id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
18080	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
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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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
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX