id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
17217	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-14.6.1-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 0x00007ff846a2adc0 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in 
  File """", line 88 in _run_code
  File """", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, scipy._lib._ccallback_c, 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.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.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, psutil._psutil_osx, psutil._psutil_posix, chimerax.alignment_algs._sw (total: 113)


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===== Log before crash start =====
Startup Messages  
---  
warning | Registration file '/Users/lukaskruckemeyer/Library/Application Support/ChimeraX/registration' has expired  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> ""/Users/lukaskruckemeyer/Documents/Universität/PhD/Structure_predictions/ChlH
> /Nostoc_ChlH_PPIX_Neurosnap-Boltz-1/output.cif""

Summary of feedback from opening
/Users/lukaskruckemeyer/Documents/Universität/PhD/Structure_predictions/ChlH
/Nostoc_ChlH_PPIX_Neurosnap-Boltz-1/output.cif  
---  
warning | Atom O39 is not in the residue template for LIG /B:1  
  
output.cif title:  
. [more info...]  
  
Chain information for output.cif #1  
---  
Chain | Description  
A | .  
  
Non-standard residues in output.cif #1  
---  
LIG — (LIG)  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

> color medium blue

> lighting flat

> color #1 #3a64d7ff

> select ::name=""LIG""

42 atoms, 46 bonds, 1 residue, 1 model selected  

> color sel orange

> ui mousemode right select

> select clear

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> open
> /Users/lukaskruckemeyer/Downloads/cryosparc_P7_J3142_008_volume_map_sharp.mrc

Opened cryosparc_P7_J3142_008_volume_map_sharp.mrc as #2, grid size
440,440,440, pixel 0.68, shown at level 0.0158, step 2, values float32  

> open
> /Users/lukaskruckemeyer/Downloads/cryosparc_P7_J3144_008_volume_map_sharp.mrc

Opened cryosparc_P7_J3144_008_volume_map_sharp.mrc as #3, grid size
440,440,440, pixel 0.68, shown at level 0.0165, step 2, values float32  

> volume #2 step 1

> volume #3 step 1

> surface dust #2 size 6.8

> surface dust #3 size 6.8

> volume #2 level 0.09804

> volume #3 level 0.1116

> view #2 clip false

> select add #3

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #3,-0.81989,0.40223,-0.40743,271.94,0.40583,0.91027,0.081981,-59.276,0.40384,-0.09813,-0.90955,247.28

> ui mousemode right ""rotate selected models""

> ui mousemode right ""translate selected models""

> view matrix models
> #3,-0.81989,0.40223,-0.40743,300.75,0.40583,0.91027,0.081981,7.1751,0.40384,-0.09813,-0.90955,231.51

> volume flip #2

Opened cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip as #4, grid size
440,440,440, pixel 0.68, shown at step 1, values float32  

> close #2

> select subtract #3

Nothing selected  

> select add #4

2 models selected  

> view matrix models #4,1,0,0,-40.725,0,1,0,5.26,0,0,1,10.228

> select subtract #4

Nothing selected  

> select add #3

2 models selected  

> ui mousemode right ""rotate selected models""

> ui mousemode right ""translate selected models""

> view matrix models
> #3,-0.81989,0.40223,-0.40743,271.92,0.40583,0.91027,0.081981,-77.776,0.40384,-0.09813,-0.90955,257.09

> view matrix models
> #3,-0.81989,0.40223,-0.40743,232.84,0.40583,0.91027,0.081981,-54.341,0.40384,-0.09813,-0.90955,243.02

> view matrix models
> #3,-0.81989,0.40223,-0.40743,226.09,0.40583,0.91027,0.081981,-53.148,0.40384,-0.09813,-0.90955,242.88

> ui mousemode right ""translate selected models""

> ui mousemode right ""rotate selected models""

> view matrix models
> #3,0.91121,0.15081,-0.38333,2.8257,-0.28049,0.90867,-0.30925,109.44,0.30169,0.38932,0.8703,-89.648

> ui mousemode right ""translate selected models""

> view matrix models
> #3,0.91121,0.15081,-0.38333,0.2304,-0.28049,0.90867,-0.30925,101.38,0.30169,0.38932,0.8703,-84.426

> matchmaker #3 to #4

No 'to' model specified  

> fitmap #3 inMap #4

Fit map cryosparc_P7_J3144_008_volume_map_sharp.mrc in map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip using 93678 points  
correlation = 0.2863, correlation about mean = 0.07494, overlap = 718.5  
steps = 120, shift = 2.32, angle = 12.2 degrees  
  
Position of cryosparc_P7_J3144_008_volume_map_sharp.mrc (#3) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
0.87724344 0.34026154 -0.33862373 9.17238215  
-0.44705404 0.83605653 -0.31804428 132.72338424  
0.17489034 0.43038536 0.88554040 -82.91424940  
Axis 0.62288960 -0.42737828 -0.65525289  
Axis point 271.76070074 77.16439868 0.00000000  
Rotation angle (degrees) 36.92523028  
Shift along axis 3.32009168  
  

> hide #!3 models

> hide #!4 models

> select subtract #3

Nothing selected  

> show #!4 models

> volume #4 level 0.1121

> show #!3 models

> hide #!4 models

> volume flip #3

Opened cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip as #2, grid size
440,440,440, pixel 0.68, shown at step 1, values float32  

> close #3

> show #!4 models

> fitmap #2 inMap #4

Fit map cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip in map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip using 93678 points  
correlation = 0.295, correlation about mean = 0.1092, overlap = 731.8  
steps = 124, shift = 4.62, angle = 10.3 degrees  
  
Position of cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip (#2) relative
to cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
0.83637651 0.48870777 -0.24827209 -16.45094484  
-0.54635926 0.77986309 -0.30545885 156.22040741  
0.04433812 0.39112437 0.91926919 -60.52736312  
Axis 0.54357354 -0.22833620 -0.80770687  
Axis point 239.87809802 118.73060784 0.00000000  
Rotation angle (degrees) 39.84733788  
Shift along axis 4.27529386  
  

> ui mousemode right ""rotate selected models""

> select add #2

2 models selected  

> view matrix models
> #2,-0.70817,-0.25695,0.65763,156.59,0.13971,0.86201,0.48725,-68.834,-0.69208,0.43693,-0.57456,269.74

> fitmap #2 inMap #4

Fit map cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip in map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip using 93678 points  
correlation = 0.2795, correlation about mean = 0.06207, overlap = 745.8  
steps = 68, shift = 1.07, angle = 5.19 degrees  
  
Position of cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip (#2) relative
to cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
-0.73606997 -0.23061148 0.63641130 199.83138753  
0.09301636 0.89679966 0.43254864 -64.32156799  
-0.67048412 0.37758273 -0.63865665 274.28912318  
Axis -0.04079130 0.96987324 0.24017069  
Axis point 153.57248499 0.00000000 105.23263123  
Rotation angle (degrees) 137.64319495  
Shift along axis -4.65894103  
  

> view matrix models
> #2,-0.70315,-0.22165,0.67561,147.11,0.11442,0.90252,0.41517,-60.611,-0.70177,0.36923,-0.60925,286.2

> ui mousemode right ""translate selected models""

> view matrix models
> #2,-0.70315,-0.22165,0.67561,142.38,0.11442,0.90252,0.41517,-65.138,-0.70177,0.36923,-0.60925,291.24

> fitmap #2 inMap #4

Fit map cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip in map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip using 93678 points  
correlation = 0.3138, correlation about mean = 0.02515, overlap = 931.1  
steps = 244, shift = 4.81, angle = 15.2 degrees  
  
Position of cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip (#2) relative
to cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
-0.80766532 -0.34336504 0.47935079 248.21616837  
-0.08625325 0.87300833 0.48001752 -40.69123273  
-0.58329847 0.34634794 -0.73471491 285.52213504  
Axis -0.12135756 0.96477090 0.23342977  
Axis point 166.06607561 0.00000000 109.12087265  
Rotation angle (degrees) 146.58315099  
Shift along axis -2.73126014  
  

> fitmap #2 inMap #4

Fit map cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip in map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip using 93678 points  
correlation = 0.3138, correlation about mean = 0.02511, overlap = 931.1  
steps = 48, shift = 0.00287, angle = 0.0102 degrees  
  
Position of cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip (#2) relative
to cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
-0.80771457 -0.34332921 0.47929346 248.22781884  
-0.08633861 0.87306561 0.47989800 -40.67100510  
-0.58321763 0.34623907 -0.73483038 285.54515181  
Axis -0.12136583 0.96478813 0.23335425  
Axis point 166.06794169 0.00000000 109.13398180  
Rotation angle (degrees) 146.58874104  
Shift along axis -2.73210344  
  

> view matrix models
> #2,-0.80771,-0.34333,0.47929,210.43,-0.086339,0.87307,0.4799,-38.913,-0.58322,0.34624,-0.73483,300.19

> fitmap #2 inMap #4

Fit map cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip in map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip using 93678 points  
correlation = 0.8799, correlation about mean = 0.5716, overlap = 4218  
steps = 164, shift = 2.26, angle = 22.4 degrees  
  
Position of cryosparc_P7_J3144_008_volume_map_sharp.mrc z flip (#2) relative
to cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
-0.84335283 -0.45720298 0.28234984 301.24773314  
-0.38261248 0.87985278 0.28189850 30.82670487  
-0.37731113 0.12970932 -0.91695790 318.08822868  
Axis -0.22345081 0.96854311 0.10951704  
Axis point 183.02742212 0.00000000 130.05866548  
Rotation angle (degrees) 160.09004584  
Shift along axis -2.62097611  
  

> ui mousemode right ""translate selected models""

> ui mousemode right select

> select clear

> select add #1

10488 atoms, 10708 bonds, 1329 residues, 1 model selected  
Drag select of 5 atoms, 164 residues, 4 bonds  

> ui mousemode right ""translate selected models""

> view matrix models #1,1,0,0,21.19,0,1,0,175.71,0,0,1,138.03

> view matrix models #1,1,0,0,109.02,0,1,0,144.01,0,0,1,153.56

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,-0.25421,-0.92045,-0.2969,94.591,-0.83659,0.055246,0.54503,132.19,-0.48527,0.38693,-0.78409,152.9

> ui mousemode right ""move picked models""

> ui mousemode right ""translate selected models""

> view matrix models
> #1,-0.25421,-0.92045,-0.2969,118.71,-0.83659,0.055246,0.54503,157.37,-0.48527,0.38693,-0.78409,166.83

> fitmap #1 inMap #4

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms  
average map value = 0.02819, steps = 144  
shifted from previous position = 3.99  
rotated from previous position = 7.05 degrees  
atoms outside contour = 8990, contour level = 0.11213  
  
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
-0.18594866 -0.95673211 -0.22380072 156.79570665  
-0.87065941 0.05487494 0.48881584 154.61045561  
-0.45538476 0.28574885 -0.84319174 158.32977930  
Axis -0.63496928 0.72413914 0.26914034  
Axis point 154.15825218 0.00000000 39.78019363  
Rotation angle (degrees) 170.79873409  
Shift along axis 55.01195609  
  

> view matrix models
> #1,-0.18595,-0.95673,-0.2238,113.35,-0.87066,0.054875,0.48882,162.7,-0.45538,0.28575,-0.84319,169.69

> fitmap #1 inMap #4

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms  
average map value = 0.02819, steps = 112  
shifted from previous position = 4.09  
rotated from previous position = 0.012 degrees  
atoms outside contour = 8989, contour level = 0.11213  
  
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
-0.18581836 -0.95676976 -0.22374797 156.78949477  
-0.87060741 0.05474602 0.48892291 154.60736644  
-0.45553735 0.28564749 -0.84314366 158.31935263  
Axis -0.63501506 0.72409025 0.26916385  
Axis point 154.17103352 0.00000000 39.76072051  
Rotation angle (degrees) 170.78987736  
Shift along axis 54.99984198  
  

> view matrix models
> #1,-0.18582,-0.95677,-0.22375,113.11,-0.87061,0.054746,0.48892,155.84,-0.45554,0.28565,-0.84314,161.54

