id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16750	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-15.1.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Current thread 0x00000001ed0ab840 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in 
  File """", line 88 in _run_code
  File """", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, psutil._psutil_osx, psutil._psutil_posix, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy._lib._uarray._uarray, scipy.special._ufuncs_cxx, 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.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation (total: 104)


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===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Alphafold/AF-
> YNR021W-YeastCCDC47-model_v4.pdb"" format pdb

AF-YNR021W-YeastCCDC47-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for UPF0674 endoplasmic reticulum membrane
protein YNR021W (P53723) [more info...]  
  
Chain information for AF-YNR021W-YeastCCDC47-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | UPF0674 endoplasmic reticulum membrane protein YNR021W | YN8B_YEAST 1-404  
  
Computing secondary structure  

Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.  

> open 7tm3 fromDatabase pdb format mmcif

Summary of feedback from opening 7tm3 fetched from pdb  
---  
warnings | Atom HO5' is not in the residue template for G /q:1  
Atom HO5' is not in the residue template for G /u:1  
Atom HO5' is not in the residue template for C /v:1  
note | Fetching compressed mmCIF 7tm3 from http://files.rcsb.org/download/7tm3.cif  
  
7tm3 title:  
Structure of the rabbit 80S ribosome stalled on a 2-TMD Rhodopsin intermediate
in complex with the multipass translocon [more info...]  
  
Chain information for 7tm3 #2  
---  
Chain | Description | UniProt  
1 | Protein transport protein Sec61 subunit alpha isoform 1 | S61A1_CANLF 1-476  
2 | Protein transport protein Sec61 subunit beta | SC61B_CANLF 1-96  
3 | Protein transport protein Sec61 gamma |   
4 | Coiled-coil domain containing 47 | A0A8C0RJF2_CANLF 1-483  
5 | PAT complex subunit Asterix | A0A8C0TSD6_CANLF 1-106  
6 | Transmembrane protein 147 | A0A8C0RUW0_CANLF 1-224  
7 | Nicalin | A0A8C0S144_CANLF -41-521  
A | uL2 | G1TT27_RABIT 1-257  
B | Nascent chain |   
C | uL4 | G1SVW5_RABIT 1-425  
D | uL18 | G1SYJ6_RABIT 1-297  
E | eL6 | G1SKF7_RABIT 1-291  
F | uL30 | G1TUB1_RABIT 1-247  
G | eL8 | G1STW0_RABIT 1-319  
H | uL6 | G1SWI6_RABIT 1-192  
I | uL16 | B7NZQ2_RABIT 1-214  
J | uL5 | G1TUB8_RABIT 1-178  
K | 28S ribosomal RNA |   
L | eL13 | G1TPV0_RABIT 1-211  
M | eL14 | G1SZ12_RABIT 1-218  
N | eL15 | G1T0C1_RABIT 1-204  
O | uL13 |   
P | uL22 | G1TVT6_RABIT 1-184  
Q | eL18 |   
R | eL19 | G1TJR3_RABIT 1-196  
S | eL20 |   
T | eL21 | G1SHQ2_RABIT 1-160  
U | eL22 | G1TSG1_RABIT 1-128  
V | uL14 | G1T6D1_RABIT 1-140  
W | eL24 | G1SE28_RABIT 1-157  
X | uL23 | G1SE76_RABIT 1-156  
Y | uL24 | G1SQH0_RABIT 1-145  
Z | eL27 | G1TXF6_RABIT 1-136  
a | uL15 | G1SNY0_RABIT 1-148  
b | eL29 | G1SGR6_RABIT 1-226  
c | eL30 | G1TDL2_RABIT 1-115  
d | eL31 | G1SHG0_RABIT 1-125  
e | eL32 | G1U437_RABIT 1-135  
f | eL33 | G1SF08_RABIT 1-110  
g | eL34 | G1U945_RABIT 1-116  
h | uL29 | G1SIT5_RABIT 1-123  
i | eL36 | G1TTQ5_RABIT 1-105  
j | eL37 | U3KPD5_RABIT 1-97  
k | eL38 | G1U001_RABIT 1-70  
l | eL39 | G1TTN1_RABIT 1-51  
m | eL40 |   
n | eL41 | A0A087WNH4_RABIT 1-25  
o | eL42 | G1U344_RABIT 1-106  
p | eL43 | G1SY53_RABIT 1-92  
q | P-site tRNA |   
r | eL28 | G1U7L1_RABIT 1-137  
u | 5S ribosomal RNA |   
v | 5.8S ribosomal RNA |   
w | uL3 | G1TL06_RABIT 2-403  
  
Non-standard residues in 7tm3 #2  
---  
MG — magnesium ion  
ZN — zinc ion  
  

> hide surfaces

> select add #2

261738 atoms, 272680 bonds, 4073 pseudobonds, 12333 residues, 4 models
selected  

> hide #1 models

> show sel cartoons

> hide sel surfaces

> hide sel atoms

> ui mousemode right ""translate selected models""

> view matrix models #2,1,0,0,91.078,0,1,0,144.55,0,0,1,13.92

> ui mousemode right select

Drag select of 7189 residues, 4 pseudobonds  

> select up

207311 atoms, 217953 bonds, 4 pseudobonds, 8791 residues, 2 models selected  

> select up

223410 atoms, 234211 bonds, 4 pseudobonds, 9768 residues, 2 models selected  

> hide sel

> hide sel cartoons

Drag select of 170 residues  
Drag select of 115 residues  

> undo

> hide sel cartoons

Drag select of 1 residues  

> hide sel cartoons

Drag select of 80 residues  

> select up

1771 atoms, 1783 bonds, 106 residues, 1 model selected  

> select up

2045 atoms, 2061 bonds, 124 residues, 1 model selected  

> hide sel cartoons

> select #2/H

3113 atoms, 3132 bonds, 190 residues, 1 model selected  

> hide sel cartoons

> select #2/h

2145 atoms, 2153 bonds, 122 residues, 1 model selected  

> hide sel cartoons

> select #2/l

927 atoms, 939 bonds, 50 residues, 1 model selected  

> hide sel cartoons

> select #2/Y

2320 atoms, 2337 bonds, 134 residues, 1 model selected  

> hide sel cartoons

> show #1 models

> select add #2

261738 atoms, 272680 bonds, 4073 pseudobonds, 12333 residues, 4 models
selected  

> select add #1

265062 atoms, 276074 bonds, 4073 pseudobonds, 12737 residues, 5 models
selected  

> hide #!2 models

> show #!2 models

> select subtract #2

3324 atoms, 3394 bonds, 404 residues, 1 model selected  

> select add #2.1

3324 atoms, 3394 bonds, 3775 pseudobonds, 404 residues, 2 models selected  

> select add #2

265062 atoms, 276074 bonds, 4073 pseudobonds, 12737 residues, 5 models
selected  

> select subtract #2.1

265062 atoms, 276074 bonds, 298 pseudobonds, 12737 residues, 4 models selected  

> select add #2

265062 atoms, 276074 bonds, 4073 pseudobonds, 12737 residues, 5 models
selected  

Cell requested for row 1 is out of bounds for table with 5 rows! Resizing
table model.  

> select subtract #2

3324 atoms, 3394 bonds, 404 residues, 1 model selected  

> ui mousemode right ""translate selected models""

> view matrix models #1,1,0,0,403.28,0,1,0,187.18,0,0,1,424.89

> view matrix models #1,1,0,0,394.53,0,1,0,185.82,0,0,1,419.48

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,0.56002,-0.33857,0.75614,393.16,0.82675,0.1694,-0.53646,192.2,0.053537,0.92557,0.37478,417.35

> view matrix models
> #1,0.26457,-0.23747,0.93467,392.84,0.93401,-0.17817,-0.30965,191.97,0.24006,0.95491,0.17466,417.65

> ui mousemode right ""translate selected models""

> view matrix models
> #1,0.26457,-0.23747,0.93467,403.29,0.93401,-0.17817,-0.30965,255.1,0.24006,0.95491,0.17466,469.12

> view matrix models
> #1,0.26457,-0.23747,0.93467,448.77,0.93401,-0.17817,-0.30965,264.22,0.24006,0.95491,0.17466,357.33

> view matrix models
> #1,0.26457,-0.23747,0.93467,483.59,0.93401,-0.17817,-0.30965,268.86,0.24006,0.95491,0.17466,303.25

> view matrix models
> #1,0.26457,-0.23747,0.93467,506.25,0.93401,-0.17817,-0.30965,360.23,0.24006,0.95491,0.17466,246.58

> view matrix models
> #1,0.26457,-0.23747,0.93467,496.04,0.93401,-0.17817,-0.30965,408.91,0.24006,0.95491,0.17466,279.83

> view matrix models
> #1,0.26457,-0.23747,0.93467,484.16,0.93401,-0.17817,-0.30965,401.09,0.24006,0.95491,0.17466,286.08

> mmaker #1 to #2/4

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7tm3, chain 4 (#2) with AF-YNR021W-YeastCCDC47-model_v4.pdb, chain
A (#1), sequence alignment score = 399.9  
RMSD between 107 pruned atom pairs is 1.140 angstroms; (across all 318 pairs:
14.395)  
  

> view matrix models
> #1,0.37726,0.42539,-0.82263,488.41,-0.11789,0.9031,0.41294,397.28,0.91857,-0.058808,0.39085,289.4

> color #1 #ff2600ff

> rainbow sel

> save /Users/annguyen/Desktop/image1.png supersample 3

> color #1 #ff9300ff

> set bgColor white

> set bgColor #ffffff00

> save /Users/annguyen/Desktop/image2.png supersample 3

> close session

> open /Users/annguyen/Downloads/cryosparc_P4_J457_class_01_final_volume.mrc

Opened cryosparc_P4_J457_class_01_final_volume.mrc as #1, grid size
192,192,192, pixel 2.18, shown at level 1.33, step 1, values float32  

> volume #1 level 0.3098

> save /Users/annguyen/Desktop/image3.png supersample 3

> open /Users/annguyen/Downloads/cryosparc_P4_J457_class_00_final_volume.mrc

Opened cryosparc_P4_J457_class_00_final_volume.mrc as #2, grid size
192,192,192, pixel 2.18, shown at level 0.858, step 1, values float32  

> volume #2 level 0.3912

> save /Users/annguyen/Desktop/image4.png supersample 3

> open ""/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Chimera
> sessions/10-01-25-Fit map of ChaeRibo-Sec72 local refinement.cxs"" format
> session

Opened cryosparc_P4_J32_010_volume_map.mrc as #2, grid size 450,450,450, pixel
0.97, shown at level 0.286, step 1, values float32  
Opened cryosparc_P4_J429_class_01_final_volume.mrc as #14, grid size
192,192,192, pixel 2.02, shown at level 0.465, step 1, values float32  
Opened cryosparc_P4_J431_003_volume_map.mrc z flip as #16, grid size
400,400,400, pixel 0.97, shown at level 0.162, step 1, values float32  
Opened cryosparc_P4_J430_004_volume_map_sharp.mrc z flip as #17, grid size
400,400,400, pixel 0.97, shown at level 0.351, step 1, values float32  
Opened cryosparc_P4_J436_003_volume_map.mrc as #1, grid size 400,400,400,
pixel 0.97, shown at level 0.669, step 2, values float32  
Opened cryosparc_P4_J436_003_volume_map.mrc z flip as #5, grid size
400,400,400, pixel 0.97, shown at level 0.126, step 1, values float32  
Opened cryosparc_P4_J437_003_volume_map.mrc as #6, grid size 400,400,400,
pixel 0.97, shown at level 0.669, step 2, values float32  
Opened cryosparc_P4_J437_003_volume_map.mrc z flip as #12, grid size
400,400,400, pixel 0.97, shown at level 0.0853, step 1, values float32  
Opened cryosparc_P4_J439_003_volume_map.mrc as #13, grid size 400,400,400,
pixel 0.97, shown at level 0.669, step 2, values float32  
Opened cryosparc_P4_J439_003_volume_map.mrc z flip as #18, grid size
400,400,400, pixel 0.97, shown at level 0.228, step 1, values float32  
Opened 241024_P4_J458_004_volume_map.mrc as #19, grid size 400,400,400, pixel
0.97, shown at level 0.0325, step 1, values float32  
Opened emd_12977 map of 7old.map as #20, grid size 486,486,486, pixel 1.1,
shown at level 2.25, step 1, values float32  
Opened cryosparc_P4_J508_007_volume_map.mrc as #21, grid size 432,432,432,
pixel 0.97, shown at level 0.107, step 1, values float32  
Opened cryosparc_P4_J513_005_volume_map.mrc as #22, grid size 432,432,432,
pixel 0.97, shown at level 0.0523, step 1, values float32  
Opened cryosparc_P4_J458_004_1 to 60 uM.mrc as #23, grid size 400,400,400,
pixel 0.97, shown at level 0.0277, step 1, values float32  
Opened cryosparc_P4_J459_004_1 to 60 uM.mrc z flip as #25, grid size
400,400,400, pixel 0.97, shown at level 0.0372, step 1, values float32  
opened ChimeraX session  

> hide #!20 models

> hide #!22 models

> hide #!8 models

> open /Users/annguyen/Downloads/cryosparc_P4_J470_004_volume_map.mrc

Opened cryosparc_P4_J470_004_volume_map.mrc as #24, grid size 432,432,432,
pixel 0.97, shown at level 0.643, step 2, values float32  

> volume #24 level 0.6425

> volume #24 step 1

> volume #24 level 0.2073

> ui tool show ""Side View""

> ui tool show EMalign

> show #!23 models

> hide #!23 models

> show #!20 models

Aligning the volumes using EMalign took 66.59 seconds  
  
Rotation:  
[[0.224 0.542 0.810],  
[-0.974 0.144 0.173]  
[-0.023 -0.828 0.560]]  
Translation:  
[-22.500, -68.625, -24.750]  
Reflection:  
1  
  
Applying 'Fit in Map' to perform additional refinement:  
Fit map cryosparc_P4_J470_004_volume_map.mrc in map emd_12977 map of 7old.map
using 3779673 points  
correlation = 0.2031, correlation about mean = 0.01422, overlap = 6.094e+05  
steps = 524, shift = 57.7, angle = 21.2 degrees  
  
