![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 months ago
Closed 4 months ago
#18080 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.5-x86_64-i386-64bit
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: Segmentation fault
Current thread 0x00007ff846ff0fc0 (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.surface._surface, 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, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atom_search.ast, chimerax.chem_group._chem_group, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PIL._imagingmath (total: 125)
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{
"uptime" : 430000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
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"modelCode" : "MacBookPro16,1",
"coalitionID" : 6860,
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"captureTime" : "2025-06-25 18:16:04.0955 +1000",
"codeSigningMonitor" : 0,
"incident" : "9F5D496E-1236-4B8F-837B-CFDF4789ABAF",
"pid" : 46339,
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"bug_type" : "309",
"procLaunch" : "2025-06-07 16:47:06.7791 +1000",
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "324B8216-C495-C2F1-1769-3322C698A086",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
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"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
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"bridgeVersion" : {"build":"21P5077","train":"8.5"},
"sleepWakeUUID" : "FEBC0A99-094E-408D-8EFF-CB14ABF7574F",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4548493312\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10f1c8000-10f1cc000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":46339},
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
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/dongju/Desktop/Research projects-
> Monash/Modelling_GPR3_OEA/cryosparc_P161_J67_004_volume_map.mrc"
Opened cryosparc_P161_J67_004_volume_map.mrc as #1, grid size 288,288,288,
pixel 0.75, shown at level 0.0482, step 2, values float32
> volume #1 step 1
> volume #1 level 0.04046
> volume #1 level 0.0763
> open 8ww2
8ww2 title:
GPR3/Gs complex [more info...]
Chain information for 8ww2 #2
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short |
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
N | Nb35 |
R | G-protein coupled receptor 3 | GPR3_HUMAN 1-330
Non-standard residues in 8ww2 #2
---
OLA — oleic acid
PLM — palmitic acid
Y01 — cholesterol hemisuccinate
> hide atoms
> show cartoons
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select add #2
7792 atoms, 7943 bonds, 3 pseudobonds, 1025 residues, 2 models selected
> view matrix models
> #2,0.87528,0.48295,0.025505,-53.678,0.48227,-0.87556,0.028443,191.41,0.036068,-0.012595,-0.99927,268.69
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.87528,0.48295,0.025505,-43.924,0.48227,-0.87556,0.028443,155.38,0.036068,-0.012595,-0.99927,239.44
> view matrix models
> #2,0.87528,0.48295,0.025505,-83.849,0.48227,-0.87556,0.028443,149.43,0.036068,-0.012595,-0.99927,240.47
> ui tool show "Fit in Map"
> fitmap #2 inMap #1
Fit molecule 8ww2 (#2) to map cryosparc_P161_J67_004_volume_map.mrc (#1) using
7792 atoms
average map value = 0.1191, steps = 300
shifted from previous position = 9.18
rotated from previous position = 43.5 degrees
atoms outside contour = 2740, contour level = 0.076296
Position of 8ww2 (#2) relative to cryosparc_P161_J67_004_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.96878402 -0.24789375 0.00249685 3.35268084
-0.24710133 -0.96640024 -0.07079219 286.54509380
0.01996190 0.06796537 -0.99748798 229.46459950
Axis 0.99215567 -0.12488001 0.00566603
Axis point 0.00000000 139.43229763 119.70920918
Rotation angle (degrees) 175.99018772
Shift along axis -31.15722066
> fitmap #2 inMap #1
Fit molecule 8ww2 (#2) to map cryosparc_P161_J67_004_volume_map.mrc (#1) using
7792 atoms
average map value = 0.1191, steps = 28
shifted from previous position = 0.0144
rotated from previous position = 0.00891 degrees
atoms outside contour = 2748, contour level = 0.076296
Position of 8ww2 (#2) relative to cryosparc_P161_J67_004_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.96879775 -0.24784059 0.00244760 3.34754125
-0.24705438 -0.96642225 -0.07065541 286.52369625
0.01987669 0.06784611 -0.99749780 229.48026603
Axis 0.99215917 -0.12485375 0.00563206
Axis point 0.00000000 139.42849517 119.70748752
Rotation angle (degrees) 175.99761294
Shift along axis -31.15981858
> select subtract #2
Nothing selected
> addh
Summary of feedback from adding hydrogens to 8ww2 #2
---
warnings | Not adding hydrogens to /A LYS 17 CB because it is missing heavy-atom bond partners
Not adding hydrogens to /A LYS 24 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A ARG 31 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A GLU 50 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 58 CB because it is missing heavy-atom bond
partners
39 messages similar to the above omitted
notes | Termini for 8ww2 (#2) chain A determined from SEQRES records
Termini for 8ww2 (#2) chain B determined from SEQRES records
Termini for 8ww2 (#2) chain G determined from SEQRES records
Termini for 8ww2 (#2) chain N determined from SEQRES records
Termini for 8ww2 (#2) chain R determined from SEQRES records
Chain-initial residues that are actual N termini: /N GLN 1
Chain-initial residues that are not actual N termini: /A SER 13, /A THR 204,
/A THR 263, /B GLU 3, /G SER 8, /R LEU 37, /R THR 242
Chain-final residues that are actual C termini: /A LEU 394, /B SER 342
Chain-final residues that are not actual C termini: /A ARG 61, /A SER 251, /G
ARG 62, /N SER 128, /R HIS 232, /R CYS 313
Missing OXT added to C-terminal residue /B SER 342
777 hydrogen bonds
Adding 'H' to /A SER 13
Adding 'H' to /A THR 204
Adding 'H' to /A THR 263
Adding 'H' to /B GLU 3
Adding 'H' to /G SER 8
2 messages similar to the above omitted
/G ARG 62 is not terminus, removing H atom from 'C'
/N SER 128 is not terminus, removing H atom from 'C'
/R CYS 313 is not terminus, removing H atom from 'C'
7631 hydrogens added
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 59 residues in model #2 to IUPAC-IUB
standards.
8ww2 title:
GPR3/Gs complex [more info...]
Chain information for 8ww2
---
Chain | Description | UniProt
2.2/A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short |
2.2/B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
2.2/G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
2.2/N | Nb35 |
2.2/R | G-protein coupled receptor 3 | GPR3_HUMAN 1-330
Non-standard residues in 8ww2 #2.2
---
OLA — oleic acid
PLM — palmitic acid
Y01 — cholesterol hemisuccinate
> clipper associate #1 toModel #2
Opened cryosparc_P161_J67_004_volume_map.mrc as #2.1.1.1, grid size
288,288,288, pixel 0.75, shown at step 1, values float32
> isolde sim start /A-R
Loading residue template for OLA from internal database
Loading residue template for PLM from internal database
Loading residue template for Y01 from internal database
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim pause
> volume #2.1.1.1 level 0.1096
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 23 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #2.1.1.1 level 0.0201
> save "/Users/dongju/Desktop/Research projects-
> Monash/Modelling_GPR3_OEA/GPR3_8ww2_after_ISOLDE_004.pdb" relModel #2.1.1.1
> save "/Users/dongju/Desktop/Research projects-
> Monash/Modelling_GPR3_OEA/J67_after_ISOLDE.mrc" models #2.1.1.1
> select add #2
15424 atoms, 15575 bonds, 3 pseudobonds, 1025 residues, 22 models selected
> select add #2
15424 atoms, 15575 bonds, 3 pseudobonds, 1025 residues, 22 models selected
> open 8ww2
8ww2 title:
GPR3/Gs complex [more info...]
Chain information for 8ww2 #1
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short |
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
N | Nb35 |
R | G-protein coupled receptor 3 | GPR3_HUMAN 1-330
Non-standard residues in 8ww2 #1
---
OLA — oleic acid
PLM — palmitic acid
Y01 — cholesterol hemisuccinate
> hide sel atoms
> show sel cartoons
> select add #1
23216 atoms, 23518 bonds, 6 pseudobonds, 2050 residues, 24 models selected
> hide sel atoms
> show sel cartoons
> select add #2
23216 atoms, 23518 bonds, 6 pseudobonds, 2050 residues, 24 models selected
> select add #2
23216 atoms, 23518 bonds, 6 pseudobonds, 2050 residues, 24 models selected
> select add #2
23216 atoms, 23518 bonds, 6 pseudobonds, 2050 residues, 24 models selected
> select subtract #2.1
23216 atoms, 23518 bonds, 6 pseudobonds, 2050 residues, 19 models selected
> select add #2.2
23216 atoms, 23518 bonds, 6 pseudobonds, 2050 residues, 19 models selected
> select subtract #2.3
23216 atoms, 23518 bonds, 6 pseudobonds, 2050 residues, 18 models selected
> select subtract #1
15424 atoms, 15575 bonds, 3 pseudobonds, 1025 residues, 16 models selected
> select add #1
23216 atoms, 23518 bonds, 6 pseudobonds, 2050 residues, 18 models selected
> hide #!2 models
> hide #!2.1 models
> hide #!2.2 models
> hide #2.3 models
> select subtract #1
15424 atoms, 15575 bonds, 3 pseudobonds, 1025 residues, 16 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/R
Alignment identifier is 1/R
> select #1/R:169
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:169
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/R:175
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/R:175
5 atoms, 4 bonds, 1 residue, 1 model selected
> open /Users/dongju/Downloads/cryosparc_P161_J68_005_volume_map.mrc
Opened cryosparc_P161_J68_005_volume_map.mrc as #3, grid size 288,288,288,
pixel 0.75, shown at level 0.0511, step 2, values float32
> open /Users/dongju/Downloads/cryosparc_P161_J69_004_volume_map.mrc
Opened cryosparc_P161_J69_004_volume_map.mrc as #4, grid size 288,288,288,
pixel 0.75, shown at level 0.0544, step 2, values float32
> open /Users/dongju/Downloads/cryosparc_P161_J70_003_volume_map.mrc
Opened cryosparc_P161_J70_003_volume_map.mrc as #5, grid size 288,288,288,
pixel 0.75, shown at level 0.054, step 2, values float32
> hide #!1 models
> tile #3 #4 #5 columns 3
3 models tiled
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #3 step 1
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #4 step 1
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #5 step 1
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #4 level 0.08238
> volume #5 level 0.09146
> volume #3 level 0.07913
> tile #3 #4 #5 columns 3 spacingFactor 1.3
3 models tiled
> tile #3 #4 #5 columns 3 spacingFactor 1.1
3 models tiled
> tile #3 #4 #5 columns 3 spacingFactor 0.8
3 models tiled
> show #!1 models
> select #1/R:41-67,73-92,106-144,146-167,192-230,243-270,275-298,301-313
1568 atoms, 1591 bonds, 212 residues, 1 model selected
> select #1/R:218
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/R:218
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/R:270
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/R:270
4 atoms, 3 bonds, 1 residue, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open /Users/dongju/Downloads/cryosparc_P161_J65_003_volume_map.mrc
Opened cryosparc_P161_J65_003_volume_map.mrc as #6, grid size 288,288,288,
pixel 0.75, shown at level 0.0485, step 2, values float32
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!1 models
> volume #6 step 1
> volume #6 level 0.0771
> volume #6 level 0.04849
> volume #6 level 0.0771
> show #!5 models
> show #!4 models
> hide #!6 models
> show #!3 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open /Users/dongju/Downloads/cryosparc_P161_J72_022_volume_map.mrc
Opened cryosparc_P161_J72_022_volume_map.mrc as #7, grid size 288,288,288,
pixel 0.75, shown at level 0.054, step 2, values float32
> hide #!3 models
> hide #!4 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #7 step 1
> volume #7 level 0.08411
> volume #7 level 0.06233
> open /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series.cs
Unrecognized file suffix '.cs'
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open
> /Users/dongju/Downloads/cryosparc_P161_J74_00239_volume_series/J74_class_00_00239_volume.mrc
Opened J74_class_00_00239_volume.mrc as #8, grid size 80,80,80, pixel 2.7,
shown at level 0.371, step 1, values float32
> open
> /Users/dongju/Downloads/cryosparc_P161_J74_00239_volume_series/J74_class_01_00239_volume.mrc
Opened J74_class_01_00239_volume.mrc as #9, grid size 80,80,80, pixel 2.7,
shown at level 0.367, step 1, values float32
> open
> /Users/dongju/Downloads/cryosparc_P161_J74_00239_volume_series/J74_class_02_00239_volume.mrc
Opened J74_class_02_00239_volume.mrc as #10, grid size 80,80,80, pixel 2.7,
shown at level 0.373, step 1, values float32
> open
> /Users/dongju/Downloads/cryosparc_P161_J74_00239_volume_series/J74_class_03_00239_volume.mrc
Opened J74_class_03_00239_volume.mrc as #11, grid size 80,80,80, pixel 2.7,
shown at level 0.35, step 1, values float32
> open
> /Users/dongju/Downloads/cryosparc_P161_J74_00239_volume_series/J74_class_04_00239_volume.mrc
Opened J74_class_04_00239_volume.mrc as #12, grid size 80,80,80, pixel 2.7,
shown at level 0.383, step 1, values float32
> open
> /Users/dongju/Downloads/cryosparc_P161_J74_00239_volume_series/J74_class_05_00239_volume.mrc
Opened J74_class_05_00239_volume.mrc as #13, grid size 80,80,80, pixel 2.7,
shown at level 0.364, step 1, values float32
> hide #!5 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> tile #8 #9 #10 #11 #12 #13 columns 3 spacingFactor 0.8
6 models tiled
> tile #8 #9 #10 #11 #12 #13 columns 3 spacingFactor 1
6 models tiled
> tile #8 #9 #10 #11 #12 #13 columns 3 spacingFactor 1.2
6 models tiled
> set bgColor white
> set bgColor black
> set bgColor white
> set bgColor black
> volume #8-13 level 0.4
> volume #8-13 level 0.45
> volume #8-13 level 0.48
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> open
> /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series/J73_class_00_00145_volume.mrc
Opened J73_class_00_00145_volume.mrc as #14, grid size 80,80,80, pixel 2.7,
shown at level 0.38, step 1, values float32
> open
> /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series/J73_class_01_00145_volume.mrc
Opened J73_class_01_00145_volume.mrc as #15, grid size 80,80,80, pixel 2.7,
shown at level 0.349, step 1, values float32
> open
> /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series/J73_class_02_00145_volume.mrc
Opened J73_class_02_00145_volume.mrc as #16, grid size 80,80,80, pixel 2.7,
shown at level 0.365, step 1, values float32
> open
> /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series/J73_class_03_00145_volume.mrc
Opened J73_class_03_00145_volume.mrc as #17, grid size 80,80,80, pixel 2.7,
shown at level 0.381, step 1, values float32
> open
> /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series/J73_class_04_00145_volume.mrc
Opened J73_class_04_00145_volume.mrc as #18, grid size 80,80,80, pixel 2.7,
shown at level 0.377, step 1, values float32
> open
> /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series/J73_class_05_00145_volume.mrc
Opened J73_class_05_00145_volume.mrc as #19, grid size 80,80,80, pixel 2.7,
shown at level 0.378, step 1, values float32
> open
> /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series/J73_class_06_00145_volume.mrc
Opened J73_class_06_00145_volume.mrc as #20, grid size 80,80,80, pixel 2.7,
shown at level 0.362, step 1, values float32
> open
> /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series/J73_class_07_00145_volume.mrc
Opened J73_class_07_00145_volume.mrc as #21, grid size 80,80,80, pixel 2.7,
shown at level 0.384, step 1, values float32
> open
> /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series/J73_class_08_00145_volume.mrc
Opened J73_class_08_00145_volume.mrc as #22, grid size 80,80,80, pixel 2.7,
shown at level 0.36, step 1, values float32
> open
> /Users/dongju/Downloads/cryosparc_P161_J73_00145_volume_series/J73_class_09_00145_volume.mrc
Opened J73_class_09_00145_volume.mrc as #23, grid size 80,80,80, pixel 2.7,
shown at level 0.368, step 1, values float32
> volume #14-23 level 0.48
> tile #14-23 columns 5
10 models tiled
> tile #14-23 columns 5 spacingFactor 1.2
10 models tiled
> tile #14-23 columns 4 spacingFactor 1.2
10 models tiled
> volume #14-23 level 0.5.2
Invalid "level" argument: Expected a number
> volume #14-23 level 0.52
> volume #14-23 level 0.55
> volume #14-23 level 0.6
> open /Users/dongju/Downloads/cryosparc_P161_J77_006_volume_map.mrc
Opened cryosparc_P161_J77_006_volume_map.mrc as #24, grid size 288,288,288,
pixel 0.75, shown at level 0.0487, step 2, values float32
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> hide #!21 models
> hide #!22 models
> hide #!23 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #24 step 1
> volume #24 color #ff8ffc
> volume #24 level 0.07336
> volume #24 level 0.0947
> volume #24 level 0.08485
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> open /Users/dongju/Downloads/cryosparc_P161_J75_004_volume_map.mrc
Opened cryosparc_P161_J75_004_volume_map.mrc as #25, grid size 288,288,288,
pixel 0.75, shown at level 0.0514, step 2, values float32
> hide #!24 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #25 step 1
> volume #25 level 0.07913
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #25 level 0.1017
> open /Users/dongju/Downloads/cryosparc_P161_J78_004_volume_map.mrc
Opened cryosparc_P161_J78_004_volume_map.mrc as #26, grid size 288,288,288,
pixel 0.75, shown at level 0.0522, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #26 step 1
> hide #!25 models
> volume #26 level 0.08951
> show #!25 models
> show #!24 models
> tile #24-26 columns 3 spacingFactor 1
3 models tiled
> volume #26 color #ff959d
> open /Users/dongju/Downloads/cryosparc_P161_J80_006_volume_map.mrc
Opened cryosparc_P161_J80_006_volume_map.mrc as #27, grid size 288,288,288,
pixel 0.75, shown at level 0.0485, step 2, values float32
> hide #!24 models
> hide #!25 models
> hide #!26 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #27 step 1
> volume #27 level 0.09433
> show #!26 models
> show #!5 models
> hide #!26 models
> volume #27 level 0.07906
> open
> /Users/dongju/Downloads/cryosparc_P161_8ww2_receptor_only_mask_12A_mask_th0.0051_ns4_ngs15.mrc
Opened cryosparc_P161_8ww2_receptor_only_mask_12A_mask_th0.0051_ns4_ngs15.mrc
as #28, grid size 288,288,288, pixel 0.75, shown at level 0.998, step 2,
values float32
> hide #!27 models
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 84, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 150, in status
r.draw_background()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1220, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 84, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 150, in status
r.draw_background()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1220, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open /Users/dongju/Downloads/cryosparc_P161_J80_004_volume_map.mrc
Opened cryosparc_P161_J80_004_volume_map.mrc as #29, grid size 288,288,288,
pixel 0.75, shown at level 0.0514, step 2, values float32
> hide #!28 models
> show #!26 models
> select add #27
4 atoms, 3 bonds, 1 residue, 3 models selected
> show #!28 models
> hide #!26 models
> show #!26 models
> hide #!5 models
> volume #24 level 0.1013
> volume #26 level 0.03793
> volume #26 level 0.06106
> volume #26 level 0.07351
> open /Users/dongju/Downloads/cryosparc_P161_J81_004_volume_map.mrc
Opened cryosparc_P161_J81_004_volume_map.mrc as #30, grid size 288,288,288,
pixel 0.75, shown at level 0.0499, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #30 step 1
> volume #30 level 0.09329
> volume #30 level 0.07421
> volume #24 level 0.121
> volume #24 level 0.1013
> volume #24 level 0.06516
> volume #24 level 0.04382
> volume #30 level 0.06033
> volume #30 level 0.04645
> volume #30 level 0.04299
> volume #30 level 0.05339
> volume #30 level 0.07074
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #30 level 0.06554
> volume #30 level 0.0638
> volume #30 level 0.05686
> volume #30 level 0.04992
> volume #24 level 0.08157
> volume #26 level 0.1215
> volume #26 level 0.08596
> volume #26 level 0.05928
> volume #25 level 0.07047
> volume #25 level 0.06354
> volume #25 level 0.04969
> volume #25 level 0.06701
> volume #25 level 0.0774
> volume #26 level 0.08062
> volume #26 level 0.07173
> volume #26 level 0.06283
> open 8X2K
8x2k title:
a lipid receptor complex structure [more info...]