> fitmap #1 inMap #4

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms  
average map value = 0.02526, steps = 80  
shifted from previous position = 1.64  
rotated from previous position = 2.34 degrees  
atoms outside contour = 9095, contour level = 0.11213  
  
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
-0.22202901 -0.94576215 -0.23714357 153.75489113  
-0.86861097 0.08136122 0.48876920 151.60021012  
-0.44296512 0.31450645 -0.83956393 150.03868344  
Axis -0.62124940 0.73375701 0.27504514  
Axis point 147.50765612 0.00000000 37.52220316  
Rotation angle (degrees) 171.93758020  
Shift along axis 56.98499354  
  

> view matrix models
> #1,-0.22203,-0.94576,-0.23714,113.14,-0.86861,0.081361,0.48877,156.52,-0.44297,0.31451,-0.83956,162.78

> fitmap #1 inMap #4

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms  
average map value = 0.02526, steps = 96  
shifted from previous position = 2.54  
rotated from previous position = 0.0138 degrees  
atoms outside contour = 9094, contour level = 0.11213  
  
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
-0.22180819 -0.94579105 -0.23723491 153.75294201  
-0.86867013 0.08113974 0.48870086 151.60592053  
-0.44295973 0.31447674 -0.83957790 150.04121389  
Axis -0.62134051 0.73368233 0.27503855  
Axis point 147.52370869 0.00000000 37.52308817  
Rotation angle (degrees) 171.94056900  
Shift along axis 56.96477110  
  

> view matrix models
> #1,-0.22181,-0.94579,-0.23723,114.12,-0.86867,0.08114,0.4887,157.39,-0.44296,0.31448,-0.83958,167.25

> fitmap #1 inMap #4

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms  
average map value = 0.02723, steps = 172  
shifted from previous position = 5.24  
rotated from previous position = 5.9 degrees  
atoms outside contour = 9114, contour level = 0.11213  
  
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
-0.13490079 -0.97251154 -0.18979746 150.08247201  
-0.87413881 0.02661192 0.48494653 152.76441055  
-0.46656523 0.23132900 -0.85370005 158.95220827  
Axis -0.65353310 0.71318767 0.25349129  
Axis point 155.05911123 0.00000000 39.72525194  
Rotation angle (degrees) 168.81160147  
Shift along axis 51.15882932  
  

> view matrix models
> #1,-0.1349,-0.97251,-0.1898,110.96,-0.87414,0.026612,0.48495,160.87,-0.46657,0.23133,-0.8537,170.03

> fitmap #1 inMap #4

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms  
average map value = 0.02941, steps = 112  
shifted from previous position = 1.96  
rotated from previous position = 7.93 degrees  
atoms outside contour = 8981, contour level = 0.11213  
  
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
-0.08978721 -0.99333150 -0.07232408 153.55651177  
-0.89661512 0.04900216 0.44009103 155.80500859  
-0.43361225 0.10436141 -0.89503581 159.66080783  
Axis -0.66799785 0.71885144 0.19243563  
Axis point 162.66452536 0.00000000 42.95499378  
Rotation angle (degrees) 165.44581769  
Shift along axis 40.14966272  
  

> view matrix models
> #1,-0.089787,-0.99333,-0.072324,113.87,-0.89662,0.049002,0.44009,162.98,-0.43361,0.10436,-0.89504,170.11

> fitmap #1 inMap #4

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms  
average map value = 0.02941, steps = 84  
shifted from previous position = 2.19  
rotated from previous position = 0.0101 degrees  
atoms outside contour = 8983, contour level = 0.11213  
  
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
-0.08988318 -0.99331555 -0.07242392 153.55896469  
-0.89665845 0.04905614 0.43999673 155.80221831  
-0.43350276 0.10448782 -0.89507410 159.66508838  
Axis -0.66796981 0.71887738 0.19243611  
Axis point 162.65002070 0.00000000 42.96852171  
Rotation angle (degrees) 165.45497239  
Shift along axis 40.15526578  
  

> view matrix models
> #1,-0.089883,-0.99332,-0.072424,110.71,-0.89666,0.049056,0.44,157.69,-0.4335,0.10449,-0.89507,166.97

> fitmap #1 inMap #4

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms  
average map value = 0.03285, steps = 100  
shifted from previous position = 0.894  
rotated from previous position = 9.21 degrees  
atoms outside contour = 8864, contour level = 0.11213  
  
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
0.02897633 -0.98821484 -0.15030569 152.29081384  
-0.86617015 -0.09987528 0.48966743 151.80297446  
-0.49890844 0.11600153 -0.85885622 156.24821762  
Axis -0.71120291 0.66349993 0.23228916  
Axis point 0.00000000 160.99919506 90.51598125  
Rotation angle (degrees) 164.76967376  
Shift along axis 28.70635991  
  

> view matrix models
> #1,0.028976,-0.98821,-0.15031,115.89,-0.86617,-0.099875,0.48967,163.18,-0.49891,0.116,-0.85886,175.76

> fitmap #1 inMap #4

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms  
average map value = 0.02737, steps = 136  
shifted from previous position = 3.29  
rotated from previous position = 1.9 degrees  
atoms outside contour = 9130, contour level = 0.11213  
  
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
0.01334314 -0.99204106 -0.12520583 153.85365063  
-0.87387827 -0.07242560 0.48071955 156.58648538  
-0.48596164 0.10300035 -0.86788951 164.24666864  
Axis -0.70533494 0.67365830 0.22065158  
Axis point 0.00000000 166.93460678 93.21399045  
Rotation angle (degrees) 164.46905700  
Shift along axis 33.20871686  
  

> view matrix models
> #1,0.013343,-0.99204,-0.12521,107.86,-0.87388,-0.072426,0.48072,153.89,-0.48596,0.103,-0.86789,165.41

> fitmap #1 inMap #4

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms  
average map value = 0.03413, steps = 180  
shifted from previous position = 4  
rotated from previous position = 9.53 degrees  
atoms outside contour = 8705, contour level = 0.11213  
  