Position of cryosparc_P4_J470_004_volume_map.mrc (#24) relative to emd_12977
map of 7old.map (#20) coordinates:  
Matrix rotation and translation  
0.88423432 -0.42930989 -0.18390931 224.94048323  
0.28488345 0.18374703 0.94078606 -126.92981832  
-0.37009598 -0.88426806 0.28477871 557.64594680  
Axis -0.92706142 0.09457609 0.36278436  
Axis point 0.00000000 311.71591871 403.53963021  
Rotation angle (degrees) 79.84102241  
Shift along axis -18.23294052  
  
\----------------------------------------------------------------------------------------  
Stats before alignment:  
correlation = 0.0756, correlation about mean = 0.0620, overlap = 551750.015  
\----------------------------------------------------------------------------------------  
Stats after alignning with EMalign:  
correlation = 0.0880, correlation about mean = 0.0843, overlap = 460238.537  
\----------------------------------------------------------------------------------------  
Stats after refining with Fit in Map:  
correlation = 0.1191, correlation about mean = 0.1156, overlap = 622991.638  
\----------------------------------------------------------------------------------------  

> hide #!20 models

> clip off

Aligning the volumes using EMalign took 44.26 seconds  
  
Rotation:  
[[0.414 -0.775 -0.478],  
[0.902 0.279 0.329]  
[-0.121 -0.568 0.814]]  
Translation:  
[56.250, 29.250, -60.750]  
Reflection:  
1  
  
Applying 'Fit in Map' to perform additional refinement:  
Fit map cryosparc_P4_J470_004_volume_map.mrc in map emd_12977 map of 7old.map
using 3779088 points  
correlation = 0.2432, correlation about mean = 0.09047, overlap = 7.632e+05  
steps = 516, shift = 33.2, angle = 14.5 degrees  
  
Position of cryosparc_P4_J470_004_volume_map.mrc (#24) relative to emd_12977
map of 7old.map (#20) coordinates:  
Matrix rotation and translation  
0.95882622 -0.28389857 0.00733729 82.15337832  
0.06446600 0.24274092 0.96794677 -101.80044306  
-0.27657976 -0.92761976 0.25104816 544.04216957  
Axis -0.97302763 0.14573962 0.17882166  
Axis point 0.00000000 306.92126698 345.66523677  
Rotation angle (degrees) 76.92021498  
Shift along axis 2.51265733  
  
\----------------------------------------------------------------------------------------  
Stats before alignment:  
correlation = 0.1191, correlation about mean = 0.1156, overlap = 622991.638  
\----------------------------------------------------------------------------------------  
Stats after alignning with EMalign:  
correlation = 0.1204, correlation about mean = 0.1169, overlap = 629921.297  
\----------------------------------------------------------------------------------------  
Stats after refining with Fit in Map:  
correlation = 0.1511, correlation about mean = 0.1477, overlap = 790859.233  
\----------------------------------------------------------------------------------------  

> show #!20 models

> color #24 #b2ffff93 models

> color #24 #b2ffff94 models

> volume #25 level 0.2488

> volume #25 level 0.3123

> hide #!25 models

> volume #25 level 0.4441

> hide #!25 models

> volume #25 level 0.5044

> hide #!20 models

> hide #!25 models

> volume #24 level 0.4157

> color #24 #b2ffffff models

> volume #24 level 0.4494

> volume #24 level 0.5086

> show #!1 models

> select add #24

2 models selected  

> view matrix models
> #24,0.81486,0.39076,0.42815,-505.06,-0.35236,0.9204,-0.16942,358.66,-0.46027,-0.012808,0.88769,38.433

> volume #2 level 0.05095

> hide #!2 models

> volume #1 level 0.3733

> hide #!1 models

> volume #24 level 0.4635

> volume #24 level 0.4607

> volume #24 level 0.4691

> volume #24 level 0.3931

> volume #24 level 0.3678

> volume #24 level 0.3565

> volume #24 level 0.2777

> volume #24 level 0.2327

> volume #24 level 0.2298

> volume #24 level 0.2045

> volume #24 level 0.2383

> volume #24 level 0.2862

> volume #24 level 0.289

> volume #24 level 0.3171

> volume #24 level 0.3199

> volume #24 level 0.3396

> volume #24 level 0.3537

> volume #24 level 0.3594

> volume #24 level 0.365

> volume #24 level 0.41

> volume #24 level 0.4128

> volume #24 level 0.4241

> volume #24 level 0.4382

> volume #24 level 0.4438

> volume #24 level 0.4607

> volume #24 level 0.4663

> volume #24 level 0.4832

> volume #24 level 0.4945

> volume #24 level 0.4973

> show #!7 models

> view matrix models
> #24,0.81486,0.39076,0.42815,-566.23,-0.35236,0.9204,-0.16942,342.63,-0.46027,-0.012808,0.88769,14.796