Chain information for 8x2k #31
---
Chain | Description | UniProt
A | Soluble cytochrome b562,G-protein coupled receptor 3 | C562_ECOLX -105--1, GPR3_HUMAN 1-330
B | Isoform Gnas-2 of Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | GNAS2_HUMAN 26-394
C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_HUMAN 2-340
D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
E | scfv16 |
Non-standard residues in 8x2k #31
---
5YM — (Z)-N-(2-hydroxyethyl)octadec-9-enamide
> show #!31 cartoons
> hide #!31 atoms
> select ::name="OLA"
73 atoms, 71 bonds, 2 residues, 2 models selected
> show #!31 atoms
> hide #!31 atoms
> show #!31 cartoons
> select ::name="OLA"
73 atoms, 71 bonds, 2 residues, 2 models selected
> show #!31 atoms
> hide #!31 atoms
> show #!31 cartoons
> select OLA
Expected an objects specifier or a keyword
> ui tool show "File History"
> select #31 ligand
Expected a keyword
> select #31 lipid
Expected a keyword
> select #31 ligands
Expected a keyword
> select #31 ligand
Expected a keyword
> select #31 lipid
Expected a keyword
> select ::name="OLA"
73 atoms, 71 bonds, 2 residues, 2 models selected
> show #!31 atoms
> hide #!31 atoms
> select ::name="OLA
Nothing selected
> select ::name="OLA"
73 atoms, 71 bonds, 2 residues, 2 models selected
> style #!31 stick
Changed 8570 atom styles
> select ::name="OLA"
73 atoms, 71 bonds, 2 residues, 2 models selected
> show #31 target ab
> select ::name="OLA"
73 atoms, 71 bonds, 2 residues, 2 models selected
> select ::name="Y01"
119 atoms, 125 bonds, 2 residues, 2 models selected
> select ::name="5YM"
23 atoms, 22 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
8547 atoms, 8715 bonds, 6 pseudobonds, 1113 residues, 2 models selected
> hide sel atoms
> select add #31
8570 atoms, 8737 bonds, 6 pseudobonds, 1114 residues, 2 models selected
> select subtract #31
Nothing selected
> hide #!31 models
> open /Users/dongju/Downloads/cryosparc_P161_J84_007_volume_map.mrc
Opened cryosparc_P161_J84_007_volume_map.mrc as #32, grid size 288,288,288,
pixel 0.75, shown at level 0.0495, step 2, values float32
> open /Users/dongju/Downloads/cryosparc_P161_J85_005_volume_map.mrc
Opened cryosparc_P161_J85_005_volume_map.mrc as #33, grid size 288,288,288,
pixel 0.75, shown at level 0.0487, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #32 step 1
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #33 step 1
> tile #32 #33
2 models tiled
> tile #32 #33 spacingFactor 1
2 models tiled
> tile #32 #33 spacingFactor 0.8
2 models tiled
> volume #32 level 0.06332
> volume #33 level 0.06644
> volume #32 level 0.04605
> volume #33 level 0.05353
> volume #33 level 0.04546
> volume #33 level 0.04062
> volume #33 level 0.0503
> open /Users/dongju/Downloads/cryosparc_P161_J86_class_02_00294_volume.mrc
Opened cryosparc_P161_J86_class_02_00294_volume.mrc as #34, grid size
80,80,80, pixel 2.7, shown at level 0.377, step 1, values float32
> open /Users/dongju/Downloads/cryosparc_P161_J86_class_01_00294_volume.mrc
Opened cryosparc_P161_J86_class_01_00294_volume.mrc as #35, grid size
80,80,80, pixel 2.7, shown at level 0.37, step 1, values float32
> open /Users/dongju/Downloads/cryosparc_P161_J86_class_00_00294_volume.mrc
Opened cryosparc_P161_J86_class_00_00294_volume.mrc as #36, grid size
80,80,80, pixel 2.7, shown at level 0.367, step 1, values float32
> tile #34-46 spacingFactor 0.8
3 models tiled
> tile #34-46 spacingFactor 1
3 models tiled
> tile #34-46 columns 3 spacingFactor 1
3 models tiled
> volume #34 level 0.3461
> volume #34 level 0.3717
> volume #34 level 0.3288
> volume #35 level 0.2813
> volume #36 level 0.2577
> open /Users/dongju/Downloads/cryosparc_P161_J87_class_02_00412_volume.mrc
Opened cryosparc_P161_J87_class_02_00412_volume.mrc as #37, grid size
80,80,80, pixel 2.7, shown at level 0.372, step 1, values float32
> open /Users/dongju/Downloads/cryosparc_P161_J87_class_01_00412_volume.mrc
Opened cryosparc_P161_J87_class_01_00412_volume.mrc as #38, grid size
80,80,80, pixel 2.7, shown at level 0.348, step 1, values float32
> open /Users/dongju/Downloads/cryosparc_P161_J87_class_00_00412_volume.mrc
Opened cryosparc_P161_J87_class_00_00412_volume.mrc as #39, grid size
80,80,80, pixel 2.7, shown at level 0.366, step 1, values float32
> tile #37-39 columns 3 spacingFactor 1
3 models tiled
> volume #37 level 0.2957
> volume #37 level 0.2578
> volume #38 level 0.2979
> volume #38 level 0.2567
> volume #39 level 0.2668
> volume #39 level 0.2095
> volume #39 level 0.2512
> open /Users/dongju/Downloads/cryosparc_P161_J88_003_volume_map.mrc
Opened cryosparc_P161_J88_003_volume_map.mrc as #40, grid size 288,288,288,
pixel 0.75, shown at level 0.051, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #40 step 1
> volume #40 level 0.06686
> volume #40 level 0.07392
> open /Users/dongju/Downloads/cryosparc_P161_J89_002_volume_map.mrc
Opened cryosparc_P161_J89_002_volume_map.mrc as #41, grid size 288,288,288,
pixel 0.75, shown at level 0.0506, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #41 step 1
> volume #41 level 0.09116
> volume #41 level 0.049
> open /Users/dongju/Downloads/cryosparc_P161_J90_003_volume_map.mrc
Opened cryosparc_P161_J90_003_volume_map.mrc as #42, grid size 288,288,288,
pixel 0.75, shown at level 0.0507, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #42 step 1
> volume #42 level 0.04716
> open /Users/dongju/Downloads/cryosparc_P161_J91_002_volume_map.mrc
Opened cryosparc_P161_J91_002_volume_map.mrc as #43, grid size 288,288,288,
pixel 0.75, shown at level 0.0509, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #43 step 1
> volume #43 level 0.06735
> volume #43 level 0.05584
> volume #42 level 0.05968
> volume #43 level 0.04762
> volume #43 level 0.04597
> tile #40-43 columns 2 spacingFactor 1
4 models tiled
> volume #40 level 0.06686
> volume #41 level 0.05711
> volume #41 level 0.05387
> volume #42 level 0.05615
> volume #43 level 0.05255
> volume #43 level 0.04104
> volume #43 level 0.02953
> volume #43 level 0.04762
> volume #43 level 0.03939
> volume #43 level 0.06899
> volume #43 level 0.05748
> volume #42 level 0.05436
> volume #40 level 0.06156
> open "/Users/dongju/Downloads/emd_38015 (2).map"
Opened emd_38015 (2).map as #44, grid size 320,320,320, pixel 0.85, shown at
level 0.177, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #44 step 1
> volume #44 level 0.5649
> volume #44 level 0.493
> volume #44 level 0.4354
> volume #44 level 0.2485
> volume #44 level 0.723
> volume #44 level 0.5073
> volume #43 level 0.05584
> volume #44 level 0.5649
> open /Users/dongju/Downloads/cryosparc_P161_J92_003_volume_map.mrc
Opened cryosparc_P161_J92_003_volume_map.mrc as #45, grid size 288,288,288,
pixel 0.75, shown at level 0.0499, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #45 step 1
> volume #45 color #ff928c
> volume #45 level 0.05159
> volume #45 level 0.04644
> volume #45 level 0.04816
> volume #45 level 0.0825
> volume #45 level 0.06704
> volume #45 level 0.05846
> volume #45 level 0.08078
> volume #45 level 0.06704
> volume #45 level 0.05502
> volume #42 level 0.07939
> volume #42 level 0.07403
> volume #42 level 0.133
> volume #42 level 0.07761
> volume #42 level 0.06151
> volume #42 level 0.05436
> volume #42 level 0.06509
> volume #44 level 0.4786
> volume #44 level 0.493
> open /Users/dongju/Downloads/cryosparc_P161_J93_004_volume_map.mrc
Opened cryosparc_P161_J93_004_volume_map.mrc as #46, grid size 288,288,288,
pixel 0.75, shown at level 0.0469, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #46 step 1
> volume #46 level 0.06435
> volume #46 level 0.0494
> volume #46 level 0.07929
> volume #46 level 0.05189
> volume #46 level 0.0768
> volume #46 level 0.05687
> volume #45 level 0.04301
> volume #45 level 0.09795
> volume #46 level 0.07929
> volume #46 level 0.05687
> tile #45-46 columns 2 spacingFactor 1
2 models tiled
> tile #45-46 columns 2 spacingFactor 0.8
2 models tiled
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #45 level 0.06361
> volume #45 level 0.04301
> volume #46 level 0.08407
> volume #46 level 0.07414
> volume #46 level 0.05677
> volume #46 level 0.05429
> volume #46 level 0.04935
> volume #33 level 0.07289
> volume #33 level 0.06644
> volume #33 level 0.0503
> volume #33 level 0.04707
> volume #33 level 0.03739
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #44 level 0.4211
> view matrix models #44-46
Invalid "models" argument: Expected model id and 12 comma-separated numbers
> view initial #44
> lighting simple
> lighting soft
> lighting full
