume #3 level 0.0318
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select /A:604
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> show #!1 models
> hide #!1 models
> select /A:231
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.04861
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> volume #1 level 0.4571
> hide #!1 models
> select /A:603
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> show #!1 models
> hide #!1 models
> select /A:605
24 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> volume #1 level 0.5381
> volume #1 level 0.7948
> volume #1 level 0.4436
> volume #1 level 0.4706
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.8353
> volume #1 level 0.4706
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!1 models
> volume #3 level 0.03357
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #3 level 0.02826
> volume #3 level 0.03357
> volume #3 level 0.04065
> show #!1 models
> volume #1 level 0.3828
> hide #!1 models
> volume #3 level 0.03622
> volume #3 level 0.03357
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> volume #1 level 0.4301
> volume #1 level 0.4503
> volume #1 level 0.4436
> show #!3 models
> volume #3 level 0.05127
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> volume #3 level 0.04596
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #1 level 0.4031
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> open 33154 fromDatabase emdb_fits format ccp4
Summary of feedback from opening 33154 fetched from emdb_fits
---
notes | Fetching compressed map 33154 from https://files.wwpdb.org/pub/emdb/structures/EMD-33154/map/emd_33154.map.gz
Fetching map header 33154 from
https://files.wwpdb.org/pub/emdb/structures/EMD-33154/header/emd-33154.xml
Fetching compressed mmCIF 7xe4 from http://files.rcsb.org/download/7xe4.cif
Fetching CCD C14 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/C14/C14.cif
Fetching CCD D10 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/0/D10/D10.cif
Fetching CCD D12 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/2/D12/D12.cif
Fetching CCD DD9 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/9/DD9/DD9.cif
Fetching CCD HP6 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/6/HP6/HP6.cif
Fetching CCD NAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif
Fetching CCD XKP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/XKP/XKP.cif
Opened emdb 33154 as #4, grid size 224,224,224, pixel 0.92, shown at level
0.01, step 1, values float32, fit PDB 7xe4
7xe4 title:
structure of a membrane-bound glycosyltransferase [more info...]
Chain information for 7xe4 #5
---
Chain | Description | UniProt
F | 1,3-beta-glucan synthase component FKS1 | FKS1_YEAST 1-1876
Non-standard residues in 7xe4 #5
---
C14 — tetradecane
D10 — decane
D12 — dodecane
DD9 — nonane
HP6 — heptane
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
XKP —
(11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl
decanoate
> select add #5
12529 atoms, 12835 bonds, 10 pseudobonds, 1530 residues, 3 models selected
> select add #4
12529 atoms, 12835 bonds, 10 pseudobonds, 1530 residues, 5 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.86725,0.45253,-0.2076,173.55,-0.088087,0.27094,0.95856,-21.349,0.49002,0.8496,-0.19511,-7.4292,#5,-0.86725,0.45253,-0.2076,173.55,-0.088087,0.27094,0.95856,-21.349,0.49002,0.8496,-0.19511,-7.4292
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.71393,0.63567,-0.29366,148.63,-0.01025,0.40985,0.91209,-38.223,0.70015,0.65418,-0.28609,-0.53684,#5,-0.71393,0.63567,-0.29366,148.63,-0.01025,0.40985,0.91209,-38.223,0.70015,0.65418,-0.28609,-0.53684
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.71393,0.63567,-0.29366,196.82,-0.01025,0.40985,0.91209,41.09,0.70015,0.65418,-0.28609,59.182,#5,-0.71393,0.63567,-0.29366,196.82,-0.01025,0.40985,0.91209,41.09,0.70015,0.65418,-0.28609,59.182
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.86827,0.12771,-0.47937,282.81,-0.36197,0.49769,0.78821,82.573,0.33925,0.8579,-0.3859,87.659,#5,-0.86827,0.12771,-0.47937,282.81,-0.36197,0.49769,0.78821,82.573,0.33925,0.8579,-0.3859,87.659
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.86827,0.12771,-0.47937,285.04,-0.36197,0.49769,0.78821,76.609,0.33925,0.8579,-0.3859,84.03,#5,-0.86827,0.12771,-0.47937,285.04,-0.36197,0.49769,0.78821,76.609,0.33925,0.8579,-0.3859,84.03
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.82789,0.45334,-0.33028,232.85,-0.02596,0.55725,0.82994,31.043,0.56029,0.69567,-0.44957,83.596,#5,-0.82789,0.45334,-0.33028,232.85,-0.02596,0.55725,0.82994,31.043,0.56029,0.69567,-0.44957,83.596
> fitmap #4 inMap #1
Fit map emdb 33154 in map cryosparc_P1078_J1017_002_volume_map_sharp.mrc using
104898 points
correlation = 0.8147, correlation about mean = 0.471, overlap = 1137
steps = 108, shift = 4.72, angle = 10.5 degrees
Position of emdb 33154 (#4) relative to
cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.77559150 0.44110259 -0.45153775 245.46031073
-0.19104122 0.51774969 0.83392956 51.53255230
0.60163202 0.73305099 -0.31729348 58.39718054
Axis -0.08185163 -0.85452901 -0.51291372
Axis point 118.21635546 0.00000000 61.69084670
Rotation angle (degrees) 141.95878126
Shift along axis -94.08010205
> fitmap #5 inMap #1
Fit molecule 7xe4 (#5) to map cryosparc_P1078_J1017_002_volume_map_sharp.mrc
(#1) using 12529 atoms