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
0.16362504 -0.96780624 -0.19125356 151.13600788  
-0.86379252 -0.23419786 0.44610967 151.79460746  
-0.47653889 0.09220868 -0.87430443 154.69072662  
Axis -0.75892627 0.61178280 0.22305318  
Axis point 0.00000000 148.64095788 88.33728425  
Rotation angle (degrees) 166.51687288  
Shift along axis 12.66850183  
  

> hide #!2 models

> color #4 #b2b2b27e models

> color #4 #b2b2b280 models

> view #4 clip false

> view matrix models
> #1,0.16363,-0.96781,-0.19125,109.24,-0.86379,-0.2342,0.44611,158.08,-0.47654,0.092209,-0.8743,164.78

> fitmap #1 inMap #4

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms  
average map value = 0.03674, steps = 144  
shifted from previous position = 2.11  
rotated from previous position = 8.52 degrees  
atoms outside contour = 8707, contour level = 0.11213  
  
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
0.23610261 -0.96966647 -0.06326528 149.17646777  
-0.87188706 -0.24013981 0.42678544 152.62195743  
-0.42903205 -0.04560498 -0.90213729 156.49401629  
Axis -0.78030569 0.60418221 0.16151433  
Axis point 0.00000000 149.58775587 78.59419460  
Rotation angle (degrees) 162.38041224  
Shift along axis 1.08425099  
  

> volume #4 level 0.1309

> volume #4 level 0.1544

> view matrix models
> #1,0.2361,-0.96967,-0.063265,140.87,-0.87189,-0.24014,0.42679,146.5,-0.42903,-0.045605,-0.90214,185.27

> view matrix models
> #1,0.2361,-0.96967,-0.063265,121.67,-0.87189,-0.24014,0.42679,172.34,-0.42903,-0.045605,-0.90214,182.5

> fitmap #1 inMap #4

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms  
average map value = 0.01981, steps = 160  
shifted from previous position = 4.3  
rotated from previous position = 9.4 degrees  
atoms outside contour = 9845, contour level = 0.15443  
  
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
0.22182187 -0.97446967 0.03469746 158.45108148  
-0.93056349 -0.20092926 0.30607028 166.05675350  
-0.29128447 -0.10018127 -0.95137641 170.81146053  
Axis -0.77719325 0.62363074 0.08399620  
Axis point 0.00000000 161.25202690 79.48097211  
Rotation angle (degrees) 164.84933588  
Shift along axis -5.24150106  
  

> view matrix models
> #1,0.22182,-0.97447,0.034697,113.73,-0.93056,-0.20093,0.30607,158.59,-0.29128,-0.10018,-0.95138,170.61

> fitmap #1 inMap #4

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms  
average map value = 0.1115, steps = 180  
shifted from previous position = 8.56  
rotated from previous position = 18.7 degrees  
atoms outside contour = 7148, contour level = 0.15443  
  
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
0.34157459 -0.91285471 -0.22365840 150.42082873  
-0.91383675 -0.37818340 0.14791791 157.89255807  
-0.21961145 0.15386226 -0.96337802 154.95048317  
Axis 0.81901540 -0.55758946 -0.13530621  
Axis point 0.00000000 129.97610643 90.08411631  
Rotation angle (degrees) 179.79207512  
Shift along axis 14.19198575  
  

> volume #4 level 0.09334

> surface dust #4 size 6.8

> hide #1 models

> show #1 models

> show #!2 models

> hide #!4 models

> volume #2 level 0.09

> volume #2 level 0.12

> volume #4 level 0.12

> hide #1 models

> show #!4 models

> hide #!2 models

> show #1 models

> view matrix models
> #1,0.34157,-0.91285,-0.22366,109.7,-0.91384,-0.37818,0.14792,163.18,-0.21961,0.15386,-0.96338,165.15

> ui mousemode right select

> select clear

> hide #1 models

> select clear

> hide #!4 models

> show #!4 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #1 models

> select clear

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> hide #!4 models

> hide #1 models

> open
> ""/Users/lukaskruckemeyer/Downloads/cryosparc_P125_J409_class_00_final_volume
> (1).mrc""

Opened cryosparc_P125_J409_class_00_final_volume (1).mrc as #3, grid size
140,140,140, pixel 3.12, shown at level 0.732, step 1, values float32  

> volume #3 level 0.7634

> volume #3 color #78ff78

> volume #3 color #44ff7b

> volume #3 color #2ba14d

> volume #3 color #9899a1

> volume #3 color #9899a1a5

> volume #3 color #9899a1a6

> view #4 clip false

No displayed objects specified.  

> view #4 clip false

No displayed objects specified.  

> view #3 clip false

> open
> /Users/lukaskruckemeyer/Documents/Universität/PhD/Structure_predictions/FeCh/fold_2024_09_10_13_07_fech_dim_2chlorophyll/fold_2024_09_10_13_07_fech_dim_2chlorophyll_model_0.cif

Chain information for fold_2024_09_10_13_07_fech_dim_2chlorophyll_model_0.cif
#5  
---  
Chain | Description  
A B | .  
  

> color #5 #57fd61ff

> color #5 #42c04aff

> view #5 clip false

> select add #5

6336 atoms, 6516 bonds, 8 pseudobonds, 776 residues, 2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models #5,1,0,0,103.87,0,1,0,261.6,0,0,1,289.26

> view matrix models #5,1,0,0,214.22,0,1,0,230.81,0,0,1,309.84

> view #5 clip false

> ui mousemode right ""rotate selected models""

> view matrix models
> #5,0.55061,0.68349,-0.47924,214.83,-0.60357,-0.070618,-0.79417,237.14,-0.57665,0.72654,0.37365,311.04

> view matrix models
> #5,0.57054,0.69546,-0.43683,214.69,-0.57861,-0.037082,-0.81476,236.88,-0.58283,0.71761,0.38124,311.1

> view matrix models
> #5,0.63211,0.62128,-0.46309,214.51,-0.63523,0.073234,-0.76884,236.94,-0.44375,0.78016,0.44095,310.1

> ui mousemode right ""translate selected models""

> view matrix models
> #5,0.63211,0.62128,-0.46309,211.2,-0.63523,0.073234,-0.76884,228.16,-0.44375,0.78016,0.44095,312.94