> lighting simple
> view
> ui mousemode right "rotate selected models"
> ui mousemode right select
> select #46
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #46,0.95507,-0.005669,-0.29632,34.061,0.0087808,-0.99884,0.04741,94.834,-0.29625,-0.047882,-0.95391,218.55
> view matrix models
> #46,0.96129,0.027545,-0.27417,27.619,0.041247,-0.99816,0.044335,91.619,-0.27245,-0.053927,-0.96066,217.35
> view matrix models
> #46,0.96268,0.011121,-0.27041,28.792,0.044789,-0.99192,0.11866,82.831,-0.26691,-0.12634,-0.9554,223.77
> ui mousemode right select
> ui mousemode right "rotate selected models"
> view matrix models
> #46,0.18365,-0.1684,0.96846,1.3672,-0.10944,-0.98259,-0.1501,126.38,0.97688,-0.07842,-0.19888,7.0163
> view matrix models
> #46,0.14922,-0.18429,0.97148,6.3867,-0.10719,-0.9797,-0.16939,127.85,0.98298,-0.078857,-0.16594,2.9727
> view matrix models
> #46,0.14339,-0.20306,0.96861,9.2664,-0.19365,-0.96556,-0.17376,136.06,0.97054,-0.16265,-0.17778,14.281
> view matrix models
> #46,0.22128,-0.17314,0.95972,-1.2419,-0.19739,-0.9717,-0.12979,132.51,0.95503,-0.16072,-0.24919,23.189
> view matrix models
> #46,0.21533,-0.18803,0.95827,1.0979,-0.26654,-0.95534,-0.12756,137.95,0.93946,-0.22795,-0.25583,32.56
> ui mousemode right select
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #7 level 0.09557
> volume #7 level 0.05358
> volume #7 level 0.07633
> volume #24 level 0.049
> view
> volume #24 level 0.04386
> volume #33 level 0.0635
> volume #33 level 0.03581
> volume #42 level 0.03708
> volume #42 level 0.04268
> view
> volume #42 level 0.07069
> volume #42 level 0.05949
> volume #45 level 0.06811
> volume #45 level 0.04301
> volume #45 level 0.03942
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #45 level 0.05018
> volume #45 level 0.05556
> volume #45 level 0.04839
> open "/Users/dongju/Downloads/cryosparc_P161_J44_010_volume_map (2).mrc"
Opened cryosparc_P161_J44_010_volume_map (2).mrc as #47, grid size
288,288,288, pixel 0.75, shown at level 0.0507, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #47 step 1
> volume #47 level 0.09491
> volume #47 level 0.05955
Drag select of 47 cryosparc_P161_J44_010_volume_map (2).mrc
> select clear
Drag select of 47 cryosparc_P161_J44_010_volume_map (2).mrc
> select clear
> volume #47 level 0.05365
> volume #47 level 0.05513
> set bgColor white
> set bgColor #ffffff00
> view
> volume #47 level 0.05807
> volume #47 level 0.05955
> volume #47 level 0.07428
> volume #47 level 0.06544
> open "/Users/dongju/Downloads/cryosparc_P161_J51_008_volume_map (1).mrc"
Opened cryosparc_P161_J51_008_volume_map (1).mrc as #48, grid size
288,288,288, pixel 0.75, shown at level 0.0521, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #48 step 1
> volume #48 level 0.04671
> volume #48 level 0.0615
> volume #48 level 0.05209
> volume #48 level 0.07361
> volume #48 level 0.05209
> volume #48 level 0.09244
> volume #48 level 0.0494
> open /Users/dongju/Downloads/cryosparc_P161_J54_class_02_00142_volume.mrc
Opened cryosparc_P161_J54_class_02_00142_volume.mrc as #49, grid size
128,128,128, pixel 1.69, shown at level 0.179, step 1, values float32
> open /Users/dongju/Downloads/cryosparc_P161_J54_class_01_00142_volume.mrc
Opened cryosparc_P161_J54_class_01_00142_volume.mrc as #50, grid size
128,128,128, pixel 1.69, shown at level 0.188, step 1, values float32
> open /Users/dongju/Downloads/cryosparc_P161_J54_class_00_00142_volume.mrc
Opened cryosparc_P161_J54_class_00_00142_volume.mrc as #51, grid size
128,128,128, pixel 1.69, shown at level 0.198, step 1, values float32
> volume #49 level 0.2314
> view
> volume #49 level 0.2431
Drag select of 50 cryosparc_P161_J54_class_01_00142_volume.mrc
> select clear
> volume #50 level 0.1882
> volume #50 level 0.1684
> volume #50 level 0.218
Drag select of 51 cryosparc_P161_J54_class_00_00142_volume.mrc
> select clear
> volume #51 level 0.2199
> volume #51 level 0.2557
> volume #51 level 0.2447
> open /Users/dongju/Downloads/cryosparc_P161_J56_007_volume_map.mrc
Opened cryosparc_P161_J56_007_volume_map.mrc as #52, grid size 288,288,288,
pixel 0.75, shown at level 0.0563, step 2, values float32
> open /Users/dongju/Downloads/cryosparc_P161_J55_004_volume_map.mrc
Opened cryosparc_P161_J55_004_volume_map.mrc as #53, grid size 288,288,288,
pixel 0.75, shown at level 0.0495, step 2, values float32
> volume #52 level 0.06859
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #52 step 1
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #53 step 1
> volume #53 level 0.04477
> volume #53 level 0.05585
> volume #52 level 0.06412
> open /Users/dongju/Downloads/cryosparc_P161_J62_003_volume_map.mrc
Opened cryosparc_P161_J62_003_volume_map.mrc as #54, grid size 288,288,288,
pixel 0.75, shown at level 0.0493, step 2, values float32
> view
> volume #54 color #ffad92
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #54 step 1
> volume #54 level 0.04316
> volume #54 level 0.06148
> volume #54 level 0.04927
> volume #54 level 0.04622
> volume #54 level 0.05385
> volume #54 level 0.05843
> volume #54 level 0.04927
> volume #54 level 0.05079
> open
> /Users/dongju/Downloads/cryosparc_P138_J63_molmap_mask_th0.0064_ns8_ngs10.mrc
Opened cryosparc_P138_J63_molmap_mask_th0.0064_ns8_ngs10.mrc as #55, grid size
288,288,288, pixel 0.75, shown at level 1, step 2, values float32
> volume #55 level 0.9884
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #55 step 1
> view
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting simple
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting simple
> graphics silhouettes false
> lighting simple
> volume #55 color #83a2ff
> volume #55 color #83a2ff80
> select #54
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #54,0.044887,0.99862,0.027264,0.51408,0.92813,-0.051783,0.36864,-25.226,0.36954,0.0087578,-0.92917,179.74
> view matrix models
> #54,0.044887,0.99862,0.027264,0.56339,0.92813,-0.051783,0.36864,-25.348,0.36954,0.0087578,-0.92917,179.97
> ui mousemode right "rotate selected models"
> view matrix models
> #54,0.031293,-0.92551,-0.37744,247.28,-0.94743,-0.14778,0.28381,196.47,-0.31844,0.34871,-0.88147,213.53
> view matrix models
> #54,0.089047,-0.92584,-0.36727,239.98,-0.94005,-0.2,0.27625,201.97,-0.32922,0.32065,-0.88814,218.36
> view matrix models
> #54,0.4429,-0.78218,-0.43822,194.26,-0.80449,-0.56246,0.19085,234.5,-0.39577,0.26802,-0.87837,230.03
> view matrix models
> #54,0.51821,-0.78489,-0.33971,175.87,-0.78232,-0.59553,0.18257,236.46,-0.3456,0.17115,-0.92264,239.51
> view matrix models
> #54,0.12681,-0.90345,-0.40951,238.07,-0.93186,-0.24999,0.26296,207.75,-0.33994,0.34826,-0.87359,215.06
> view matrix models
> #54,0.3627,-0.864,-0.34922,201.99,-0.92188,-0.27783,-0.2701,266.64,0.13634,0.4199,-0.89727,158.61
> view matrix models
> #54,0.34857,-0.86918,-0.35076,204.23,-0.93414,-0.29154,-0.20587,262.53,0.076673,0.39942,-0.91356,168.95
> view matrix models
> #54,0.32551,-0.8868,-0.32808,206.14,-0.94048,-0.2678,-0.20925,261.09,0.097701,0.37667,-0.92118,169.88
> view matrix models
> #54,0.95477,0.061799,-0.29087,34.608,0.061071,-0.99807,-0.011589,208.35,-0.29102,-0.0066992,-0.95669,255.92
> view matrix models
> #54,0.97768,-0.00084969,-0.21011,30.065,-0.0039945,-0.99989,-0.014543,215.89,-0.21008,0.015058,-0.97757,247.12
> view matrix models
> #54,0.97883,-0.045487,-0.19957,33.497,-0.0074596,-0.98227,0.1873,192.81,-0.20455,-0.18184,-0.96182,265.51
> view matrix models
> #54,0.97496,-0.061475,-0.21372,37.106,-0.020733,-0.98197,0.18788,194.15,-0.22141,-0.17874,-0.95866,266.66
> view matrix models
> #54,0.9749,-0.057148,-0.21517,36.814,-0.020685,-0.98556,0.16804,196.65,-0.22166,-0.15937,-0.96201,265.02
> ui mousemode right zoom
> ui mousemode right select
> select clear
> select #54
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #54,-0.16569,0.9642,-0.20704,52.006,0.98524,0.17099,0.0078431,-16.285,0.042963,-0.20268,-0.9783,242.71
> volume #55 level 0.9981
> view matrix models
> #54,0.94256,-0.10668,-0.31656,56.359,-0.034997,-0.97395,0.22403,190.98,-0.33221,-0.20008,-0.92174,276.93
> view matrix models
> #54,0.94237,-0.088029,-0.32279,55.089,-0.044773,-0.98927,0.13907,202.74,-0.33157,-0.1166,-0.9362,269.64
> ui mousemode right "translate selected models"
> view matrix models
> #54,0.94237,-0.088029,-0.32279,54.081,-0.044773,-0.98927,0.13907,202.74,-0.33157,-0.1166,-0.9362,265.26
> ui mousemode right "rotate selected models"
> view matrix models
> #54,0.13436,0.98091,-0.14059,9.7097,0.98359,-0.11478,0.13916,-0.173,0.12037,-0.15698,-0.98024,225.37
> ui mousemode right select