average map value = 0.5176, steps = 108
shifted from previous position = 4.28
rotated from previous position = 10.4 degrees
atoms outside contour = 5925, contour level = 0.40307
Position of 7xe4 (#5) relative to
cryosparc_P1078_J1017_002_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.77580956 0.44096383 -0.45129860 245.45501288
-0.19028465 0.51843695 0.83367553 51.42373913
0.60159063 0.73264864 -0.31829969 58.48259859
Axis -0.08201767 -0.85477760 -0.51247278
Axis point 118.18885277 0.00000000 61.73225462
Rotation angle (degrees) 141.98375373
Shift along axis -94.05824869
> volume #4 level 0.01035
> surface dust #4 size 9.2
> volume #4 level 0.008252
> volume #4 level 0.009126
> select clear
> hide #!2 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #4 level 0.007727
> show #!5 models
> hide #!3 models
> color #4 #ffb2ff7f models
> color #4 #ffb2ffa2 models
> color #4 #ffb2ffd0 models
> color #4 #ffb2ffd1 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> color #5 #941100ff
> color #4 #ffb2ffaa models
> color #4 #ffb2ffab models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> volume #4 level 0.00965
> volume #4 level 0.006328
> volume #4 level 0.009126
> show #!1 models
> hide #!1 models
> show #!3 models
> volume #3 level 0.0285
> volume #4 level 0.009126
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!4 models
> hide #!5 models
> hide #!3 models
> hide #!4 models
> show #!5 models
> color #5 #0433ffff
> select #5/F:1357
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/F:639
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> select #5/F:619
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #5/F:617
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/F:618
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> hide #!1 models
> show #!4 models
> volume #4 level 0.008601
> fitmap #5 inMap #4
Fit molecule 7xe4 (#5) to map emdb 33154 (#4) using 12529 atoms
average map value = 0.0173, steps = 56
shifted from previous position = 0.0796
rotated from previous position = 0.0627 degrees
atoms outside contour = 2448, contour level = 0.0086013
Position of 7xe4 (#5) relative to emdb 33154 (#4) coordinates:
Matrix rotation and translation
1.00000000 0.00005862 0.00004014 -0.00661266
-0.00005862 1.00000000 -0.00007132 0.02208420
-0.00004015 0.00007131 1.00000000 -0.00293560
Axis 0.70843877 0.39881019 -0.58229283
Axis point 0.00000000 -6.44294241 277.04962384
Rotation angle (degrees) 0.00576774
Shift along axis 0.00583212
> volume #4 level 0.008601
> show #!3 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!2 models
> show #!4 models
> volume #1 level 0.4236
> volume #4 level 0.009126
> volume #1 level 0.4133
> show #!2 models
> hide #!2 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> volume #4 level 0.008077
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!4 models
> show #!1 models
> hide #!4 models
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> volume #1 level 0.4031
> volume #1 level 0.4133
> volume #1 level 0.4031
> surface dust #1 size 13
> ui tool show "Hide Dust"
> surface dust #1 size 1.3
> surface undust #1
> volume #1 level 0.4338
> volume #1 level 0.5363
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!2 models
> select #2:1248
Nothing selected
> select #2:1209
12 atoms, 11 bonds, 1 residue, 1 model selected
> hide #!3 models
> show sel atoms
> color sel orange red
> show #!4 models
> hide #!4 models
> show #!1 models
> volume #1 level 0.3826
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #3 level 0.02985
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.4338
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
Desktop color scheme is light
> view matrix models
> #2,-0.66534,0.63156,0.39805,104.96,-0.71668,-0.68965,-0.10371,419.38,0.20902,-0.35428,0.91148,37.72
[Repeated 2 time(s)]
> show #!1 models
> volume #1 level 0.4953
> show #!4 models
> show #!2 models
> hide #!4 models
> hide #!1 models
> show #!1 models
> save /Users/shamiul/projects/fks1/apo_drug_sac_model44.cxs includeMaps true
——— End of log from Tue Jan 20 09:48:17 2026 ———
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: MLY33LL/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 13822.61.10
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.7.3 (24G419)
Kernel Version: Darwin 24.6.0
Time since boot: 7 hours, 13 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL E2414H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.11
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.5
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pytz: 2025.2
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.0.0
roman-numerals-py: 4.0.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.0.4
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.3
urllib3: 2.6.2
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
Change History (2)
comment:1 by , 2 hours 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 , 82 minutes ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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I'm not sure CGSDatagramReadStream::mainQueueWakeup() means the computer was waking up.
The crash is in dialog.exec() called on the ChimeraX save dialog. I tried showing the save dialog and sleeping and waking Mac laptop with ChimeraX 1.11 also locking screen and relogging in. No crash.