> view matrix models
> #5,0.63211,0.62128,-0.46309,214.6,-0.63523,0.073234,-0.76884,225.4,-0.44375,0.78016,0.44095,303.83

> view matrix models
> #5,0.63211,0.62128,-0.46309,217.15,-0.63523,0.073234,-0.76884,226.09,-0.44375,0.78016,0.44095,301.5

> ui mousemode right ""rotate selected models""

> view matrix models
> #5,0.59334,0.7434,-0.30871,217.12,-0.46969,0.0082807,-0.88279,225.19,-0.65372,0.66879,0.35408,303.07

> ui mousemode right ""rotate selected models""

> ui mousemode right ""translate selected models""

> view matrix models
> #5,0.59334,0.7434,-0.30871,217.72,-0.46969,0.0082807,-0.88279,223.25,-0.65372,0.66879,0.35408,298.32

> ui mousemode right select

> select clear

> view #5 clip false

> select clear

> select add #3

2 models selected  

> select add #5

6336 atoms, 6516 bonds, 8 pseudobonds, 776 residues, 4 models selected  

> select clear

> select add #5

6336 atoms, 6516 bonds, 8 pseudobonds, 776 residues, 2 models selected  

> select add #3

6336 atoms, 6516 bonds, 8 pseudobonds, 776 residues, 4 models selected  

> ui mousemode right ""translate selected models""

> view matrix models
> #3,1,0,0,-1.4264,0,1,0,7.3595,0,0,1,26.278,#5,0.59334,0.7434,-0.30871,216.3,-0.46969,0.0082807,-0.88279,230.6,-0.65372,0.66879,0.35408,324.6

> ui mousemode right rotate

> ui mousemode right select

> select clear

> color #3 #9899a15b models

> color #3 #bcbdc55b models

> color #3 #bcbdc55c models

> hide #!5 models

> show #!5 models

> hide #!5 models

> open
> /Users/lukaskruckemeyer/Documents/Universität/PhD/Structure_predictions/FeCh/fold_2025_03_25_15_20_syn_fech_tetramere_4x_chla/fold_2025_03_25_15_20_syn_fech_tetramere_4x_chla_model_0.cif

Chain information for
fold_2025_03_25_15_20_syn_fech_tetramere_4x_chla_model_0.cif #6  
---  
Chain | Description  
A B C D | .  
  

> select add #6

12672 atoms, 13032 bonds, 16 pseudobonds, 1552 residues, 2 models selected  

> view #6 clip false

> ui mousemode right ""translate selected models""

> view matrix models #6,1,0,0,184.35,0,1,0,270.73,0,0,1,323.94

> ui mousemode right ""rotate selected models""

> view matrix models
> #6,-0.64496,0.74122,0.18604,180.16,0.22232,-0.050929,0.97364,271.11,0.73116,0.66932,-0.13194,326.01

> view #6 clip false

> fitmap #6 inMap #3

Fit molecule fold_2025_03_25_15_20_syn_fech_tetramere_4x_chla_model_0.cif (#6)
to map cryosparc_P125_J409_class_00_final_volume (1).mrc (#3) using 12672
atoms  
average map value = 0.754, steps = 140  
shifted from previous position = 53.2  
rotated from previous position = 35.6 degrees  
atoms outside contour = 6268, contour level = 0.7634  
  
Position of fold_2025_03_25_15_20_syn_fech_tetramere_4x_chla_model_0.cif (#6)
relative to cryosparc_P125_J409_class_00_final_volume (1).mrc (#3)
coordinates:  
Matrix rotation and translation  
-0.64383139 0.37053803 0.66946450 216.74374107  
0.54253430 -0.39590511 0.74088844 223.67438389  
0.53957176 0.84021468 0.05386655 302.95226335  
Axis 0.41853385 0.54733279 0.72474563  
Axis point 21.43629069 -1.09450152 -0.00000000  
Rotation angle (degrees) 173.18524080  
Shift along axis 432.70224723  
  

> ui mousemode right ""rotate selected models""

> ui mousemode right select

> select clear

> volume #3 level 0.7033

> select clear

> view #3 clip false

> surface dust #3 size 31.2

> color #6 #8fdb8fff

> color #6 #91db8eff

> color #6 #a1f39eff

> select clear

> show #!5 models

> hide #!6 models

> color #5 #378f43ff

> hide #!5 models

> show #!6 models

> select clear

> show #!5 models

> hide #!6 models

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

> hide #!5 models

> show #!6 models

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

> hide #!6 models

> show #!6 models

> show #!5 models

> select add #3

2 models selected  

> select add #5

6336 atoms, 6516 bonds, 8 pseudobonds, 776 residues, 4 models selected  

> select add #6

19008 atoms, 19548 bonds, 24 pseudobonds, 2328 residues, 6 models selected  

> ui mousemode right ""translate selected models""

> view matrix models
> #3,1,0,0,-0.39312,0,1,0,7.9458,0,0,1,26.354,#5,0.59334,0.7434,-0.30871,217.33,-0.46969,0.0082807,-0.88279,231.19,-0.65372,0.66879,0.35408,324.68,#6,-0.64383,0.37054,0.66946,216.35,0.54253,-0.39591,0.74089,231.62,0.53957,0.84021,0.053867,329.31

> ui mousemode right ""rotate selected models""

> view matrix models
> #3,0.79418,0.41093,0.44768,-152.37,0.25463,0.44388,-0.85915,278.82,-0.55177,0.79631,0.24788,159.15,#5,-0.014454,0.8932,-0.44942,245.83,0.50424,-0.38162,-0.77467,177.05,-0.86344,-0.23781,-0.44487,290.74,#6,-0.046813,0.50773,0.86024,247.31,-0.3867,-0.80325,0.45305,173.02,0.92102,-0.31144,0.23394,292.77

> ui mousemode right select

> select clear

> hide #!5 models

> select clear

> show #!5 models

> select add #5

6336 atoms, 6516 bonds, 8 pseudobonds, 776 residues, 2 models selected  

> select add #6

19008 atoms, 19548 bonds, 24 pseudobonds, 2328 residues, 4 models selected  

> select add #3

19008 atoms, 19548 bonds, 24 pseudobonds, 2328 residues, 6 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #3,0.81484,0.35706,0.45666,-147.53,0.28997,0.43107,-0.85446,272.63,-0.50194,0.82867,0.24771,141.21,#5,0.017241,0.91413,-0.40506,245.83,0.52816,-0.35231,-0.77261,177.09,-0.84897,-0.20062,-0.48888,290.82,#6,-0.084501,0.54426,0.83465,247.3,-0.41387,-0.78114,0.46747,173.04,0.90641,-0.30593,0.29126,292.82

> view matrix models
> #3,0.80497,0.39352,0.44403,-149.08,0.2417,0.46597,-0.85115,275.26,-0.54185,0.79247,0.27998,148.18,#5,0.0025192,0.89864,-0.43868,246.5,0.48096,-0.3857,-0.78735,178,-0.87674,-0.209,-0.43318,290.65,#6,-0.065182,0.51555,0.85437,247.94,-0.36207,-0.81007,0.46119,174.02,0.92987,-0.27928,0.23947,292.81

> select subtract #3

19008 atoms, 19548 bonds, 24 pseudobonds, 2328 residues, 4 models selected  

> select subtract #5

12672 atoms, 13032 bonds, 16 pseudobonds, 1552 residues, 2 models selected  

> select subtract #6

Nothing selected  

> hide #!5 models

> hide #!6 models

> show #!5 models

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

> show #!6 models

> hide #!5 models

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

> hide #!6 models

> hide #!3 models

> show #!3 models

> show #!2 models

> show #1 models

> show #!4 models

> show #!6 models

> show #!5 models

> delete #5

> delete #6

> hide #!3 models

> show #!3 models

> close #3

> open
> /Users/lukaskruckemeyer/Downloads/cryosparc_P7_J3164_007_volume_map_sharp.mrc

Opened cryosparc_P7_J3164_007_volume_map_sharp.mrc as #3, grid size
440,440,440, pixel 0.68, shown at level 0.0173, step 2, values float32  

> volume #3 level 0.01093

> volume #3 step 1

> volume #3 level 0.12

> volume flip #3

Opened cryosparc_P7_J3164_007_volume_map_sharp.mrc z flip as #5, grid size
440,440,440, pixel 0.68, shown at step 1, values float32  

> close #3

> hide #!2 models

> hide #1 models

> select add #5

2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models #5,1,0,0,-10.375,0,1,0,-4.9797,0,0,1,20.481

> view matrix models #5,1,0,0,-30.581,0,1,0,15.507,0,0,1,22.982

> select up

10488 atoms, 10708 bonds, 1329 residues, 7 models selected  

> fitmap #5 inMap #4

Fit map cryosparc_P7_J3164_007_volume_map_sharp.mrc z flip in map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip using 100332 points  
correlation = 0.3006, correlation about mean = 0.07433, overlap = 757.6  
steps = 152, shift = 5.27, angle = 6.03 degrees  
  
Position of cryosparc_P7_J3164_007_volume_map_sharp.mrc z flip (#5) relative
to cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
0.99468960 -0.06119212 -0.08275334 27.34927905  
0.06293562 0.99784380 0.01862438 0.40014333  
0.08143524 -0.02373361 0.99639601 3.90233440  
Axis -0.20156818 -0.78132096 0.59068420  
Axis point -59.03960295 0.00000000 325.70546604  
Rotation angle (degrees) 6.03126561  
Shift along axis -3.52033741  
  

> view matrix models
> #1,0.34157,-0.91285,-0.22366,140.34,-0.91384,-0.37818,0.14792,250.8,-0.21961,0.15386,-0.96338,243.54,#4,1,0,0,-10.084,0,1,0,92.88,0,0,1,88.615,#2,-0.84335,-0.4572,0.28235,291.16,-0.38261,0.87985,0.2819,123.71,-0.37731,0.12971,-0.91696,406.7,#5,0.99469,-0.061192,-0.082753,17.265,0.062936,0.99784,0.018624,93.281,0.081435,-0.023734,0.9964,92.517

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> select subtract #2

10488 atoms, 10708 bonds, 1329 residues, 5 models selected  

> select subtract #1

4 models selected  

> select subtract #4

2 models selected  

> select subtract #5

Nothing selected  

> select add #5

2 models selected  

> view matrix models
> #5,0.99469,-0.061192,-0.082753,12.666,0.062936,0.99784,0.018624,80.163,0.081435,-0.023734,0.9964,80.867

> fitmap #5 inMap #4

Fit map cryosparc_P7_J3164_007_volume_map_sharp.mrc z flip in map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip using 100332 points  
correlation = 0.99, correlation about mean = 0.9371, overlap = 5773  
steps = 84, shift = 1.16, angle = 5.95 degrees  
  
Position of cryosparc_P7_J3164_007_volume_map_sharp.mrc z flip (#5) relative
to cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
0.99999762 -0.00217361 0.00020144 0.38027762  
0.00217323 0.99999597 0.00182782 -0.58813910  
-0.00020541 -0.00182738 0.99999831 0.30024801  
Axis -0.64194425 0.07145441 0.76341459  
Axis point 269.04956351 157.84447119 0.00000000  
Rotation angle (degrees) 0.16311971  
Shift along axis -0.05692846  
  

> select subtract #5

Nothing selected  

> view #5 clip false

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> surface dust #4 size 6.8

> surface dust #5 size 6.8

> surface dust #4 size 6.8

> surface dust #5 size 6.8

> surface dust #4 size 6.8

> surface dust #5 size 6.8

> show #1 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!5 models

> show #!4 models

> hide #!5 models

> show #!5 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> color #5 #ffb2b281 models