> select clear
> volume #6 level 0.06216
> volume #6 color #9489ff
> volume #6 level 0.04572
> volume #6 level 0.06664
> volume #6 level 0.05618
> volume #6 level 0.04871
> volume #24 level 0.06271
> volume #24 level 0.049
> volume #24 level 0.06957
Drag select of 24 cryosparc_P161_J77_006_volume_map.mrc
> select clear
> volume #24 level 0.06443
> volume #24 level 0.05414
> volume #24 level 0.05072
> volume #24 level 0.05243
> volume #24 level 0.06957
> ui mousemode right "translate selected models"
> ui mousemode right select
> volume #26 level 0.04983
> volume #26 level 0.07212
> volume #26 level 0.06283
> volume #26 level 0.08141
> ui mousemode right "translate selected models"
> ui mousemode right select
> select #25
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #25,0.75969,0.38221,-0.52611,34.791,0.45013,-0.89296,0.0012527,-45.751,-0.46931,-0.23777,-0.85042,272.03
> ui mousemode right select
> select clear
> volume #25 level 0.1009
> volume #25 level 0.08102
> volume #25 color #63bfff
> volume #25 level 0.07017
> volume #25 level 0.06112
> volume #25 level 0.05208
> volume #25 level 0.06112
> volume #25 level 0.05931
> select #30
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #30,-0.68895,0.66493,-0.28847,168.69,0.60337,0.74666,0.28007,-377.71,0.40162,0.018903,-0.91561,310.54
> view matrix models
> #30,-0.68895,0.66493,-0.28847,192.73,0.60337,0.74666,0.28007,-503.61,0.40162,0.018903,-0.91561,433.97
> ui mousemode right select
> select #30
2 models selected
> select #30
2 models selected
> select #30
2 models selected
> select #30
2 models selected
> select #30
2 models selected
> select #30
2 models selected
> select #30
2 models selected
> select #30
2 models selected
> select #30
2 models selected
> hide #!30 models
> show #!30 models
> select subtract #30
Nothing selected
> volume #30 level 0.03543
> volume #30 level 0.04449
> volume #30 level 0.09159
> volume #30 level 0.06985
> volume #30 level 0.05536
> ui mousemode right "translate selected models"
> ui mousemode right select
> volume #42 color #d5876c
> volume #42 level 0.07443
> volume #42 level 0.07069
> volume #42 level 0.06696
> volume #42 level 0.06322
> volume #42 level 0.06135
Drag select of 42 cryosparc_P161_J90_003_volume_map.mrc
> select clear
> open /Users/dongju/Downloads/cryosparc_P161_J71_map.mrc
Opened cryosparc_P161_J71_map.mrc as #56, grid size 288,288,288, pixel 0.75,
shown at level 0.0493, step 2, values float32
> volume #41 level 0.04878
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #56 step 1
> volume #56 level 0.04189
> volume #56 level 0.0387
> volume #56 level 0.07802
> open "/Users/dongju/Downloads/cryosparc_P163_J35_008_volume_map (1).mrc"
Opened cryosparc_P163_J35_008_volume_map (1).mrc as #57, grid size
288,288,288, pixel 0.75, shown at level 0.112, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #57 step 1
> volume #57 color #ff75c0
> volume #57 level 0.1523
Drag select of 57 cryosparc_P163_J35_008_volume_map (1).mrc
> select clear
> volume #57 level 0.1174
> open "/Users/dongju/Downloads/cryosparc_P163_J46_009_volume_map (1).mrc"
Opened cryosparc_P163_J46_009_volume_map (1).mrc as #58, grid size
288,288,288, pixel 0.75, shown at level 0.117, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #58 step 1
> volume #58 level 0.1174
> volume #58 level 0.1302
> volume #58 level 0.1195
> open "/Users/dongju/Downloads/cryosparc_P163_J51_008_volume_map (2).mrc"
Opened cryosparc_P163_J51_008_volume_map (2).mrc as #59, grid size
288,288,288, pixel 0.75, shown at level 0.119, step 2, values float32
> volume #59 color #85fc5f
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #59 step 1
> volume #59 level 0.1554
> volume #59 level 0.1486
> volume #59 level 0.1349
> tile #58-59 columns 2
2 models tiled
> tile #58-59 columns 2 spacingFactor 1
2 models tiled
> tile #58-59 columns 2 spacingFactor 0.5
2 models tiled
> tile #58-59 columns 2 spacingFactor 0.7
2 models tiled
> volume #59 level 0.1235
> volume #59 color #4ba5f8
> volume #58 color #ff8681
> volume #58 level 0.1131
> volume #59 level 0.1099
> volume #59 level 0.1395
> volume #59 level 0.1144
> open /Users/dongju/Downloads/cryosparc_P161_run_class001.mrc
Opened cryosparc_P161_run_class001.mrc as #60, grid size 288,288,288, pixel
0.75, shown at level 0.00175, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #60 step 1
> volume #60 level 0.002935
Drag select of 60 cryosparc_P161_run_class001.mrc
> select clear
> volume #60 level 0.001967
> volume #60 color #7092eb
Drag select of 60 cryosparc_P161_run_class001.mrc
> select clear
Drag select of 60 cryosparc_P161_run_class001.mrc
> select clear
> volume #60 level 0.002397
Drag select of 60 cryosparc_P161_run_class001.mrc
> select clear
Drag select of 60 cryosparc_P161_run_class001.mrc
> select clear
> select #47
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #47,-0.84423,-0.18459,-0.5032,270.72,-0.16257,0.98278,-0.087778,28.952,0.51074,0.0077016,-0.8597,163.45
> ui mousemode right "translate selected models"
> view matrix models
> #47,-0.84423,-0.18459,-0.5032,276.69,-0.16257,0.98278,-0.087778,98.496,0.51074,0.0077016,-0.8597,179.05
> ui mousemode right select
> select clear
> select #30
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #30,-0.84114,0.50506,-0.19338,159.96,0.43533,0.84448,0.31199,-153.77,0.32088,0.17825,-0.9302,133.11
> view matrix models
> #30,-0.84114,0.50506,-0.19338,162.05,0.43533,0.84448,0.31199,-140.73,0.32088,0.17825,-0.9302,140.27
> ui mousemode right select
> select #47
2 models selected
Drag select of 47 cryosparc_P161_J44_010_volume_map (2).mrc
> ui mousemode right "translate selected models"
> view matrix models
> #47,-0.20523,0.86583,-0.45631,86.524,0.86746,0.37682,0.32483,34.352,0.4532,-0.32917,-0.82841,224.88
> ui mousemode right "rotate selected models"
> view matrix models
> #47,-0.3803,0.7969,-0.46938,114.84,0.79726,0.53971,0.27035,30.172,0.46877,-0.2714,-0.84059,218.15
> view matrix models
> #47,-0.39197,0.82691,-0.40321,105.06,0.81143,0.51728,0.27204,30.933,0.43352,-0.22055,-0.87374,220.17
> view matrix models
> #47,-0.496,0.83248,-0.24689,97.588,0.79377,0.54997,0.25975,30.642,0.35201,-0.067136,-0.93358,218.91
> view matrix models
> #47,-0.53984,0.73625,-0.40806,131.88,0.70939,0.65887,0.25029,28.791,0.45314,-0.15436,-0.87797,211.14
> view matrix models
> #47,-0.24383,0.86729,-0.43401,87.975,0.85659,0.40244,0.32295,32.897,0.45475,-0.29302,-0.84103,222.14
> ui mousemode right select
> select clear
> volume #30 level 0.08072
> volume #30 level 0.09884
> select #30
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #30,0.28817,-0.88836,-0.35746,203.42,-0.87201,-0.3977,0.28538,134.79,-0.39568,0.22947,-0.88926,208.39
> view matrix models
> #30,0.78674,0.56073,-0.25812,-13.648,0.57098,-0.81995,-0.040874,57.449,-0.23456,-0.11522,-0.96525,235.26
> ui mousemode right select
> select clear
> volume #30 level 0.07348
> volume #60 level 0.002504
> open /Users/dongju/Downloads/cryosparc_P161_J97_005_volume_map.mrc
Opened cryosparc_P161_J97_005_volume_map.mrc as #61, grid size 288,288,288,
pixel 0.75, shown at level 0.0477, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #61 step 1
> select #61
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #61,-0.94615,0.13199,-0.29559,234.33,-0.014714,0.89462,0.44658,-38.832,0.32338,0.42689,-0.84451,132.37
> view matrix models
> #61,-0.4934,0.49563,-0.71478,193.37,0.047505,0.8359,0.54682,-50.917,0.86851,0.23584,-0.43598,45.706
> view matrix models
> #61,-0.50616,0.39283,-0.76778,212.23,0.40972,0.89289,0.18674,-55.13,0.75891,-0.22005,-0.61289,128.42
> view matrix models
> #61,-0.70179,0.39954,-0.58979,212.32,0.41459,0.90233,0.11794,-48.689,0.57931,-0.16175,-0.7989,163.47
> ui mousemode right "translate selected models"
> view matrix models
> #61,0.99398,-0.06137,0.090732,6.3966,-0.1026,-0.81174,0.57494,243.61,0.038367,-0.58079,-0.81315,297.34
> ui mousemode right "rotate selected models"
> view matrix models
> #61,0.99188,-0.073784,0.10362,6.49,-0.12305,-0.76308,0.63449,233.58,0.032253,-0.64208,-0.76596,299.25
> view matrix models
> #61,0.99565,-0.048721,0.079446,6.1397,-0.082855,-0.85303,0.51524,252.92,0.042667,-0.51958,-0.85336,294.84
> view matrix models
> #61,0.99557,-0.049404,0.080013,6.1572,-0.083896,-0.85099,0.51844,252.44,0.042478,-0.52285,-0.85136,294.98
> view matrix models
> #61,0.99735,-0.030738,0.065954,5.5504,-0.056294,-0.90026,0.43169,264.91,0.046106,-0.43426,-0.89961,290.48
> view matrix models
> #61,0.90682,0.42016,-0.033726,-22.348,0.37909,-0.77795,0.50109,195.44,0.1843,-0.46719,-0.86474,274.81
> view matrix models
> #61,0.91057,0.41251,-0.026589,-22.752,0.35981,-0.7593,0.54222,190.73,0.20348,-0.50329,-0.83982,273.76
> view matrix models
> #61,0.9254,0.35716,-0.12681,-6.6388,0.36524,-0.75107,0.55,188.32,0.1012,-0.55528,-0.82548,289.06
> ui mousemode right select
> select clear
> volume #61 color #ea7348
> volume #61 level 0.06096
> select clear
Drag select of 61 cryosparc_P161_J97_005_volume_map.mrc
> select clear
> volume #61 level 0.05436
> volume #61 level 0.04114
> volume #61 level 0.04246
Drag select of 61 cryosparc_P161_J97_005_volume_map.mrc
> select clear
Drag select of 61 cryosparc_P161_J97_005_volume_map.mrc
> select clear
> volume #60 level 0.001913
> volume #60 level 0.001537
> volume #60 level 0.001806
> volume #61 level 0.0475
> volume #61 level 0.04251
> volume #61 level 0.06277
> volume #61 level 0.04286
> volume #61 level 0.0582
> volume #61 level 0.05445
> volume #61 level 0.03787
> volume #61 level 0.04772
> volume #61 level 0.0539
> volume #61 level 0.03921
> volume #61 level 0.04462
> volume #61 level 0.03668
> open "/Users/dongju/Downloads/emd_38015 (3).map"
Opened emd_38015 (3).map as #62, grid size 320,320,320, pixel 0.85, shown at
level 0.177, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #62 step 1
> volume #62 level 0.5198
> select #62
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #62,0.99158,0.051256,0.11889,-15.104,-0.052578,0.99858,0.0080081,136.81,-0.11832,-0.014192,0.99287,27.751
> ui mousemode right "rotate selected models"
> view matrix models
> #62,0.75026,-0.65967,0.044023,124.05,0.62245,0.72724,0.28928,45.254,-0.22285,-0.18964,0.95623,70.572
> view matrix models
> #62,0.72365,-0.6893,0.03451,132.93,0.60299,0.65578,0.45426,35.362,-0.33575,-0.30792,0.8902,110.7
> ui mousemode right "translate selected models"
> view matrix models
> #62,0.71972,-0.69351,0.032493,123.88,0.59831,0.6433,0.47769,-111.81,-0.35219,-0.32436,0.87793,93.288
> ui mousemode right select
> select clear
> volume #62 color #aad543
> volume #61 level 0.0684
> volume #62 level 0.5649
> volume #62 level 0.4447
> volume #61 level 0.03932
> volume #62 level 0.4748
> volume #62 level 0.5048
> volume #61 level 0.05518
> open /Users/dongju/Downloads/cryosparc_P161_J100_map_half_A.mrc
Opened cryosparc_P161_J100_map_half_A.mrc as #63, grid size 288,288,288, pixel
0.75, shown at level 0.0515, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #63 step 1
> select #63
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #63,0.99801,-0.060914,0.016539,26.528,0.060397,0.99772,0.030138,227.28,-0.018337,-0.029079,0.99941,63.56
> ui mousemode right "rotate selected models"
> view matrix models
> #63,-0.62778,0.39342,-0.67165,226.67,0.15178,0.90818,0.3901,188.34,0.76345,0.14295,-0.62984,136.25
> view matrix models
> #63,-0.63571,-0.47405,-0.60922,314.17,-0.58042,0.81385,-0.02761,322.25,0.5089,0.33605,-0.79252,160.37
> view matrix models
> #63,-0.83153,-0.49385,-0.2543,299.18,-0.51146,0.8593,0.0036653,306.57,0.21671,0.13311,-0.96712,232.45
> view matrix models
> #63,-0.86286,-0.37857,-0.33489,298.81,-0.40708,0.91324,0.01651,288.15,0.29959,0.15058,-0.94211,218.96
> ui mousemode right select
> select clear
> volume #63 level 0.07522
> open /Users/dongju/Downloads/cryosparc_P161_J100_map_locres.mrc
Opened cryosparc_P161_J100_map_locres.mrc as #64, grid size 288,288,288, pixel
0.75, shown at level 5.35, step 2, values float32
> select #64
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #64,0.98064,0.086853,0.17549,0.41923,-0.090425,0.99583,0.012443,342.46,-0.17368,-0.028071,0.9844,96.506
> ui mousemode right "rotate selected models"
> view matrix models
> #64,-0.9163,0.14974,-0.37144,262.75,0.027421,0.94875,0.31484,299.93,0.39955,0.2783,-0.87345,214.97
> view matrix models
> #64,-0.78378,-0.34145,-0.51876,319.51,-0.48645,0.8568,0.17102,382.5,0.38608,0.3864,-0.83764,200.38
> view matrix models
> #64,-0.72934,-0.11997,-0.67356,307.05,-0.36782,0.89888,0.23818,357.22,0.57687,0.42146,-0.69971,159.86
> view matrix models
> #64,-0.69238,-0.52474,-0.49523,327.07,-0.61599,0.78729,0.027021,420.87,0.37571,0.32377,-0.86834,211.95
> view matrix models
> #64,-0.82974,-0.17149,-0.53115,307.2,-0.28107,0.95054,0.13217,354.34,0.48221,0.25896,-0.8369,203.9
> ui mousemode right select
> select #64
2 models selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #64 step 1
> volume #64 level 6.342
> close #64
> ui tool show "Surface Color"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open /Users/dongju/Downloads/cryosparc_P161_J100_map_locres.mrc
Opened cryosparc_P161_J100_map_locres.mrc as #64, grid size 288,288,288, pixel
0.75, shown at level 5.35, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color sample #63.1 map #64 palette
> 2.5,#ff0000:3.5,#ffff00:4.5,#00ff00:5.5,#00ffff:6.5,#0000ff
Map values for surface "surface": minimum 0, mean 0, maximum 0
> color sample #61.1 map #64 palette
> 2.5,#ff0000:3.5,#ffff00:4.5,#00ff00:5.5,#00ffff:6.5,#0000ff
Map values for surface "surface": minimum 0, mean 0, maximum 0
> color single #61.1
> color sample #61.1 map #64 palette #ff0000:#ffff00:#00ff00:#00ffff:#0000ff
Map values for surface "surface": minimum 0, mean 0, maximum 0
> color sample #61.1 map #64 palette #ff0000:#ffff00:#00ff00:#00ffff:#0000ff
Map values for surface "surface": minimum 0, mean 0, maximum 0
> color sample #61.1 map #64 palette
> 0,#ff0000:0,#ffff00:0,#00ff00:0,#00ffff:0,#0000ff
Map values for surface "surface": minimum 0, mean 0, maximum 0
> color single #61.1
> color sample #63.1 map #64 palette
> 2.5,#ff0000:3.5,#ffff00:4.5,#00ff00:5.5,#00ffff:6.5,#0000ff
Map values for surface "surface": minimum 0, mean 0, maximum 0
> color sample #63.1 map #64 palette
> 2,#ff0000:2.5,#ffff00:3,#00ff00:4.5,#00ffff:5.5,#0000ff
Map values for surface "surface": minimum 0, mean 0, maximum 0
> color sample #63.1 map #63 palette
> 2,#ff0000:2.5,#ffff00:3,#00ff00:4.5,#00ffff:5.5,#0000ff
Map values for surface "surface": minimum 0.07522, mean 0.07522, maximum
0.07523
> color sample #63.1 map #63 palette
> 2.5,#ff0000:3,#ffff00:3.5,#00ff00:4.5,#00ffff:5.5,#0000ff
Map values for surface "surface": minimum 0.07522, mean 0.07522, maximum
0.07523
> color sample #63.1 map #63 palette
> 2.5,#ff0000:3.5,#ffff00:4.5,#00ff00:5.5,#00ffff:6.5,#0000ff
Map values for surface "surface": minimum 0.07522, mean 0.07522, maximum
0.07523
> color sample #63.1 map #64 palette
> 2.5,#ff0000:3.5,#ffff00:4.5,#00ff00:5.5,#00ffff:6.5,#0000ff
Map values for surface "surface": minimum 0, mean 0, maximum 0
> color sample #61.1 map #64 palette
> 2.5,#ff0000:3.5,#ffff00:4.5,#00ff00:5.5,#00ffff:6.5,#0000ff
Map values for surface "surface": minimum 0, mean 0, maximum 0
> color single #61.1
> close #64
> close #63
> volume #61 level 0.05397
> volume #60 color #5a86ef
> volume #60 level 0.002396
> select clear
Drag select of 60 cryosparc_P161_run_class001.mrc
> select clear
> volume #60 level 0.002298
Drag select of 61 cryosparc_P161_J97_005_volume_map.mrc
> select clear
> volume #61 level 0.06486
> volume #61 level 0.05518
> volume #61 level 0.0576
> volume #61 level 0.06365
> tile #60-61
2 models tiled
> select #61
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #61,-0.20992,-0.97379,-0.087548,238.7,-0.96548,0.22058,-0.13855,65.31,0.15423,0.055443,-0.98648,145.45
> view matrix models
> #61,-0.90591,-0.10548,-0.41011,256.41,-0.12197,0.99243,0.014168,-128.99,0.40552,0.062855,-0.91192,108.65
> view matrix models
> #61,-0.84196,-0.13266,-0.52298,265.57,-0.1603,0.98704,0.0076999,-123.48,0.51518,0.090317,-0.85231,86.783
> view matrix models
> #61,-0.84255,-0.13305,-0.52193,265.56,-0.16055,0.987,0.0075702,-123.43,0.51413,0.090176,-0.85296,86.987
> ui mousemode right select
> select clear
> tile #60-61 columns 2 spaingFactor 1
Expected a keyword
> tile #60-61 columns 2 spacingFactor 1
2 models tiled
> tile #60-61 columns 2 spacingFactor 0.8
2 models tiled
> tile #60-61 columns 2 spacingFactor 0.9
2 models tiled
> volume #61 level 0.06607
> volume #60 level 0.002445
> tile #60-61 columns 2 spacingFactor 0.6
2 models tiled
> volume #61 level 0.03825
> volume #60 level 0.002002
> volume #60 level 0.001658
> volume #60 level 0.00215
> volume #61 level 0.05035
> volume #60 level 0.002396
> volume #61 level 0.05397
> volume #44 color #6ce6ff
> select #44
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #44,0.7259,-0.65031,0.22397,66.641,0.55466,0.74603,0.36849,-282.48,-0.40672,-0.14326,0.90225,-8.3567
> view matrix models
> #44,0.7259,-0.65031,0.22397,66.637,0.55466,0.74603,0.36849,-282.44,-0.40672,-0.14326,0.90225,-8.3806
> ui mousemode right select
> select clear
> open "/Users/dongju/Downloads/emd_42023 (2).map"
Opened emd_42023 (2).map as #63, grid size 256,256,256, pixel 0.86, shown at
level 0.167, step 1, values float32
> select #63
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #63,1,0,0,-20.61,0,1,0,-156.64,0,0,1,-66.319
> ui mousemode right "rotate selected models"
> view matrix models
> #63,-0.97631,0.20061,0.081134,168.14,0.21204,0.812,0.54377,-224.96,0.043204,0.54809,-0.8353,89.084
> view matrix models
> #63,0.89146,-0.035537,-0.4517,47.972,-0.10357,-0.98651,-0.12678,69.705,-0.4411,0.1598,-0.88311,187.33
> view matrix models
> #63,0.891,-0.051501,-0.45107,49.557,-0.087143,-0.99447,-0.05859,60.689,-0.44556,0.091512,-0.89056,195.57
> view matrix models
> #63,0.89091,-0.053244,-0.45104,49.738,-0.088873,-0.99434,-0.058166,60.818,-0.44539,0.091907,-0.89061,195.52
> ui mousemode right select
> select clear
> volume #63 level 0.2612
> open /Users/dongju/Downloads/emd_37881.map
Opened emd_37881.map as #64, grid size 256,256,256, pixel 1.1, shown at level
0.322, step 1, values float32
> volume #64 level 0.6891
> select #64
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #64,1,0,0,-32.534,0,1,0,-18.188,0,0,1,-138.88
> ui mousemode right select
> select clear
> volume #64 level 1.03
> open
> /Users/dongju/Downloads/cryosparc_P161_J101_component_000/J101_component_000_frame_000.mrc
Opened J101_component_000_frame_000.mrc as #65, grid size 288,288,288, pixel
0.75, shown at level 0.0514, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #65 step 1
> volume #65 color #ff7f8d
>
Incomplete command: vseries
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #65 style image
> volume #65 style surface
> hide #!65 models
> show #!65 models
> volume #65 change image level -0.006732,0 level 0.05131,0.8 level 0.2737,1
> volume #65 style image colorMode opaque8 showOutlineBox true imageMode "box
> faces"
> volume #65 style mesh
> volume #65 style surface
> volume #65 style image colorMode auto8 imageMode "full region"
> volume #65 style surface
> ui mousemode right "crop volume"
> ui mousemode right select
> select clear
> set bgColor white
> set bgColor black
> set bgColor transparent
> set bgColor white
> set bgColor #ffffff00
> ui mousemode right "move planes"
> volume #65 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 108 tiltedSlabSpacing 0.75 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #!65 region all imageMode "full region"
> volume unzone #!65
> mousemode rightMode "crop volume"
> volume #!65 planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> volume #!65 showOutlineBox false
> volume #!65 region all imageMode "full region"
> volume unzone #!65
> mousemode rightMode "crop volume"
> volume #!65 region all imageMode "full region"
> volume unzone #!65
> mousemode rightMode "crop volume"
> volume #65 orthoplanes xyz positionPlanes 144,144,144 style image region all
> mousemode rightMode "move planes"
> volume #65 style image region all imageMode "tilted slab" tiltedSlabAxis
> 0,0,1 tiltedSlabOffset 108 tiltedSlabSpacing 0.75 tiltedSlabPlaneCount 10
> mousemode rightMode "rotate slab"
> volume #!65 planes z style image imageMode "full region"
> mousemode rightMode "move planes"
> ui mousemode right "crop volume"
> volume #65 region 0,0,143,287,287,257
> volume #65 region 0,0,143,287,287,287
> volume #65 style surface
> close #65
> volume #64 color #7c50ff
> volume #64 region 0,0,0,255,255,255
> volume #64 region 11,0,0,255,255,255
> volume #63 level 0.3177
> volume #63 color #ffdb44
> volume #63 level 0.28
> volume #63 region 0,0,0,255,255,255
> volume #62 region 96,0,0,319,319,319
> volume #62 region 92,0,0,319,319,319
> volume #62 level 0.656
> volume #62 level 0.5735
> volume #62 level 0.491
> volume #62 level 0.5185
> volume #61 region 0,0,0,287,287,287
> ui mousemode right select
> select #61
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #61,-0.91049,-0.30014,0.28447,208.27,-0.012093,0.70694,0.70717,-159.24,-0.41335,0.64043,-0.64729,134.11
> ui mousemode right "rotate selected models"
> view matrix models
> #61,-0.862,-0.47334,0.18142,233.97,-0.4897,0.87004,-0.056726,-35.845,-0.13099,-0.13774,-0.98177,227.54
> view matrix models
> #61,0.78289,-0.61232,-0.11024,102.81,-0.4373,-0.6676,0.60257,50.512,-0.44256,-0.42353,-0.79042,270.82
> view matrix models
> #61,0.97076,0.23918,-0.0203,-21.77,0.20457,-0.78014,0.59121,-6.1939,0.12557,-0.57808,-0.80626,227.33
> view matrix models
> #61,0.13752,0.37645,0.91617,-54.5,-0.26925,-0.87592,0.40033,78.508,0.9532,-0.30173,-0.019098,14.58
> view matrix models
> #61,-0.37962,0.31395,0.87024,14.42,-0.17868,-0.94783,0.264,92.345,0.90772,-0.055278,0.41591,-58.143
> ui mousemode right select
> select clear
> select #61
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #61,0.94414,0.078156,0.32014,-37.975,-0.11776,-0.82732,0.54925,61.513,0.30779,-0.55627,-0.7719,209.94
> ui mousemode right select
> select #61
2 models selected
> select clear
> volume #61 level 0.06849
> volume #61 level 0.04793
> volume #61 level 0.05276
> open /Users/dongju/Downloads/cryosparc_P163_J46_009_volume_map.mrc
Opened cryosparc_P163_J46_009_volume_map.mrc as #65, grid size 288,288,288,
pixel 0.75, shown at level 0.117, step 2, values float32
> volume #65 color #fc65ed
> volume #65 level 0.1391
> volume #65 level 0.1083
> volume #65 level 0.1155
> volume #65 level 0.1337
> volume #63 level 0.2894
> volume #63 level 0.28
> volume #63 color #ff835e
> volume #63 level 0.3083
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #65 step 1
> volume #63 level 0.2612
> select #65
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #65,0.93557,-0.34281,-0.084758,27.627,-0.25377,-0.81958,0.5137,-75.094,-0.24557,-0.45909,-0.85377,210.93
> ui mousemode right select
> select clear
> volume #65 level 0.1042
> volume #65 level 0.1258
> volume #65 level 0.118
> open /Users/dongju/Downloads/cryosparc_P161_J97_005_volume_map_sharp.mrc
Opened cryosparc_P161_J97_005_volume_map_sharp.mrc as #66, grid size
288,288,288, pixel 0.75, shown at level 0.0993, step 2, values float32
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #66 step 1
> select #66
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #66,1,-0.00010955,1.6327e-05,-1.3257,0.00010955,1,0.00047679,53.573,-1.6379e-05,-0.00047679,1,-13.767
> ui mousemode right "rotate selected models"
> view matrix models
> #66,-0.90835,-0.27533,0.31478,200.97,-0.089159,0.86289,0.49746,23.877,-0.40859,0.4238,-0.80836,181.85
> view matrix models
> #66,-0.5662,0.57279,-0.59274,171.2,0.20296,0.79384,0.57325,-8.595,0.79889,0.20427,-0.56573,48.212
> view matrix models
> #66,-0.13312,0.7085,-0.69304,120.53,0.071561,0.70431,0.70628,0.81845,0.98851,0.044423,-0.14446,-1.006
> view matrix models
> #66,-0.19566,0.56408,-0.8022,154.81,0.76572,0.59894,0.2344,-11.604,0.61269,-0.5684,-0.54912,150.05
> view matrix models
> #66,-0.8811,-0.4681,-0.067514,260.51,-0.38784,0.79685,-0.46326,168.13,0.27065,-0.38199,-0.88365,203.47
> view matrix models
> #66,-0.97152,-0.23503,-0.030291,241.08,-0.18806,0.84246,-0.50486,146.08,0.14417,-0.48478,-0.86267,226
> view matrix models
> #66,-0.96966,-0.16566,0.17979,210.48,-0.23481,0.83585,-0.49621,150.92,-0.068074,-0.52336,-0.84939,251.72
> view matrix models
> #66,-0.94169,0.0060802,0.33642,171.82,-0.18433,0.82713,-0.53092,150.18,-0.28149,-0.56198,-0.77778,271.23
> view matrix models
> #66,-0.88594,-0.074842,-0.45772,261.1,-0.095359,0.9952,0.021845,62.11,0.45389,0.063001,-0.88883,136.1
> ui mousemode right "translate selected models"
> view matrix models
> #66,-0.88594,-0.074842,-0.45772,265.76,-0.095359,0.9952,0.021845,76.726,0.45389,0.063001,-0.88883,154.19
> ui mousemode right select
> select clear
> volume #66 level 0.1919
> volume #66 level 0.175
> volume #66 level 0.1498
> volume #66 level 0.2172
> volume #66 level 0.2003
> volume #66 level 0.1414
> volume #66 level 0.1245
> volume #66 level 0.1666
> open /Users/dongju/Downloads/cryosparc_P161_J104_007_volume_map.mrc
Opened cryosparc_P161_J104_007_volume_map.mrc as #67, grid size 288,288,288,
pixel 0.75, shown at level 0.0404, step 2, values float32
> select #67
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #67,0.99937,-0.034572,-0.0083988,16.21,0.034508,0.99937,-0.0076891,122.19,0.0086593,0.0073944,0.99994,29.575
> ui mousemode right "rotate selected models"
> view matrix models
> #67,0.42712,-0.89905,0.096289,160.95,0.86718,0.37715,-0.32521,133.05,0.25606,0.2224,0.94073,-14.302