> view matrix models
> #24,0.81486,0.39076,0.42815,-268.56,-0.35236,0.9204,-0.16942,-79.513,-0.46027,-0.012808,0.88769,80.645

> view matrix models
> #24,0.81486,0.39076,0.42815,-305.94,-0.35236,0.9204,-0.16942,-70.442,-0.46027,-0.012808,0.88769,68.055

> ui mousemode right ""rotate selected models""

> view matrix models
> #24,-0.2131,0.20263,-0.95579,406.52,-0.075588,0.97191,0.2229,-268.19,0.9741,0.11975,-0.19179,-20.854

> view matrix models
> #24,-0.96541,-0.26056,-0.0091224,433.93,-0.22953,0.8328,0.50374,-277.62,-0.12366,0.48841,-0.86381,373.54

> view matrix models
> #24,-0.99084,0.13161,0.030162,338.08,0.111,0.66681,0.73692,-395.16,0.076877,0.73352,-0.67531,209.86

> view matrix models
> #24,-0.98485,0.16651,0.048353,323.14,0.15176,0.69297,0.70481,-402.47,0.083848,0.70148,-0.70774,224.92

> ui mousemode right ""translate selected models""

> view matrix models
> #24,-0.98485,0.16651,0.048353,365.7,0.15176,0.69297,0.70481,-213.67,0.083848,0.70148,-0.70774,359.72

> view matrix models
> #24,-0.98485,0.16651,0.048353,422.13,0.15176,0.69297,0.70481,-162.82,0.083848,0.70148,-0.70774,259.43

> fitmap #7 inMap #24

Fit molecule 7old (#7) to map cryosparc_P4_J470_004_volume_map.mrc (#24) using
214209 atoms  
average map value = 0.255, steps = 272  
shifted from previous position = 32.6  
rotated from previous position = 12.8 degrees  
atoms outside contour = 166436, contour level = 0.4973  
  
Position of 7old (#7) relative to cryosparc_P4_J470_004_volume_map.mrc (#24)
coordinates:  
Matrix rotation and translation  
-0.99195802 -0.08597927 0.09288084 537.06027100  
-0.10979205 0.94963433 -0.29349676 135.06712643  
-0.06296820 -0.30133404 -0.95143723 646.59826071  
Axis -0.04964939 0.98730837 -0.15085465  
Axis point 284.89643728 0.00000000 322.85872966  
Rotation angle (degrees) 175.47315242  
Shift along axis 9.14583899  
  

> color #24 #b2ffffcf models

> color #24 #b2ffffff models

> view matrix models
> #24,-0.98485,0.16651,0.048353,299.66,0.15176,0.69297,0.70481,-284,0.083848,0.70148,-0.70774,156.33

> view matrix models
> #24,-0.98485,0.16651,0.048353,386.04,0.15176,0.69297,0.70481,-144.87,0.083848,0.70148,-0.70774,261.84

> color #24 #b2ffffd3 models

> view matrix models
> #24,-0.98485,0.16651,0.048353,417.11,0.15176,0.69297,0.70481,-156.27,0.083848,0.70148,-0.70774,232.68

> volume flip #24 axis z

Opened cryosparc_P4_J470_004_volume_map.mrc z flip as #26, grid size
432,432,432, pixel 1.24, shown at step 1, values float32  

> volume #24 color #b2ffff

> view matrix models
> #24,-0.98485,0.16651,0.048353,472.39,0.15176,0.69297,0.70481,-155.59,0.083848,0.70148,-0.70774,202

> hide #!26 models

> show #!26 models

> hide #!24 models

> select subtract #24

Nothing selected  

> select add #26

2 models selected  

> color #26 #b2ffffff models

> view matrix models
> #26,-0.98485,0.16651,0.048353,336.66,0.15176,0.69297,0.70481,-97.35,0.083848,0.70148,-0.70774,209.36

> view matrix models
> #26,-0.98485,0.16651,0.048353,175.16,0.15176,0.69297,0.70481,20.1,0.083848,0.70148,-0.70774,148.72

> view matrix models
> #26,-0.98485,0.16651,0.048353,171.21,0.15176,0.69297,0.70481,47.196,0.083848,0.70148,-0.70774,131.73

> ui mousemode right ""rotate selected models""

> view matrix models
> #26,0.51227,-0.2572,-0.81941,91.979,-0.74447,0.34271,-0.57299,670.99,0.42819,0.90355,-0.015918,-172.36

> view matrix models
> #26,-0.12566,-0.077561,-0.98904,256.86,-0.77327,0.63221,0.048665,460.39,0.6215,0.77091,-0.13942,-161.72

> close #26

> show #!24 models

> ui mousemode right ""translate selected models""

> select add #24

2 models selected  

> view matrix models
> #24,-0.98485,0.16651,0.048353,464.88,0.15176,0.69297,0.70481,-108.42,0.083848,0.70148,-0.70774,232.32

> color #24 #b2ffffd7 models

> color #24 #b2ffffd6 models

> ui mousemode right ""translate selected models""

> view matrix models
> #24,-0.98485,0.16651,0.048353,466.82,0.15176,0.69297,0.70481,-146.01,0.083848,0.70148,-0.70774,226.3

> view matrix models
> #24,-0.98485,0.16651,0.048353,421.12,0.15176,0.69297,0.70481,-111.7,0.083848,0.70148,-0.70774,205.63

> view matrix models
> #24,-0.98485,0.16651,0.048353,418.89,0.15176,0.69297,0.70481,-165.44,0.083848,0.70148,-0.70774,234.98

> volume #24 level 0.6606

> fitmap #7 inMap #24

Fit molecule 7old (#7) to map cryosparc_P4_J470_004_volume_map.mrc (#24) using
214209 atoms  
average map value = 0.2548, steps = 160  
shifted from previous position = 26.5  
rotated from previous position = 3.67 degrees  
atoms outside contour = 187584, contour level = 0.66059  
  
Position of 7old (#7) relative to cryosparc_P4_J470_004_volume_map.mrc (#24)
coordinates:  
Matrix rotation and translation  
-0.98776464 -0.07472793 0.13688219 522.41411799  
-0.11720443 0.93473165 -0.33546964 153.16751387  
-0.10287916 -0.34740824 -0.93205332 667.73111883  
Axis -0.04897138 0.98348548 -0.17423582  
Axis point 285.83482002 0.00000000 331.17234155  
Rotation angle (degrees) 172.99859438  
Shift along axis 8.71200957  
  

> view matrix models
> #24,-0.98485,0.16651,0.048353,400.13,0.15176,0.69297,0.70481,-163.68,0.083848,0.70148,-0.70774,205.82

> hide #!24 models

> select subtract #24

Nothing selected  

> hide #!7 models

> show #!24 models

> color #24 #b2ffffff models

> volume #24 level 0.4523

> volume #24 level 0.3059

> close #24

> open ""/Volumes/TOSHIBA EXT/CryoSparc
> /cryosparc_P4_J470_004_volume_map_sharp.mrc-2.download/""

'/Volumes/TOSHIBA EXT/CryoSparc
/cryosparc_P4_J470_004_volume_map_sharp.mrc-2.download/' has no suffix  

> show #!22 models

> hide #!22 models

> show #!21 models

> hide #!21 models

> close session

> open ""/Volumes/TOSHIBA EXT/CryoSparc /cryosparc_P4_J520_mask.mrc""

Opened cryosparc_P4_J520_mask.mrc as #1, grid size 432,432,432, pixel 0.97,
shown at level 0.922, step 2, values float32  

> open ""/Volumes/TOSHIBA EXT/CryoSparc /cryosparc_P4_J470_004_volume_map
> (1).mrc""

Opened cryosparc_P4_J470_004_volume_map (1).mrc as #2, grid size 432,432,432,
pixel 0.97, shown at level 0.643, step 2, values float32  

> volume #1 color #b2b2b2bc

> volume #1 color #b2b2b2bd

> volume #2 step 1

> volume #2 level 0.4234

> volume #2 level 0.1376

> ui tool show ""Side View""

> volume #2 level 0.1618

> volume #2 level 0.1296

> save /Users/annguyen/Desktop/image5.png supersample 3

> save /Users/annguyen/Desktop/image6.png supersample 3

> close session

> open ""/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Chimera
> sessions/13-02-25 fit TPR domian in map of RiboSec72.cxs""

Opened cryosparc_P26_J18_003_volume_map.mrc as #1, grid size 320,320,320,
pixel 1.34, shown at level 0.245, step 1, values float32  
Opened cryosparc_P26_J18_003_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 1.34, shown at level 1.28, step 2, values float32  
Opened cryosparc_P4_J508_007_volume_map.mrc as #15, grid size 432,432,432,
pixel 0.97, shown at level 0.469, step 1, values float32  
Opened cryosparc_P4_J532_002_with particle substraction center.mrc as #16,
grid size 432,432,432, pixel 0.97, shown at level 0.0316, step 1, values
float32  
Opened cryosparc_P4_J521_005_wo particle substraction side.mrc as #17, grid
size 432,432,432, pixel 0.97, shown at level 0.111, step 1, values float32  
Opened cryosparc_P4_J527_005_wo particle substrction center.mrc as #18, grid
size 432,432,432, pixel 0.97, shown at level 0.111, step 1, values float32  
Opened cryosparc_P4_J531_002_with particle substraction side.mrc as #19, grid
size 432,432,432, pixel 0.97, shown at level 0.05, step 1, values float32  
opened ChimeraX session  

> save /Users/annguyen/Desktop/image7.png supersample 3

> hide #!16 models

> show #!17 models

> hide #!17 models

> show #!18 models

> hide #!18 models

> show #!19 models

> hide #!19 models

> show #!18 models

> hide #!18 models

> show #!17 models

> hide #!17 models

> show #!16 models

> save /Users/annguyen/Desktop/image8.png supersample 3

> hide #!16 models

> show #!17 models

> color #17 #919191d3 models

> color #17 #919191bd models

> volume #17 level 0.1193

> volume #17 level 0.1401

> volume #17 level 0.1027

> ui tool show ""Hide Dust""

> surface dust #17 size 5.82

> color #17 #91919187 models

> color #17 #91919184 models

> color #17 #91919185 models

> clip off

> volume #17 level 0.1484

> volume #17 level 0.1941

> volume #17 level 0.02374

> show #!16 models

> hide #!17 models

> save /Users/annguyen/Desktop/image9.png supersample 3

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/annguyen/Desktop/movie1.mp4

Movie saved to /Users/annguyen/Desktop/movie1.mp4  
  

> save /Users/annguyen/Desktop/image10.png supersample 3

> hide #!16 models

> show #!17 models

> volume #17 level 0.06114

> volume #17 level 0.1276

> volume #17 level 0.1235

> volume #17 level 0.111

> show #!16 models

> hide #!17 models

> volume #16 level 0.111

> volume #16 level 0.03447

> volume #16 level 0.03141

> hide #!16 models

> show #!17 models

> save /Users/annguyen/Desktop/image7.png supersample 3

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!16 models

> save /Users/annguyen/Desktop/image8.png supersample 3

> hide #!16 models

> show #!15 models

> volume #15 level 0.09918

> color #15 #588b94ad models

> color #15 #588b949d models

> color #15 #588b9497 models

> color #15 #588b9496 models

> color #15 #ecefefff models

> color #15 #929292ff models

> color #15 darkgrey models

> color #15 #a9a9a9a8 models

> open ""/Volumes/TOSHIBA EXT/CryoSparc /110125_P4_J470_004_volume_map.mrc""

Opened 110125_P4_J470_004_volume_map.mrc as #20, grid size 432,432,432, pixel
0.97, shown at level 0.643, step 2, values float32  

> fitmap #20 to #15

Expected a keyword  

> ui tool show ""Fit in Map""

> volume #20 level 0.6425

> volume #20 step 1

> fitmap #20 inMap #15

Fit map 110125_P4_J470_004_volume_map.mrc in map
cryosparc_P4_J508_007_volume_map.mrc using 805166 points  
correlation = 0.5839, correlation about mean = 0.02471, overlap = 1.385e+05  
steps = 560, shift = 10.2, angle = 23.5 degrees  
  
Position of 110125_P4_J470_004_volume_map.mrc (#20) relative to
cryosparc_P4_J508_007_volume_map.mrc (#15) coordinates:  
Matrix rotation and translation  
-0.98428643 -0.17517813 0.02220026 456.74807319  
0.15184765 -0.90388049 -0.39992794 443.73306515  
0.09012502 -0.39027259 0.91627768 73.49476206  
Axis 0.02889570 -0.20327929 0.97869432  
Axis point 208.26201902 249.13621015 0.00000000  
Rotation angle (degrees) 170.38234946  
Shift along axis -5.07478190  
  

> ui tool show EMalign

Aligning the volumes using EMalign took 41.50 seconds  
  
Rotation:  
[[1.000 -0.003 0.021],  
[0.003 1.000 -0.010]  
[-0.021 0.010 1.000]]  
Translation:  
[0.000, 0.000, 0.000]  
Reflection:  
0  
  
Applying 'Fit in Map' to perform additional refinement:  
Fit map 110125_P4_J470_004_volume_map.mrc in map
cryosparc_P4_J508_007_volume_map.mrc using 805293 points  
correlation = 0.6057, correlation about mean = 0.03729, overlap = 1.483e+05  
steps = 168, shift = 6.46, angle = 7.44 degrees  
  
Position of 110125_P4_J470_004_volume_map.mrc (#20) relative to
cryosparc_P4_J508_007_volume_map.mrc (#15) coordinates:  
Matrix rotation and translation  
-0.98360871 -0.17003199 0.06002529 445.08953919  
0.11631208 -0.85266107 -0.50935313 464.32653872  
0.13778756 -0.49402251 0.85846162 100.85272092  
Axis 0.05159898 -0.26172802 0.96376138  
Axis point 201.86600584 263.10761087 0.00000000  
Rotation angle (degrees) 171.45677611  
Shift along axis -1.36314246  
  
\----------------------------------------------------------------------------------------  
Stats before alignment:  
correlation = 0.3252, correlation about mean = 0.3136, overlap = 366124.319  
\----------------------------------------------------------------------------------------  
Stats after alignning with EMalign:  
correlation = 0.3253, correlation about mean = 0.3195, overlap = 366217.448  
\----------------------------------------------------------------------------------------  
Stats after refining with Fit in Map:  
correlation = 0.3432, correlation about mean = 0.3375, overlap = 386350.541  
\----------------------------------------------------------------------------------------  