> color #5 #ffb2b282 models

> hide #!4 models

> hide #!5 models

> show #!5 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!4 models

> show #!4 models

> hide #!5 models

> hide #!4 models

> hide #1 models

> show #1 models

> show #!4 models

> show #!5 models

> hide #!4 models

> show #!4 models

> hide #!5 models

> show #!5 models

> hide #!4 models

> hide #!5 models

> show #!4 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!4 models

> hide #!5 models

> show #!5 models

> show #!4 models

> hide #!5 models

> show #!5 models

> hide #!4 models

> hide #!5 models

> show #!4 models

> volume #4 level 0.0571

> volume #4 level 0.07887

> volume #4 level 0.07162

> volume #4 level 0.05226

> volume #4 level 0.05

> volume #4 level 0.06

> show #!5 models

> hide #!4 models

> volume #5 level 0.06

> show #!4 models

> hide #!4 models

> volume #5 level 0.04634

> view

> ui tool show ""Side View""

> view #1 clip false

> volume #5 level 0.05545

> volume #5 level 0.07366

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> volume #5 level 0.1351

> volume #5 level 0.07366

> hide #!5 models

> show #!4 models

> ui tool show ""Show Sequence Viewer""

> sequence chain /A

Alignment identifier is 1/A  

> ui tool show Matchmaker

> ui tool show ""Segment Map""

> toolshed show

> ui tool show ""Fit in Map""

> hide #!4 models

> show #!4 models

> select /A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1328

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:1151-1328

1430 atoms, 1455 bonds, 178 residues, 1 model selected  
Average map value = 0.1115 for 10488 atoms, 4968 outside contour  

> fitmap #1 inMap #4

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms  
average map value = 0.1115, steps = 136  
shifted from previous position = 0.0256  
rotated from previous position = 0.0176 degrees  
atoms outside contour = 4966, contour level = 0.06  
  
Position of output.cif (#1) relative to
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) coordinates:  
Matrix rotation and translation  
0.34150799 -0.91287025 -0.22369666 150.42327919  
-0.91392282 -0.37808190 0.14764535 157.90211567  
-0.21935671 0.15401942 -0.96341094 154.94639770  
Axis 0.81899497 -0.55763467 -0.13524357  
Axis point 0.00000000 129.97458321 90.09013044  
Rotation angle (degrees) 179.77703866  
Shift along axis 14.18871147  
  

> select /A:1328

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:1251-1328

649 atoms, 659 bonds, 78 residues, 1 model selected  
Average map value = 0.1115 for 10488 atoms, 4966 outside contour  

> fitmap #1 inMap #4 moveWholeMolecules false

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms  
average map value = 0.1115, steps = 64  
shifted from previous position = 0.0103  
rotated from previous position = 0.0183 degrees  
atoms outside contour = 4973, contour level = 0.06  
  

> ui mousemode right select

> select clear

> select /A:1328

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:1051-1328

2219 atoms, 2256 bonds, 278 residues, 1 model selected  
Drag select of 16 residues, 4 cryosparc_P7_J3142_008_volume_map_sharp.mrc z
flip  

> select /A:1328

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:1051-1328

2219 atoms, 2256 bonds, 278 residues, 1 model selected  
Average map value = 0.1115 for 10488 atoms, 4973 outside contour  

> fitmap #1 inMap #4 moveWholeMolecules false

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms  
average map value = 0.1115, steps = 64  
shifted from previous position = 0.00694  
rotated from previous position = 0.0124 degrees  
atoms outside contour = 4968, contour level = 0.06  
  

> fitmap #1 inMap #4 moveWholeMolecules false

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms  
average map value = 0.1115, steps = 96  
shifted from previous position = 0.00591  
rotated from previous position = 0.00366 degrees  
atoms outside contour = 4967, contour level = 0.06  
  

> fitmap #1 inMap #4 moveWholeMolecules false

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 10488 atoms  
average map value = 0.1115, steps = 96  
shifted from previous position = 0.00039  
rotated from previous position = 0.00827 degrees  
atoms outside contour = 4967, contour level = 0.06  
  

> fitmap sel inMap #4 moveWholeMolecules false

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 2219 atoms  
average map value = 0.2104, steps = 68  
shifted from previous position = 0.307  
rotated from previous position = 0.632 degrees  
atoms outside contour = 449, contour level = 0.06  
  
Drag select of 7 residues, 4 cryosparc_P7_J3142_008_volume_map_sharp.mrc z
flip  

> select /A:1328

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:1201-1328

1053 atoms, 1071 bonds, 128 residues, 1 model selected  
Average map value = 0.2322 for 1053 atoms, 212 outside contour  

> fitmap sel inMap #4 moveWholeMolecules false

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 1053 atoms  
average map value = 0.2338, steps = 68  
shifted from previous position = 0.0763  
rotated from previous position = 0.931 degrees  
atoms outside contour = 203, contour level = 0.06  
  

> select /A:1200

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:1051-1200

1166 atoms, 1184 bonds, 150 residues, 1 model selected  

> fitmap sel inMap #4 moveWholeMolecules false

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 1166 atoms  
average map value = 0.1914, steps = 48  
shifted from previous position = 0.0954  
rotated from previous position = 0.44 degrees  
atoms outside contour = 231, contour level = 0.06  
  

> select /A:1050

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:901-1050

1146 atoms, 1168 bonds, 150 residues, 1 model selected  

> fitmap sel inMap #4 moveWholeMolecules false

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 1146 atoms  
average map value = 0.1611, steps = 48  
shifted from previous position = 0.137  
rotated from previous position = 0.874 degrees  
atoms outside contour = 290, contour level = 0.06  
  

> select /A:900

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /A:751-900

1177 atoms, 1194 bonds, 150 residues, 1 model selected  

> fitmap sel inMap #4 moveWholeMolecules false

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 1177 atoms  
average map value = 0.1445, steps = 48  
shifted from previous position = 0.0994  
rotated from previous position = 1.55 degrees  
atoms outside contour = 353, contour level = 0.06  
  

> select /A:750

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:601-750

1171 atoms, 1195 bonds, 150 residues, 1 model selected  

> fitmap sel inMap #4 moveWholeMolecules false

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 1171 atoms  
average map value = 0.1441, steps = 64  
shifted from previous position = 0.467  
rotated from previous position = 1.4 degrees  
atoms outside contour = 368, contour level = 0.06  
  

> select /A:600

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /A:451-600

1184 atoms, 1219 bonds, 150 residues, 1 model selected  

> fitmap sel inMap #4 moveWholeMolecules false

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 1184 atoms  
average map value = 0.1402, steps = 60  
shifted from previous position = 1.57  
rotated from previous position = 5.19 degrees  
atoms outside contour = 367, contour level = 0.06  
  

> select /A:450

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:251-450

1548 atoms, 1582 bonds, 200 residues, 1 model selected  

> fitmap sel inMap #4 moveWholeMolecules false

Fit molecule output.cif (#1) to map
cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip (#4) using 1548 atoms  
average map value = 0.06931, steps = 64  
shifted from previous position = 1.68  
rotated from previous position = 5.79 degrees  
atoms outside contour = 839, contour level = 0.06  
  

> select clear

> hide #1 models

> show #1 models

> volume #4 level 0.06726

> volume #4 level 0.08

> hide #1 models

> hide #!4 models

> show #1 models

> show #!4 models

> ui tool show ""Side View""

Drag select of 1 bonds, 4 cryosparc_P7_J3142_008_volume_map_sharp.mrc z flip  

> select #4

3 models selected  

> select clear

> volume #4 level 0.04613

> volume #4 level 0.2856

> volume #4 level 0.04371

> view orient

> ui tool show ""Side View""

> volume #4 level 0.08242

> hide #1 models

> select ::name=""LIG""

42 atoms, 46 bonds, 1 residue, 1 model selected  

> show #1 models

> select add #1

10488 atoms, 10708 bonds, 1329 residues, 1 model selected  

> select subtract #1

Nothing selected  

> hide cartoons

> show cartoons

> hide cartoons

> show cartoons

> volume #4 color #c6c6c600

> volume #4 color #c6c6c60d

> volume #4 color #c6c6c6f4

Drag select of 2 residues, 4 cryosparc_P7_J3142_008_volume_map_sharp.mrc z
flip  
Drag select of 1 residues, 4 cryosparc_P7_J3142_008_volume_map_sharp.mrc z
flip  

> select clear

> ui mousemode right ""rotate selected models""

> ui mousemode right ""translate selected models""

> color #4 #c6c6c6d3 models

> color #4 #c6c6c6d4 models

> volume #4 level 0.1308

> volume #4 level 0.08726

> volume #4 level 0.04371

> volume #4 level 0.1623

> open
> /Users/lukaskruckemeyer/Downloads/cryosparc_P7_J3155_005_volume_map_sharp.mrc

Opened cryosparc_P7_J3155_005_volume_map_sharp.mrc as #3, grid size
400,400,400, pixel 0.68, shown at level 0.0157, step 2, values float32  

> hide #1 models

> hide #!3 models

> hide #!4 models

> show #!3 models

> show #!3 target m

> view #3 clip false

> volume #3 level 0.08175

> surface dust #3 size 6.8

> volume #3 level 0.1021

> volume #3 level 0.1038

> hide #!3 models

> show #1 models

> show #!4 models

> view #4 clip false

> volume #4 level 0.08

> volume #4 level 0.09

> ui mousemode right select

> select /A:577

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #4

2 models selected  

> select /A:578

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:577

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #4

2 models selected  

> select #4

2 models selected  

> select clear

> hide #!4 models

> select /A:589

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show #!4 models

> hide #!4 models

> select /A:1171

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select clear

> select /A:1172

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /A:1171

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select clear

> select /A:744

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:1172

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /A:588

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /A:588-589

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:1171

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select clear

> select /A:744

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:1171

10 atoms, 10 bonds, 1 residue, 1 model selected  

> show #!4 models

> hide #!4 models

> show #!4 models

Drag select of 3 residues, 4 cryosparc_P7_J3142_008_volume_map_sharp.mrc z
flip  

> select #4

2 models selected  

> select /A:1171

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select
> /A:7-10,32-48,61-65,67-79,91-104,118-123,131-135,140-152,156-165,167-173,176-193,197-212,215-220,249-258,264-267,280-284,289-300,316-322,353-363,378-383,390-397,400-403,425-443,446-448,462-464,473-487,498-506,526-532,536-541,581-586,594-606,621-623,636-641,655-664,684-699,705-718,732-734,737-756,773-783,788-790,795-803,807-815,819-843,852-860,866-873,881-899,903-912,928-930,942-944,948-968,983-988,992-1001,1021-1024,1037-1042,1044-1058,1064-1066,1068-1080,1084-1087,1103-1108,1115-1126,1142-1151,1173-1175,1178-1184,1208-1220,1223-1254,1259-1271,1273-1282,1284-1299,1307-1324

5576 atoms, 5600 bonds, 685 residues, 1 model selected  

> select /A:1170

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:1170-1173

39 atoms, 41 bonds, 4 residues, 1 model selected  

> volume #4 level 0.1088

> volume #4 level 0.0853

> select #4

2 models selected  

> select clear

> volume #4 level 0.1095

> show atoms

> volume #4 level 0.08046

> select /A:1-2

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select /A:1-270

2172 atoms, 2218 bonds, 270 residues, 1 model selected  

> select /A:180

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:1-180

1431 atoms, 1454 bonds, 180 residues, 1 model selected  

> select /A:180

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:179-180

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select clear

> show #!5 models

> hide #!5 models

> view #3 clip false

No displayed objects specified.  

> view #3 clip false

No displayed objects specified.  

> hide #!4 models

> hide #!3 models

> show #!4 models

> show #!3 models

> view #4 clip false

> show #!4 target m

> view #4 clip false

> select add #4

2 models selected  

> select subtract #4

Nothing selected  

> select add #3

2 models selected  

> view #4 clip false

> hide #!3 models

> hide #!4 models

> view #3 clip false

No displayed objects specified.  

> show #!3 models

> hide #1 models

> view #3 clip false

> select clear

> show #!4 models

> hide #!4 models

> hide #!3 models

> show #!4 models

> show #1 models

> view #1 clip false


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

Log:
Startup Messages  
---  
warning | Registration file '/Users/lukaskruckemeyer/Library/Application Support/ChimeraX/registration' has expired  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




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: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
      OS Loader Version: 580.140.1~8

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 1 Tag, 1 Stunde und 43 Minuten

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:
        PA278CV:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: M6LMQS089968
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort
        PA278CV:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: M6LMQS089975
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


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-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    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