> view matrix models
> #67,-0.81863,-0.10581,-0.56448,283.34,-0.032081,0.98977,-0.139,144.82,0.57342,-0.095685,-0.81366,176.55
> ui mousemode right select
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #67 step 1
> volume #67 level 0.08403
> volume #67 level 0.04837
> volume #67 level 0.0563
> volume #67 level 0.04441
> volume #67 level 0.08007
> volume #67 level 0.06818
> volume #67 level 0.06026
> volume #66 level 0.1329
> volume #67 level 0.08403
Drag select of 66 cryosparc_P161_J97_005_volume_map_sharp.mrc , 67
cryosparc_P161_J104_007_volume_map.mrc
> select clear
> volume #67 level 0.05233
> ui tool show "Side View"
> view
> tile
2 models tiled
> select clear
Drag select of 67 cryosparc_P161_J104_007_volume_map.mrc
> select #67
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #67,0.14302,0.96877,0.20258,-41.634,-0.80965,0.23224,-0.53901,71.212,-0.56922,-0.086927,0.81758,32.97
> view matrix models
> #67,-0.18784,0.4962,0.84765,-24.395,-0.75902,0.4744,-0.44591,30.02,-0.62338,-0.72714,0.28752,163.56
> view matrix models
> #67,-0.26629,0.20525,0.94179,4.9279,-0.76516,0.54919,-0.33604,10.993,-0.58619,-0.8101,0.010801,197.93
> view matrix models
> #67,-0.81719,-0.49463,-0.29587,272.59,-0.41894,0.8623,-0.28447,-65.86,0.39584,-0.10851,-0.91189,114.43
> view matrix models
> #67,-0.86081,-0.41723,-0.29142,268.74,-0.46244,0.88034,0.1056,-104.84,0.21249,0.22566,-0.95075,103.48
> view matrix models
> #67,0.64917,-0.75581,-0.085669,115.86,-0.74345,-0.65426,0.13864,84.924,-0.16083,-0.026309,-0.98663,175.18
> view matrix models
> #67,0.95992,0.27878,0.028833,-40.141,0.25782,-0.9187,0.29919,-14.82,0.1099,-0.27977,-0.95376,168.58
> view matrix models
> #67,0.99596,0.087471,0.020457,-22.985,0.079628,-0.96505,0.24968,15.058,0.041582,-0.24704,-0.96811,174.2
> ui mousemode right "translate selected models"
> view matrix models
> #67,0.99596,0.087471,0.020457,-14.345,0.079628,-0.96505,0.24968,103.68,0.041582,-0.24704,-0.96811,198.57
> ui mousemode right select
> select clear
> volume #67 level 0.09196
> select clear
> select #67
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #67,0.97906,0.18186,0.091535,-28.73,0.15103,-0.95024,0.27246,92.23,0.13653,-0.25293,-0.9578,187.82
> view matrix models
> #67,0.63356,0.75521,-0.16812,-25.132,0.74413,-0.53531,0.39963,-26.818,0.21181,-0.37829,-0.90113,187.07
> view matrix models
> #67,0.54931,0.82573,-0.12819,-26.811,0.7898,-0.46295,0.40236,-39.445,0.27289,-0.32226,-0.90646,175.17
> view matrix models
> #67,0.60895,0.7909,-0.060501,-36.096,0.55401,-0.36949,0.74602,-55.156,0.56767,-0.48781,-0.66316,137.1
> view matrix models
> #67,0.69509,0.70932,-0.11708,-31.947,0.53167,-0.39756,0.74785,-50.02,0.48392,-0.58207,-0.65347,154.97
> view matrix models
> #67,0.65686,0.75376,0.019625,-45.02,0.49817,-0.45337,0.73911,-39.853,0.56601,-0.47571,-0.6733,137
> ui mousemode right "translate selected models"
> view matrix models
> #67,0.65686,0.75376,0.019625,-43.299,0.49817,-0.45337,0.73911,-40.065,0.56601,-0.47571,-0.6733,144.52
> ui mousemode right select
> select clear
> open /Users/dongju/Downloads/cryosparc_P161_J104_007_volume_map_sharp.mrc
Opened cryosparc_P161_J104_007_volume_map_sharp.mrc as #68, grid size
288,288,288, pixel 0.75, shown at level 0.0986, step 2, values float32
> select #68
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #68,1,-6.1047e-05,0.00027243,-12.352,6.1053e-05,1,-2.3363e-05,-135.18,-0.00027243,2.3379e-05,1,-33.458
> view matrix models
> #68,1,-6.1047e-05,0.00027243,-13.342,6.1053e-05,1,-2.3363e-05,-145.75,-0.00027243,2.3379e-05,1,-36.19
> ui mousemode right "rotate selected models"
> view matrix models
> #68,0.89939,-0.0071355,-0.43708,44.669,-0.12095,-0.9649,-0.23312,103.37,-0.42007,0.26253,-0.86868,179.11
> view matrix models
> #68,0.89831,-0.030642,-0.4383,47.444,-0.09885,-0.98609,-0.13366,92.714,-0.42811,0.16339,-0.88884,192.77
> view matrix models
> #68,0.89802,-0.040174,-0.43811,48.48,-0.089691,-0.99163,-0.092914,87.999,-0.43071,0.12273,-0.8941,197.99
> view matrix models
> #68,0.89787,-0.047179,-0.43773,49.209,-0.082886,-0.99458,-0.062818,84.39,-0.43239,0.092684,-0.89691,201.7
> view matrix models
> #68,0.89893,-0.015739,-0.43781,45.721,-0.11294,-0.9739,-0.19689,99.631,-0.42328,0.22643,-0.87725,184.24
> view matrix models
> #68,0.89856,-0.023864,-0.43819,46.676,-0.10529,-0.98108,-0.16248,95.928,-0.42603,0.19214,-0.88407,188.95
> view matrix models
> #68,0.89861,-0.022647,-0.43815,46.535,-0.10644,-0.98008,-0.16765,96.493,-0.42563,0.19729,-0.88313,188.25
> view matrix models
> #68,0.065555,0.97384,0.21756,-39.434,0.98867,-0.033879,-0.14626,-126.62,-0.13506,0.22468,-0.96503,162.38
> view matrix models
> #68,-0.15873,0.86279,0.48,-30.888,-0.39568,0.38983,-0.83155,50.949,-0.90457,-0.32192,0.27951,173.07
> view matrix models
> #68,-0.080275,0.80672,0.58545,-44.558,-0.86641,0.23394,-0.44115,77.572,-0.49285,-0.54265,0.68017,109.6
> volume #68 level 0.2481
> view matrix models
> #68,-0.012401,0.78705,0.61677,-52.73,-0.9836,0.1014,-0.14918,77.623,-0.17995,-0.6085,0.77288,74.024
> view matrix models
> #68,0.20256,0.94412,0.25999,-60.087,0.8527,-0.3006,0.42725,-132.47,0.48153,0.13515,-0.86595,73.364
> view matrix models
> #68,0.15154,0.96062,0.23291,-53.8,0.95793,-0.20083,0.20505,-134.14,0.24375,0.19204,-0.95064,100.98
> volume #68 level 0.4615
> view matrix models
> #68,0.18588,0.95044,0.24922,-58.008,0.89641,-0.2679,0.35311,-134.41,0.40238,0.15776,-0.90178,82.702
> view matrix models
> #68,0.17227,0.95489,0.2419,-56.303,0.92492,-0.24129,0.29378,-134.7,0.33889,0.17313,-0.92476,90.167
> view matrix models
> #68,0.24131,0.92427,0.29578,-65.695,0.69908,-0.37696,0.60761,-125.58,0.6731,0.060151,-0.7371,47.93
> view matrix models
> #68,0.22858,0.93182,0.2819,-63.789,0.75981,-0.35179,0.54674,-129.07,0.60863,0.089218,-0.78842,56.744
> ui mousemode right "translate selected models"
> view matrix models
> #68,0.22858,0.93182,0.2819,-57.943,0.75981,-0.35179,0.54674,-130.33,0.60863,0.089218,-0.78842,82.377
> ui mousemode right "rotate selected models"
> view matrix models
> #68,0.0068193,0.99995,-0.0075008,-13.927,0.71445,0.00037614,0.69969,-175.24,0.69965,-0.01013,-0.71441,75.69
> ui mousemode right select
> select clear
> volume #68 level 0.3334
> volume #68 level 0.2907
> volume #68 level 0.2694
> volume #68 level 0.2054
> volume #67 level 0.0563
> select #62
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #62,-0.38567,0.87373,0.29641,33.576,-0.51028,0.065659,-0.8575,214.92,-0.76868,-0.48196,0.42052,267.74
> ui mousemode right rotate
> ui mousemode right select
> select clear
> volume #62 level 0.6697
> volume #62 level 0.546
> volume #62 level 0.4361
> volume #62 level 0.3536
> volume #67 level 0.04837
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #68 step 1
Drag select of 68 cryosparc_P161_J104_007_volume_map_sharp.mrc
> select clear
> volume #68 level 0.2784
> volume #68 level 0.5708
> volume #68 level 0.4977
> volume #68 level 0.4246
> volume #68 level 0.2541
> volume #68 level 0.3515
> volume #68 level 0.3028
===== Log before crash end =====
Log:
Startup Messages
---
warning | Could not find virtual screen for QCocoaScreen(0x6000023f1290, "DELL P2422H", QRect(1536,61 1920x1080), dpr=1, displayId=4128833, <NSScreen: 0x6000030f7660>) with displayId 4128833
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Could not find virtual screen for QCocoaScreen(0x6000023f1290, "DELL P2422H",
QRect(1536,61 1920x1080), dpr=1, displayId=4128833, <NSScreen:
0x6000030f7660>) with displayId 4128833
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
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: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0)
OS Loader Version: 580~2215
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 19 days, 23 hours, 32 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-019
Option ROM Version: 113-D32206U1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
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-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-Clipper: 0.23.1
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-ISOLDE: 1.8
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
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
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
pycollada: 0.8
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
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 , 4 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 4 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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