> select add #20

2 models selected  

> view matrix models
> #20,0.97877,0.14201,-0.1478,146.08,-0.055502,0.87778,0.47583,-221.39,0.19731,-0.45753,0.86703,132.15

> view matrix models
> #20,0.97877,0.14201,-0.1478,215.81,-0.055502,0.87778,0.47583,-305.26,0.19731,-0.45753,0.86703,167.67

> volume #20 level 0.06958

> volume #20 level 0.1269

> view matrix models
> #20,0.97877,0.14201,-0.1478,200.08,-0.055502,0.87778,0.47583,-271.99,0.19731,-0.45753,0.86703,133.16

> ui mousemode right ""move picked models""

> view matrix models
> #20,0.97877,0.14201,-0.1478,177.48,-0.055502,0.87778,0.47583,-246.68,0.19731,-0.45753,0.86703,60.84

> view matrix models
> #20,0.97877,0.14201,-0.1478,186.78,-0.055502,0.87778,0.47583,-228.7,0.19731,-0.45753,0.86703,119.27

> ui mousemode right ""rotate selected models""

> view matrix models
> #20,-0.99567,0.086636,-0.033657,591.51,-0.090674,-0.98498,0.14697,238.86,-0.020419,0.14939,0.98857,12.321

> ui mousemode right ""translate selected models""

> view matrix models
> #20,-0.99567,0.086636,-0.033657,532.39,-0.090674,-0.98498,0.14697,439.89,-0.020419,0.14939,0.98857,-40.753

> view matrix models
> #20,-0.99567,0.086636,-0.033657,411.69,-0.090674,-0.98498,0.14697,414.91,-0.020419,0.14939,0.98857,-31.323

Aligning the volumes using EMalign took 41.68 seconds  
  
Rotation:  
[[0.999 0.015 -0.035],  
[-0.016 0.999 -0.030]  
[0.034 0.031 0.999]]  
Translation:  
[0.000, 0.000, 0.000]  
Reflection:  
0  
  
Applying 'Fit in Map' to perform additional refinement:  
Fit map 110125_P4_J470_004_volume_map.mrc in map
cryosparc_P4_J508_007_volume_map.mrc using 4771418 points  
correlation = 0.9808, correlation about mean = 0.9194, overlap = 9.601e+05  
steps = 328, shift = 9.72, angle = 12.5 degrees  
  
Position of 110125_P4_J470_004_volume_map.mrc (#20) relative to
cryosparc_P4_J508_007_volume_map.mrc (#15) coordinates:  
Matrix rotation and translation  
0.99913639 0.01530929 0.03862765 -11.46678109  
-0.01606262 0.99968531 0.01926815 0.84750554  
-0.03832051 -0.01987197 0.99906789 11.76656337  
Axis -0.42611207 0.83772209 -0.34154091  
Axis point 314.14671375 0.00000000 286.47758692  
Rotation angle (degrees) 2.63235022  
Shift along axis 1.57734513  
  
\----------------------------------------------------------------------------------------  
Stats before alignment:  
correlation = 0.4967, correlation about mean = 0.4924, overlap = 559211.345  
\----------------------------------------------------------------------------------------  
Stats after alignning with EMalign:  
correlation = 0.4552, correlation about mean = 0.4506, overlap = 512497.332  
\----------------------------------------------------------------------------------------  
Stats after refining with Fit in Map:  
correlation = 0.9457, correlation about mean = 0.9456, overlap = 1064762.828  
\----------------------------------------------------------------------------------------  

> hide #!15 models

> color #20 #797979ff models

> color #20 #919191ff models

> color #20 #9191919c models

> color #20 #9191918c models

> volume #20 level 0.1139

> ui tool show ""Hide Dust""

> surface dust #20 size 5.82

> save /Users/annguyen/Desktop/image9.png supersample 3

> select add #16

4 models selected  

> select subtract #16

2 models selected  

> select subtract #20

Nothing selected  

> save /Users/annguyen/Desktop/image10.png supersample 3


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Volumes/TOSHIBA EXT/CryoSparc /cryosparc_P4_J598_003_volume_map.mrc""

Opened cryosparc_P4_J598_003_volume_map.mrc as #1, grid size 432,432,432,
pixel 0.97, shown at level 0.641, step 2, values float32  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: Z16U000NJD/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.41.5
      OS Loader Version: 11881.41.5

Software:

    System Software Overview:

      System Version: macOS 15.1.1 (24B91)
      Kernel Version: Darwin 24.1.0
      Time since boot: 7 days, 21 hours, 49 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL P3223QE:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMalign: 0.1.1
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    finufft: 2.3.1
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX