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Opened 3 hours ago
#20770 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-15.7.7-arm64-arm-64bit
ChimeraX Version: 1.10rc202505310246 (2025-05-31 02:46:39 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 0x00000001f503a2c0 (most recent call first):
File "/Applications/ChimeraX-1.10-rc2025.06.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10-rc2025.06.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10-rc2025.06.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, chimerax.map._map, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, cython.cimports.libc.math, 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._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._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, PIL._imagingmath, chimerax.segment._segment, tables._comp_lzo, tables._comp_bzip2, tables.utilsextension, numexpr.interpreter, tables.hdf5extension, tables.linkextension, tables.lrucacheextension, tables.tableextension, tables.indexesextension (total: 124)
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"uptime" : 970000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 1968042898,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,1",
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"captureTime" : "2026-07-17 09:37:40.4137 -0400",
"codeSigningMonitor" : 1,
"incident" : "474255E3-6BA4-4939-9FB7-3B74940978C7",
"pid" : 55625,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2026-07-15 10:41:18.0474 -0400",
"procStartAbsTime" : 22103538973627,
"procExitAbsTime" : 23431908552746,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10-rc2025.06.02.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"parentProc" : "launchd",
"parentPid" : 1,
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"crashReporterKey" : "CAFC4431-C50C-FE3B-31D1-590AB06F9D8C",
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"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"sleepWakeUUID" : "195812EE-1121-4A4D-9A49-08ABC19CE1DD",
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"exception" : {"codes":"0x0000000000000001, 0x0000aa1a0c68fa70","rawCodes":[1,187028854078064],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000aa1a0c68fa70 -> 0x00002a1a0c68fa70 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":55625},
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===== Log before crash start =====
UCSF ChimeraX version: 1.10rc202505310246 (2025-05-31)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/goncalvesgm/Desktop/ChimeraX-figures/NENEposter/NPCfigure-
> colorbyPodoDiff.cxs format session
Opened emdb 14321 as #3, grid size 144,144,144, pixel 13.8, shown at level
0.0605, step 1, values float32
> view name session-start
opened ChimeraX session
> select add #1
617133 atoms, 630097 bonds, 18 pseudobonds, 78030 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #2
617133 atoms, 630097 bonds, 18 pseudobonds, 78030 residues, 2 models selected
> select add #1
1234266 atoms, 1260194 bonds, 36 pseudobonds, 156060 residues, 4 models
selected
> close #10#4-9
> view
> color bychain
> hide #!2 models
> surface #1 resolution 25
101 Gaussian surfaces, threshold level 0.013 - 0.024
> surface close
> show all cartoons
> ui mousemode right select
> select clear
> color #1/10-17 red
> name frozen #1/10-17,E* luminal-ring
Missing or invalid "objects" argument: invalid objects specifier
> name frozen luminal-ring #1/10-17,E*
> color luminal-ring salmon
Drag select of 17392 residues
> select clear
> info chains
chain id #1/00 chain_id 00
chain id #1/01 chain_id 01
chain id #1/02 chain_id 02
chain id #1/03 chain_id 03
chain id #1/04 chain_id 04
chain id #1/10 chain_id 10
chain id #1/11 chain_id 11
chain id #1/12 chain_id 12
chain id #1/13 chain_id 13
chain id #1/14 chain_id 14
chain id #1/15 chain_id 15
chain id #1/16 chain_id 16
chain id #1/17 chain_id 17
chain id #1/40 chain_id 40
chain id #1/41 chain_id 41
chain id #1/A0 chain_id A0
chain id #1/A1 chain_id A1
chain id #1/A2 chain_id A2
chain id #1/A3 chain_id A3
chain id #1/A4 chain_id A4
chain id #1/A5 chain_id A5
chain id #1/A6 chain_id A6
chain id #1/B0 chain_id B0
chain id #1/B1 chain_id B1
chain id #1/C0 chain_id C0
chain id #1/C1 chain_id C1
chain id #1/C2 chain_id C2
chain id #1/C3 chain_id C3
chain id #1/C4 chain_id C4
chain id #1/D0 chain_id D0
chain id #1/D1 chain_id D1
chain id #1/D2 chain_id D2
chain id #1/D3 chain_id D3
chain id #1/D4 chain_id D4
chain id #1/D5 chain_id D5
chain id #1/E0 chain_id E0
chain id #1/E1 chain_id E1
chain id #1/F0 chain_id F0
chain id #1/F1 chain_id F1
chain id #1/F2 chain_id F2
chain id #1/F3 chain_id F3
chain id #1/H0 chain_id H0
chain id #1/H1 chain_id H1
chain id #1/H2 chain_id H2
chain id #1/H3 chain_id H3
chain id #1/I0 chain_id I0
chain id #1/I1 chain_id I1
chain id #1/I2 chain_id I2
chain id #1/I3 chain_id I3
chain id #1/J0 chain_id J0
chain id #1/J1 chain_id J1
chain id #1/J2 chain_id J2
chain id #1/J3 chain_id J3
chain id #1/J4 chain_id J4
chain id #1/K0 chain_id K0
chain id #1/K1 chain_id K1
chain id #1/K2 chain_id K2
chain id #1/K3 chain_id K3
chain id #1/L0 chain_id L0
chain id #1/L1 chain_id L1
chain id #1/L2 chain_id L2
chain id #1/L3 chain_id L3
chain id #1/M0 chain_id M0
chain id #1/M1 chain_id M1
chain id #1/M2 chain_id M2
chain id #1/M3 chain_id M3
chain id #1/N0 chain_id N0
chain id #1/N1 chain_id N1
chain id #1/N2 chain_id N2
chain id #1/N3 chain_id N3
chain id #1/O0 chain_id O0
chain id #1/O1 chain_id O1
chain id #1/O2 chain_id O2
chain id #1/O3 chain_id O3
chain id #1/P0 chain_id P0
chain id #1/P1 chain_id P1
chain id #1/P2 chain_id P2
chain id #1/P3 chain_id P3
chain id #1/Q0 chain_id Q0
chain id #1/Q1 chain_id Q1
chain id #1/Q2 chain_id Q2
chain id #1/Q3 chain_id Q3
chain id #1/R0 chain_id R0
chain id #1/R1 chain_id R1
chain id #1/R2 chain_id R2
chain id #1/R3 chain_id R3
chain id #1/S0 chain_id S0
chain id #1/S1 chain_id S1
chain id #1/S2 chain_id S2
chain id #1/S3 chain_id S3
chain id #1/T0 chain_id T0
chain id #1/T1 chain_id T1
chain id #1/U0 chain_id U0
chain id #1/U1 chain_id U1
chain id #1/U2 chain_id U2
chain id #1/U3 chain_id U3
chain id #1/U4 chain_id U4
chain id #1/U5 chain_id U5
chain id #1/U6 chain_id U6
chain id #1/V0 chain_id V0
chain id #1/W0 chain_id W0
chain id #2/00 chain_id 00
chain id #2/01 chain_id 01
chain id #2/02 chain_id 02
chain id #2/03 chain_id 03
chain id #2/04 chain_id 04
chain id #2/10 chain_id 10
chain id #2/11 chain_id 11
chain id #2/12 chain_id 12
chain id #2/13 chain_id 13
chain id #2/14 chain_id 14
chain id #2/15 chain_id 15
chain id #2/16 chain_id 16
chain id #2/17 chain_id 17
chain id #2/40 chain_id 40
chain id #2/41 chain_id 41
chain id #2/A0 chain_id A0
chain id #2/A1 chain_id A1
chain id #2/A2 chain_id A2
chain id #2/A3 chain_id A3
chain id #2/A4 chain_id A4
chain id #2/A5 chain_id A5
chain id #2/A6 chain_id A6
chain id #2/B0 chain_id B0
chain id #2/B1 chain_id B1
chain id #2/C0 chain_id C0
chain id #2/C1 chain_id C1
chain id #2/C2 chain_id C2
chain id #2/C3 chain_id C3
chain id #2/C4 chain_id C4
chain id #2/D0 chain_id D0
chain id #2/D1 chain_id D1
chain id #2/D2 chain_id D2
chain id #2/D3 chain_id D3
chain id #2/D4 chain_id D4
chain id #2/D5 chain_id D5
chain id #2/E0 chain_id E0
chain id #2/E1 chain_id E1
chain id #2/F0 chain_id F0
chain id #2/F1 chain_id F1
chain id #2/F2 chain_id F2
chain id #2/F3 chain_id F3
chain id #2/H0 chain_id H0
chain id #2/H1 chain_id H1
chain id #2/H2 chain_id H2
chain id #2/H3 chain_id H3
chain id #2/I0 chain_id I0
chain id #2/I1 chain_id I1
chain id #2/I2 chain_id I2
chain id #2/I3 chain_id I3
chain id #2/J0 chain_id J0
chain id #2/J1 chain_id J1
chain id #2/J2 chain_id J2
chain id #2/J3 chain_id J3
chain id #2/J4 chain_id J4
chain id #2/K0 chain_id K0
chain id #2/K1 chain_id K1
chain id #2/K2 chain_id K2
chain id #2/K3 chain_id K3
chain id #2/L0 chain_id L0
chain id #2/L1 chain_id L1
chain id #2/L2 chain_id L2
chain id #2/L3 chain_id L3
chain id #2/M0 chain_id M0
chain id #2/M1 chain_id M1
chain id #2/M2 chain_id M2
chain id #2/M3 chain_id M3
chain id #2/N0 chain_id N0
chain id #2/N1 chain_id N1
chain id #2/N2 chain_id N2
chain id #2/N3 chain_id N3
chain id #2/O0 chain_id O0
chain id #2/O1 chain_id O1
chain id #2/O2 chain_id O2
chain id #2/O3 chain_id O3
chain id #2/P0 chain_id P0
chain id #2/P1 chain_id P1
chain id #2/P2 chain_id P2
chain id #2/P3 chain_id P3
chain id #2/Q0 chain_id Q0
chain id #2/Q1 chain_id Q1
chain id #2/Q2 chain_id Q2
chain id #2/Q3 chain_id Q3
chain id #2/R0 chain_id R0
chain id #2/R1 chain_id R1
chain id #2/R2 chain_id R2
chain id #2/R3 chain_id R3
chain id #2/S0 chain_id S0
chain id #2/S1 chain_id S1
chain id #2/S2 chain_id S2
chain id #2/S3 chain_id S3
chain id #2/T0 chain_id T0
chain id #2/T1 chain_id T1
chain id #2/U0 chain_id U0
chain id #2/U1 chain_id U1
chain id #2/U2 chain_id U2
chain id #2/U3 chain_id U3
chain id #2/U4 chain_id U4
chain id #2/U5 chain_id U5
chain id #2/U6 chain_id U6
chain id #2/V0 chain_id V0
chain id #2/W0 chain_id W0
> select #1/C1,C5
16013 atoms, 16330 bonds, 2011 residues, 1 model selected
> select #1/C0,C1
32026 atoms, 32660 bonds, 4022 residues, 1 model selected
> name frozen inner-ring #1/40,41,A0-A3,B*,C0,C1,D*,F*,H*,I*,J*,U*,V*,W*
> color inner-ring paleyellow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color inner-ring pale-yellow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color inner-ring peru
> select clear
> name frozen inner-ring #1/40,41,A0-A3,B*,C0,C1,D0-D3,F*
> color inner-ring peru
> color bychain
> color inner-ring peru
> view
> color inner-ring khaki
> color luminal-ring salmon
> name frozen ycomplexes-cytosol
> #1/K0-K1,L0-L1,M0-M1,N0-N1,O0-O1,P0-P1,Q0-Q1,R0-R1,S0-S1
> color ycomplexes-cytosol dodger blue
> name frozen ycomplexes-nuc
> #1/K2-K3,L2-L3,M2-M3,N2-N3,O2-O3,P2-P3,Q2-Q3,R2-R3,S2-S3
> color ycomplexes-nuc dodger blue
> name frozen ycomplexes-nuc
> #1/K2-K3,L2-L3,M2-M3,N2-N3,O2-O3,P2-P3,Q2-Q3,R2-R3,S2-S3,T*
> color ycomplexes-nuc dodger blue
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> name frozen linker-nups #1/A4-A6,C2-C4,D4-D5
> color linker-nups dark turquoise
> name frozen FG-nups #1/00-05,H*,I*,J*,U*
> name frozen FG-nups #1/H*,I*,J*,U*
> color FG-nups gray
> select #1/J*
7015 atoms, 7100 bonds, 855 residues, 1 model selected
> select clear
> select #1/J1
1403 atoms, 1420 bonds, 171 residues, 1 model selected
> select #1/J2
1403 atoms, 1420 bonds, 171 residues, 1 model selected
> select #1/J3
1403 atoms, 1420 bonds, 171 residues, 1 model selected
> select #1/J4
1403 atoms, 1420 bonds, 171 residues, 1 model selected
> name frozen FG-nups #1/H*,I*,J1-J3,U*
> color FG-nups gray
> name frozen cyt-nups #1/00-05,J3,V0,W0
> color cyt-nups green
> color cyt-nups light green
> name frozen cyt-nups #1/00-05,J4,V0,W0
> color cyt-nups light green
> color FG-nups gray
> color FG-nups light gray
> save /Users/goncalvesgm/Desktop/ChimeraX-figures/CRD-talk-moviesandfigs/NPC-
> recolored.cxs includeMaps true
> surface #1 resolution 50
101 Gaussian surfaces, threshold level 0.004 - 0.020
> graphics silhouettes false
> lighting flat
> surface #1 resolution 100
101 Gaussian surfaces, threshold level 0.002 - 0.014
> surface #1 resolution 10
101 Gaussian surfaces, threshold level 0.045 - 0.061
> graphics silhouettes false
> surface #1 resolution 50
101 Gaussian surfaces, threshold level 0.004 - 0.020
> ui tool show "Side View"
> ui mousemode right clip
> surface #1 resolution 25
101 Gaussian surfaces, threshold level 0.013 - 0.024
> surface #1 resolution 10
101 Gaussian surfaces, threshold level 0.045 - 0.061
> name list
FG-nups [24164 atoms, 24509 bonds]
Y-complexes-all [599464 atoms, 612432 bonds, 2 models]
cyt-nups [39867 atoms, 40692 bonds]
inner-ring [140434 atoms, 143258 bonds]
linker-nups [86345 atoms, 88042 bonds]
luminal-ring [121232 atoms, 123926 bonds]
no-change-podDiff [438246 atoms, 447304 bonds, 2 models]
pododiff-high [113646 atoms, 116162 bonds, 2 models]
pododiff-low [348562 atoms, 355540 bonds, 2 models]
pododiff-mid [226180 atoms, 231172 bonds, 2 models]
ycomplexes-cytosol [93884 atoms, 95984 bonds]
ycomplexes-nuc [109804 atoms, 112266 bonds]
> color FG-nups light grey
> color FG-nups light grey target s
> name frozen FG-nups #1/H*,I*,J0-J3,U*
> color FG-nups light grey target s
> color FG-nups silver grey target s
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color FG-nups silver target s
> name side
"side" is not defined
> view name side
> surface #1 resolution 20
101 Gaussian surfaces, threshold level 0.017 - 0.028
> show #!3 models
> color #3 #b2b2b2ff models
> ui tool show "Segment Map"
Segmenting emdb 14321, density threshold 0.060491
Showing 42 region surfaces
2326 watershed regions, grouped to 42 regions
Showing emdb 14321.seg - 42 regions, 42 surfaces
> lighting simple
> ui mousemode right select
> select #4.22
1 model selected
> select add #4.11
2 models selected
> select add #4.18
3 models selected
> select add #4.16
4 models selected
> select add #4.24
5 models selected
> select add #4.9
6 models selected
> select add #4.17
7 models selected
> select add #4.13
8 models selected
> select add #4.21
9 models selected
> select add #4.12
10 models selected
> select add #4.19
11 models selected
> select add #4.15
12 models selected
> select add #4.23
13 models selected
> select add #4.10
14 models selected
> select add #4.20
15 models selected
> select add #4.14
16 models selected
> close #4.9-24
> hide #!3 models
> select #4.3
1 model selected
> select #4.2
1 model selected
Ungrouped to 4 regions
> select #4.12
1 model selected
> select add #4.10
2 models selected
> close #4.10,12
> select #4.9
1 model selected
> select #4.11
1 model selected
> select add #4.27
2 models selected
> select add #4.32
3 models selected
> close #4.11,27,32
> select #4.9
1 model selected
Ungrouped to 11 regions
> hide #!1 models
> select clear
> select #4.16
1 model selected
> select add #4.14
2 models selected
> select add #4.2
3 models selected
> select add #4.15
4 models selected
> select subtract #4.2
3 models selected
Grouped 3 regions
> select clear
> select #4.2
1 model selected
> select add #4.9
2 models selected
Grouped 2 regions
> select clear
> select #4.12
1 model selected
> select add #4.2
2 models selected
Grouped 2 regions
> select clear
> select #4.19
1 model selected
> select add #4.18
2 models selected
> select add #4.33
3 models selected
> select add #4.11
4 models selected
> close #4.11,18-19,33
> select clear
> select #4.34
1 model selected
> close #4.34
> select clear
> select #4.5
1 model selected
> select add #4.1
2 models selected
> select add #4.6
3 models selected
> select add #4.4
4 models selected
> select add #4.8
5 models selected
> select add #4.3
6 models selected
> select add #4.7
7 models selected
> close #4.1,3-8
> select clear
> select #4.31
1 model selected
> select add #4.25
2 models selected
> select add #4.26
3 models selected
> select add #4.29
4 models selected
> select add #4.28
5 models selected
> select add #4.30
6 models selected
> close #4.25-26,28-31
> select #4.38
1 model selected
> select add #4.36
2 models selected
> select add #4.35
3 models selected
> select add #4.40
4 models selected
> select add #4.37
5 models selected
> select add #4.39
6 models selected
> select add #4.17
7 models selected
> close #4.17,35-40
> select #4.10
1 model selected
> select add #4.13
2 models selected
> close #4.10,13
> select #4.2
1 model selected
> select #4.41
1 model selected
> close #4.41
> select #4.2
1 model selected
> select add #4.42
2 models selected
> select subtract #4.2
1 model selected
> close #4.42
> select #4.2
1 model selected
Ungrouped to 2 regions
> select #4.1
1 model selected
Ungrouped to 2 regions
> select #4.4
1 model selected
Ungrouped to 3 regions
> select #4.6
1 model selected
Ungrouped to 27 regions
> select #4.1
1 model selected
Ungrouped to 22 regions
> select clear
> select #4.2
1 model selected
Ungrouped to 3 regions
> select clear
> select #4.53
1 model selected
> close #4.53
> select #4.55
1 model selected
> close #4.55
> select #4.4
1 model selected
> close #4.4
> select #4.26
1 model selected
> close #4.26
> select #4.36
1 model selected
> close #4.36
> select #4.17
1 model selected
> close #4.17
> select #4.8
1 model selected
> select add #4.12
2 models selected
> select add #4.38
3 models selected
> select add #4.52
4 models selected
> close #4.8,12,38,52
> select #4.51
1 model selected
> select add #4.48
2 models selected
> select clear
> select #4.48
1 model selected
> select clear
> select #4.51
1 model selected
> select #4.41
1 model selected
> select add #4.51
2 models selected
> select add #4.25
3 models selected
> close #4.25,41,51
> select #4.27
1 model selected
> select add #4.29
2 models selected
> select add #4.19
3 models selected
> select subtract #4.19
2 models selected
> select add #4.15
3 models selected
> select subtract #4.15
2 models selected
> close #4.27,29
> select #4.30
1 model selected
> close #4.30
> select #4.31
1 model selected
> close #4.31
> select #4.11
1 model selected
Ungrouped to 6 regions
> select clear
> select #4.25
1 model selected
> select add #4.12
2 models selected
Grouped 2 regions
> select clear
> select #4.4
1 model selected
> select add #4.2
2 models selected
> select add #4.17
3 models selected
> close #4.2,4,17
> select #4.10
1 model selected
> close #4.10
> select #4.20
1 model selected
> close #4.20
> select #4.7
1 model selected
> close #4.7
> select #4.49
1 model selected
> close #4.49
> select clear
Drag select of 2921, 2716, 1826, 2460, 2477, 2479, 2524, 2553, 2559, 2572,
793, 716, 2633, 1685, 1112, 941, 2367, 2394, 2459, 2579, 408, 668, 1172, 2687,
2693, 2720, 2728, 2741, 2742, 606, 2420, 486, 1354, 3060
Grouped 34 regions
> select clear
> select #4.1
1 model selected
Ungrouped to 34 regions
> select #4.26
1 model selected
> close #4.26
> select #4.14
1 model selected
> close #4.14
> select #4.20
1 model selected
Ungrouped to 6 regions
> select clear
> select #4.14
1 model selected
Ungrouped to 0 regions
> select #4.14
1 model selected
Ungrouped to 0 regions
> select #4.14
1 model selected
> close #4.14
> select #4.11
1 model selected
> close #4.11
Drag select of 1172, 1826, 941, 2572, 2477, 486, 2728, 2479, 2633, 1685, 1112,
2420, 2741, 2742, 1354, 2553, 2459, 668, 716, 2460, 2524, 606, 2367, 2559,
2687, 2720, 2693, 3060, 793, 2921, 938, 676, 726, 727, 615
Grouped 35 regions
> show #!1 models
> lighting flat
> graphics silhouettes false
Saving 1 regions to mrc file...
Opened NE-segment.mrc as #5, grid size 35,49,36, pixel 13.8, shown at step 1,
values float32
Wrote NE-segment.mrc
> volume resample #5 onGrid #3
Opened NE-segment.mrc resampled as #6, grid size 144,144,144, pixel 13.8,
shown at step 1, values float32
> volume #6 level 0.4393
> hide #!4 models
> volume #6 level 0.1666
> volume #6 color #ffffb280
> lighting simple
> view
> volume #6 color #ebebeb
> volume #6 color #d6d6d6
> volume #6 color silver
> volume #6 color darkgrey
> volume #6 color silver
> volume #6 color #d6d6d6
> lighting flat
> graphics silhouettes false
> surface #1 resolution 30
101 Gaussian surfaces, threshold level 0.010 - 0.022
> volume #6 level 0.3094
> volume #6 step 4
> volume #6 level 0.2079
> volume #6 step 2
> vop gaussian #6 sd 5
Opened NE-segment.mrc resampled gaussian as #7, grid size 144,144,144, pixel
13.8, shown at step 1, values float32
> volume #7 level 0.3037
> lighting simple
> volume #7 level 0.2183
> volume #7 step 2
> volume #7 level 0.2016
> volume #7 step 4
> volume #7 step 2
> volume #7 color #b2ffff80
> lighting flat
> graphics silhouettes false
> volume #7 level 0.299
> volume #7 color #929292
> volume #7 color #009051
> volume #7 color #929292
> volume #7 color darkgrey
> close session
> open /Users/goncalvesgm/Desktop/ChimeraX-figures/NENEposter/NPCfigure-
> colorbyPodoDiff.cxs format session
Opened emdb 14321 as #3, grid size 144,144,144, pixel 13.8, shown at level
0.0605, step 1, values float32
> view name session-start
opened ChimeraX session
> close session
> open /Users/goncalvesgm/Desktop/ChimeraX-figures/CRD-talk-moviesandfigs/NPC-
> recolored.cxs format session
Opened emdb 14321 as #3, grid size 144,144,144, pixel 13.8, shown at level
0.0605, step 1, values float32
> view name session-start
opened ChimeraX session
> close session
> open /Users/goncalvesgm/Desktop/ChimeraX-figures/NENEposter/NPCfigure-
> colorbyPodoDiff.cxs format session
Opened emdb 14321 as #3, grid size 144,144,144, pixel 13.8, shown at level
0.0605, step 1, values float32
> view name session-start
opened ChimeraX session
> lighting simple
> show #!3 models
> hide #!9 models
> hide #!8 models
> hide #!6 models
> hide #!7 models
> hide #!5 models
> hide #!4 models
> hide #!2 models
> hide #!1 models
> vop gaussian #3 sdev 41.4
Opened emdb 14321 gaussian as #11, grid size 144,144,144, pixel 13.8, shown at
step 1, values float32
> volume #11 level 0.05756
> volume #11 level 0.04829
> ui tool show "Segment Map"
Segmenting emdb 14321 gaussian, density threshold 0.048294
Showing 8 region surfaces
52 watershed regions, grouped to 8 regions
Showing emdb 14321 gaussian.seg - 8 regions, 8 surfaces
Segmenting emdb 14321 gaussian, density threshold 0.048294
Showing 8 region surfaces
52 watershed regions, grouped to 8 regions
Showing emdb 14321 gaussian.seg - 8 regions, 8 surfaces
Segmenting emdb 14321 gaussian, density threshold 0.048294
Showing 8 region surfaces
52 watershed regions, grouped to 8 regions
Showing emdb 14321 gaussian.seg - 8 regions, 8 surfaces
Segmenting emdb 14321 gaussian, density threshold 0.048294
Showing 8 region surfaces
52 watershed regions, grouped to 8 regions
Showing emdb 14321 gaussian.seg - 8 regions, 8 surfaces
> select #12.8
1 model selected
> select add #12.4
2 models selected
> select add #12.7
3 models selected
> select add #12.2
4 models selected
> select add #12.5
5 models selected
> select add #12.1
6 models selected
> select add #12.6
7 models selected
> select add #12.3
8 models selected
> select subtract #12.8
7 models selected
> select subtract #12.4
6 models selected
> select add #12.4
7 models selected
Drag select of 71, 23 of 36740 triangles, 11 emdb 14321 gaussian
> select subtract #12.3
9 models selected
> select clear
> select add #12.1
1 model selected
> select add #12.2
2 models selected
> select add #12.3
3 models selected
> select add #12.4
4 models selected
> select add #12.5
5 models selected
> select add #12.6
6 models selected
> select add #12.7
7 models selected
> select add #12.8
8 models selected
Ungrouped to 24 regions
> select clear
> select #12.13
1 model selected
Drag select of 50, 13 of 1896 triangles, 49, 479 of 1896 triangles, 40, 446 of
4064 triangles, 45, 43 of 1852 triangles, 51, 1430 of 1896 triangles, 44, 1737
of 4064 triangles, 43, 1306 of 4008 triangles, 48, 1343 of 1852 triangles, 46,
995 of 1852 triangles, 42, 1404 of 4008 triangles, 47, 377 of 1852 triangles,
52, 1013 of 1896 triangles, 41, 468 of 4064 triangles, 11 emdb 14321 gaussian
> close #12.12-13,17,19-22,25-26,29-30,32
> hide #!11 models
> select #12.15
1 model selected
> select add #12.10
2 models selected
> select add #12.9
3 models selected
> select add #12.27
4 models selected
> close sele
Expected a models specifier or a keyword
> close selected
Expected a models specifier or a keyword
> close sel
Drag select of 66, 27822 of 31904 triangles, 65, 31829 of 31892 triangles, 68,
63, 30035 of 31888 triangles, 62, 30140 of 32052 triangles, 67, 64, 30066 of
32072 triangles, 61, 20053 of 31900 triangles
> select clear
> select #12.18
1 model selected
> select add #12.24
2 models selected
> select add #12.14
3 models selected
> select add #12.16
4 models selected
> select add #12.11
5 models selected
> select add #12.28
6 models selected
> select add #12.23
7 models selected
> select subtract #12.18
6 models selected
> select add #12.18
7 models selected
> select subtract #12.24
6 models selected
> select add #12.24
7 models selected
> select subtract #12.23
6 models selected
> select add #12.23
7 models selected
> select subtract #12.18
6 models selected
> select add #12.18
7 models selected
> select add #12.31
8 models selected
Ungrouped to 28 regions
> select clear
> select #12.7
1 model selected
> select add #12.9
2 models selected
> select add #12.12
3 models selected
> select #12.30
1 model selected
> select add #12.20
2 models selected
> select add #12.26
3 models selected
> select add #12.4
4 models selected
> select add #12.15
5 models selected
> select add #12.36
6 models selected
> select add #12.9
7 models selected
> select add #12.7
8 models selected
> select subtract #12.30
7 models selected
> select add #12.30
8 models selected
> select add #12.22
9 models selected
> select add #12.19
10 models selected
> select add #12.25
11 models selected
> select add #12.1
12 models selected
> select add #12.3
13 models selected
> select add #12.13
14 models selected
> select subtract #12.3
13 models selected
> select add #12.34
14 models selected
> select add #12.12
15 models selected
> select add #12.8
16 models selected
> select add #12.32
17 models selected
> close #12.1,4,7-9,12-13,15,19-20,22,25-26,30,32,34,36
> undo
Segmenting emdb 14321 gaussian, density threshold 0.048294
Showing 8 region surfaces
52 watershed regions, grouped to 8 regions
Showing emdb 14321 gaussian.seg - 8 regions, 8 surfaces
Segmenting emdb 14321 gaussian, density threshold 0.048294
Showing 8 region surfaces
52 watershed regions, grouped to 8 regions
Showing emdb 14321 gaussian.seg - 8 regions, 8 surfaces
Segmenting emdb 14321 gaussian, density threshold 0.048294
Showing 8 region surfaces
52 watershed regions, grouped to 8 regions
Showing emdb 14321 gaussian.seg - 8 regions, 8 surfaces
Drag select of 75, 76, 36554 of 36684 triangles, 70, 72, 73, 69, 74, 36093 of
36752 triangles, 71
Ungrouped to 24 regions
> select clear
Drag select of 43, 63, 48, 67, 40, 49, 64, 46, 42, 45, 38, 66, 52, 41, 62, 47,
39, 68, 65, 44, 51, 50, 61, 37
Ungrouped to 28 regions
> select #12.42
1 model selected
> select add #12.48
2 models selected
> select add #12.34
3 models selected
> select add #12.5
4 models selected
> select add #12.4
5 models selected
> select add #12.37
6 models selected
> select add #12.51
7 models selected
> select subtract #12.42
6 models selected
> select subtract #12.48
5 models selected
> select add #12.48
6 models selected
> select add #12.42
7 models selected
> select subtract #12.51
6 models selected
> select add #12.51
7 models selected
> select subtract #12.34
6 models selected
> select add #12.34
7 models selected
> select add #12.39
8 models selected
Ungrouped to 8 regions
Ungrouped to 0 regions
> select clear
Drag select of 43, 690 of 4008 triangles, 48, 942 of 1852 triangles, 40, 2434
of 4064 triangles, 49, 46, 1710 of 1852 triangles, 42, 1911 of 4008 triangles,
45, 1756 of 1852 triangles, 38, 2432 of 4008 triangles, 52, 891 of 1896
triangles, 41, 822 of 4064 triangles, 47, 1022 of 1852 triangles, 39, 1383 of
4008 triangles, 44, 1290 of 4064 triangles, 51, 1342 of 1896 triangles, 50,
1432 of 1896 triangles, 37, 2063 of 4064 triangles, 21, 21 of 28872 triangles,
18, 5 of 27852 triangles
> select add #12.5
19 models selected
> select subtract #12.5
18 models selected
> select subtract #12.27
17 models selected
> select #12.40
1 model selected
> show #12.39 models
> select add #12.47
2 models selected
> select add #12.44
3 models selected
> select add #12.49
4 models selected
> select add #12.38
5 models selected
> select add #12.1
6 models selected
> select add #12.7
7 models selected
> select add #12.33
8 models selected
> select subtract #12.40
7 models selected
> select add #12.40
8 models selected
> select #12.3
1 model selected
> select add #12.23
2 models selected
Grouped 2 regions
> select clear
Drag select of 16, 295 of 2656 triangles, 57, 674 of 4212 triangles, 9, 495 of
2656 triangles, 59, 654 of 4212 triangles, 55, 1091 of 4212 triangles, 56,
1090 of 4212 triangles, 1, 673 of 2656 triangles, 8, 500 of 2656 triangles,
10, 415 of 2064 triangles, 3, 587 of 2064 triangles, 15, 303 of 2064
triangles, 7, 486 of 2064 triangles
> show #!1 models
> hide #!1 models
> select #12.52
1 model selected
> select add #12.12
2 models selected
Grouped 2 regions
> view
> select #12.8
1 model selected
> select add #12.27
2 models selected
Grouped 2 regions
> select clear
Drag select of 23, 24, 21, 22, 33, 17, 77, 78, 79
Ungrouped to 6 regions
Ungrouped to 0 regions
> select #12.48
1 model selected
Ungrouped to 0 regions
> select #12.45
1 model selected
> select add #12.20
2 models selected
Grouped 2 regions
> select #12.12
1 model selected
> select add #12.23
2 models selected
Grouped 2 regions
> select #12.27
1 model selected
> select add #12.34
2 models selected
Grouped 2 regions
> select #12.51
1 model selected
> select add #12.48
2 models selected
Grouped 2 regions
Drag select of 23, 24, 21, 22, 80, 81, 82, 83
Grouped 8 regions
> show #12.1 models
> show #12.2 models
> show #12.6 models
> show #12.7 models
> hide #12.7 models
> hide #12.6 models
> hide #12.2 models
> hide #12.1 models
Ungrouped to 8 regions
> select #12.34
1 model selected
> select #12.34
1 model selected
Ungrouped to 0 regions
Drag select of 23, 21, 24, 22, 36, 20, 17, 33, 34, 19, 18, 35
Grouped 12 regions
> hide #12.3 models
> show #12.3 models
Saving 1 regions to mrc file...
Opened emdb 14321 gaussian_NE.mrc as #13, grid size 119,119,44, pixel 13.8,
shown at step 1, values float32
Wrote emdb 14321 gaussian_NE.mrc
> ui tool show "Segment Map"
> save /Users/goncalvesgm/Desktop/ChimeraX-figures/CRD-talk-
> moviesandfigs/emdb14321gaussian.seg models #12
> close #12
> vop resample #13 ongrid #3
Opened emdb 14321 gaussian_NE.mrc resampled as #12, grid size 144,144,144,
pixel 13.8, shown at step 1, values float32
> volume #12 level 0.0678
> vop gaussian #12 sdev 41.4
Opened emdb 14321 gaussian_NE.mrc resampled gaussian as #14, grid size
144,144,144, pixel 13.8, shown at step 1, values float32
> volume #14 level 0.02614
> volume #14 color silver
> volume #14 color darkgrey
> show #!1 models
> hide all cartoons
> select #1/K0,K1,L0,L1,M0,M1,N0,N1,O0,O1,P0,P1,Q0,Q1,R0,R1,S0,S1
93884 atoms, 95984 bonds, 4 pseudobonds, 11772 residues, 2 models selected
> show #1/K0,K1,L0,L1,M0,M1,N0,N1,O0,O1,P0,P1,Q0,Q1,R0,R1,S0,S1 cartoons
> show #2-3/K0,K1,L0,L1,M0,M1,N0,N1,O0,O1,P0,P1,Q0,Q1,R0,R1,S0,S1 cartoons
> show #!2 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #4/K0,K1,L0,L1,M0,M1,N0,N1,O0,O1,P0,P1,Q0,Q1,R0,R1,S0,S1 cartoons
> show #5/K0,K1,L0,L1,M0,M1,N0,N1,O0,O1,P0,P1,Q0,Q1,R0,R1,S0,S1 cartoons
> show #6/K0,K1,L0,L1,M0,M1,N0,N1,O0,O1,P0,P1,Q0,Q1,R0,R1,S0,S1 cartoons
> show #7/K0,K1,L0,L1,M0,M1,N0,N1,O0,O1,P0,P1,Q0,Q1,R0,R1,S0,S1 cartoons
> show #8,9/K0,K1,L0,L1,M0,M1,N0,N1,O0,O1,P0,P1,Q0,Q1,R0,R1,S0,S1 cartoons
> color #1/K0-S0 red
> color #1/K0,L0,M0,N0,O0,P0,Q0,R0,S0 red
> color #1/K1,L1,M1,N1,O1,P1,Q1,R1,S1 blue
> select clear
> color #2,3-9/K0,L0,M0,N0,O0,P0,Q0,R0,S0 red
> color #2,4-9/K1,L1,M1,N1,O1,P1,Q1,R1,S1 blue
> surface #1-2,3-9/K0,K1,L0,L1,M0,M1,N0,N1,O0,O1,P0,P1,Q0,Q1,R0,R1,S0,S1
> resolution 25
144 Gaussian surfaces, threshold level 0.014 - 0.023
> hide all surfaces
> hide #1 surfaces
> surface close
> volume #14 level 0.04166
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> hide #!4 models
> show #!2 models
> show #!4 models
> show #!1 models
> rename #3 id #15
> rename #6 id #3
> rename #9 id #16
> rename #7 id #6
> rename #8 id #7
> rename #5 id #9
> rename #16 id #87
> rename #87 id #5
> hide #!9 models
> hide #!1 models
> show #!1 models
> show #!9 models
> rename #9 id #8
> surface #1-2,3-9/K0,K1,L0,L1,M0,M1,N0,N1,O0,O1,P0,P1,Q0,Q1,R0,R1,S0,S1
> resolution 50
144 Gaussian surfaces, threshold level 0.008 - 0.020
> graphics silhouettes false
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting flat
> save /Users/goncalvesgm/Desktop/ChimeraX-figures/CRD-talk-
> moviesandfigs/npccartoon-lattice.cxs includeMaps true
> ui mousemode right clip
> surface #1-2,3-9/A*,B*,C*,D*,E*,F*,H*,I* resolution 50
272 Gaussian surfaces, threshold level 0.005 - 0.011
> volume #14 level 0.09456
> color #1-2,3-9/A*,B*,C*,D*,E*,F*,H*,I* cyan
> volume #14 level 0.08993
> volume #14 level 0.06726
> volume #14 color #a9a9a980
> color #1-2,3-9/A*,B*,C*,D*,E*,F*,H*,I*,J*,U*V*,W* cyan
> color #1-8/A*,B*,C*,D*,E*,F*,H*,I*,J*,U*V*,W* cyan
> hide #!1 models
> show #!1 models
> surface close
> surface #1-2,3-9/A*,B*,C*,D*,E*,F*,H*,I* resolution 50
272 Gaussian surfaces, threshold level 0.005 - 0.011
> save /Users/goncalvesgm/Desktop/ChimeraX-figures/CRD-talk-
> moviesandfigs/npccartoon-lattice.cxs includeMaps true
> open /Users/goncalvesgm/Desktop/ChimeraX-figures/CRD-talk-moviesandfigs/NPC-
> recolored.cxs
Opened emdb 14321 as #3, grid size 144,144,144, pixel 13.8, shown at level
0.0605, step 1, values float32
> view name session-start
opened ChimeraX session
> open /Users/goncalvesgm/Desktop/ChimeraX-figures/CRD-talk-
> moviesandfigs/npccartoon-lattice.cxs
Opened emdb 14321 gaussian as #11, grid size 144,144,144, pixel 13.8, shown at
level 0.0483, step 1, values float32
Opened emdb 14321 gaussian_NE.mrc as #13, grid size 119,119,44, pixel 13.8,
shown at level 0.185, step 1, values float32
Opened emdb 14321 gaussian_NE.mrc resampled as #12, grid size 144,144,144,
pixel 13.8, shown at level 0.0678, step 1, values float32
Opened emdb 14321 gaussian_NE.mrc resampled gaussian as #14, grid size
144,144,144, pixel 13.8, shown at level 0.0673, step 1, values float32
Opened emdb 14321 as #15, grid size 144,144,144, pixel 13.8, shown at level
0.0605, step 1, values float32
> view name session-start
opened ChimeraX session
> color #1/K0,L0,M0,N0,O0,P0,Q0,R0,S0 gold
> color #1-8/K0,L0,M0,N0,O0,P0,Q0,R0,S0 gold
> color #1-8/K1-S1 dark orange
> color #1-8/K1,L1,M1,N1,O1,P1,Q1,R1,S1 dark orange
> color #1-8/K0,L0,M0,N0,O0,P0,Q0,R0,S0 gold
> surface #1-8/K0,K1,L0,L1,M0,M1,N0,N1,O0,O1,P0,P1,Q0,Q1,R0,R1,S0,S1
> resolution 50
144 Gaussian surfaces, threshold level 0.008 - 0.020
> color #1-8/A*,B*,C*,D*,E*,F*,H*,I*,J*,U*V*,W* dark green
> color #1-8/A*,B*,C*,D*,E*,F*,H*,I*,J*,U*V*,W* dark blue
> ui mousemode right clip
> close surface #1-8/K1,L1,M1,N1,O1,P1,Q1,R1,S1
Expected a models specifier or a keyword
> surface #1-8/K1,L1,M1,N1,O1,P1,Q1,R1,S1 close
Expected a keyword
> surface close #1-8/K1,L1,M1,N1,O1,P1,Q1,R1,S1
> hide #1-8/K1,L1,M1,N1,O1,P1,Q1,R1,S1 cartoons
> surface #1-8/A*,B*,C*,D*,E*,F*,H*,I*,J*,U*V*,W* close
Expected a keyword
> surface close #1-8/A*,B*,C*,D*,E*,F*,H*,I*,J*,U*V*,W*
> hide #1-8/A*,B*,C*,D*,E*,F*,H*,I*,J*,U*V*,W* cartoons
> hide #!3 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!2 models
> volume #14 level 0.06874
> volume #14 level 0.04138
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> surface #1-8/A*,B*,C*,D*,E*,F*,H*,I*,J*,U*V*,W* resolution 25
320 Gaussian surfaces, threshold level 0.015 - 0.023
> volume #15 style mesh
> volume #14 style mesh
> volume #14 style image
> volume #14 style mesh
> volume #14 style surface
> volume #14 step 2
> volume #14 step 4
> volume #14 step 16
> volume #14 change image level -4.441e-17,0 level 0.09221,0.8 level 0.1882,1
> volume #14 level 0.04852
> volume #14 step 8
> volume #14 step 4
> volume #14 step 2
> volume #14 color #a9a9a900
> hide #!14 models
> hide #10 models
> show #!15 models
> volume #14
> volume #15 style surface
> volume #15 color #b2b2b2
> hide #!1 models
> show #!1 models
> hide #!1 models
> lighting simple
> show #!1 models
> hide #!1 models
> volume #15 level 0.1122
> volume #15 level 0.07343
Segmenting emdb 14321, density threshold 0.073425
Showing 40 region surfaces
2158 watershed regions, grouped to 40 regions
Showing emdb 14321.seg - 40 regions, 40 surfaces
> ui mousemode right select
Drag select of 2818, 20 of 59392 triangles, 2792, 2510 of 7784 triangles,
2797, 71 of 7784 triangles, 2778, 1292 of 7784 triangles, 2798, 2298 of 7332
triangles, 2789, 1118 of 7332 triangles, 2790, 2436 of 4516 triangles, 2796,
2338 of 4516 triangles, 2779, 97 of 4516 triangles, 2788, 143 of 4516
triangles, 2783, 2718 of 4200 triangles, 2777, 1068 of 4200 triangles, 2785,
1131 of 4200 triangles, 15 emdb 14321
> select subtract #9.2
14 models selected
> hide #!15 models
> select #9.14
1 model selected
> select add #9.9
2 models selected
> select add #9.21
3 models selected
> select add #9.15
4 models selected
> select clear
> select #9.34
1 model selected
> select add #9.36
2 models selected
> select add #9.35
3 models selected
> select add #9.38
4 models selected
> select subtract #9.35
3 models selected
> select add #9.33
4 models selected
> select add #9.37
5 models selected
> select add #9.40
6 models selected
> select clear
> select #9.39
1 model selected
> select add #9.35
2 models selected
> select #9.6
1 model selected
Drag select of 2815, 2818, 2816, 2814, 2813, 2817, 2812, 2819, 2679, 2692,
2761, 2760, 2753, 2757, 2748, 2755
Ungrouped to 68 regions, but did not show all surfaces, see Options
> select subtract #9.58
51 models selected
> select subtract #9.85
50 models selected
> select add #9.85
51 models selected
> select clear
> select add #9.88
1 model selected
> select add #9.57
2 models selected
> select add #9.58
3 models selected
> select #9.74
1 model selected
> select add #9.70
2 models selected
> select subtract #9.70
1 model selected
> select #9.71
1 model selected
> select add #9.70
2 models selected
> select add #9.81
3 models selected
> select add #9.80
4 models selected
> select add #9.84
5 models selected
> select add #9.46
6 models selected
Deleted 6 regions
> select #9.64
1 model selected
> select add #9.65
2 models selected
> select add #9.66
3 models selected
> select add #9.69
4 models selected
Deleted 4 regions
> select #9.54
1 model selected
> select add #9.50
2 models selected
> select add #9.76
3 models selected
> select add #9.75
4 models selected
> select add #9.79
5 models selected
> select add #9.78
6 models selected
> select add #9.42
7 models selected
Deleted 7 regions
> select #9.92
1 model selected
> select add #9.89
2 models selected
Deleted 2 regions
Drag select of 2810, 1071 of 4808 triangles, 2630, 245 of 4832 triangles,
2805, 646 of 4808 triangles, 2665, 369 of 4832 triangles, 2800, 499 of 3944
triangles, 2645, 1551 of 4652 triangles, 2673, 280 of 4832 triangles
Deleted 7 regions
> select add #9.62
1 model selected
> select add #9.63
2 models selected
> select add #9.55
3 models selected
Deleted 3 regions
> select #9.86
1 model selected
> select add #9.87
2 models selected
Deleted 2 regions
Drag select of 2787, 2775, 2782, 2786, 1459, 1038, 2791, 1439, 1381, 1437,
1384, 1361, 1467, 1404, 2776, 1413, 1013
Grouped 17 regions
Showing 45 region surfaces
Drag select of 2793, 999 of 7784 triangles, 2797, 341 of 7784 triangles, 2794,
482 of 7332 triangles, 2795, 905 of 7332 triangles, 2790, 70 of 4516
triangles, 2796, 64 of 4516 triangles, 2779, 1509 of 4516 triangles, 2788,
1516 of 4516 triangles, 2784, 1664 of 4200 triangles, 2777, 736 of 4200
triangles, 2785, 594 of 4200 triangles
> select clear
Drag select of 2793, 999 of 7784 triangles, 2797, 341 of 7784 triangles, 2794,
482 of 7332 triangles, 2795, 905 of 7332 triangles, 2790, 70 of 4516
triangles, 2796, 64 of 4516 triangles, 2779, 1509 of 4516 triangles, 2788,
1505 of 4516 triangles, 2784, 1664 of 4200 triangles, 2777, 736 of 4200
triangles, 2785, 594 of 4200 triangles
Deleted 11 regions
> select #9.10
1 model selected
Drag select of 2798, 32 of 7332 triangles, 2781, 13 of 44168 triangles, 2653,
13 of 4652 triangles
> select add #9.12
5 models selected
> select subtract #9.3
4 models selected
Deleted 4 regions
> select #9.6
1 model selected
> select #9.25
1 model selected
> select add #9.6
2 models selected
> select add #9.8
3 models selected
Deleted 3 regions
> select #9.35
1 model selected
> select add #9.33
2 models selected
> select add #9.37
3 models selected
> select add #9.40
4 models selected
> select add #9.34
5 models selected
> select add #9.39
6 models selected
> select add #9.36
7 models selected
> select add #9.38
8 models selected
Deleted 8 regions
> select #9.26
1 model selected
> select add #9.28
2 models selected
> select add #9.27
3 models selected
> select add #9.41
4 models selected
> select add #9.29
5 models selected
> select add #9.5
6 models selected
> select add #9.58
7 models selected
> select add #9.88
8 models selected
> select add #9.57
9 models selected
> select add #9.74
10 models selected
> select add #9.4
11 models selected
Deleted 11 regions
> select #9.30
1 model selected
> select add #9.31
2 models selected
> select add #9.32
3 models selected
Deleted 3 regions
> select clear
> select #9.3
1 model selected
> select #9.1
1 model selected
> select #9.22
1 model selected
Deleted 1 regions
> select #9.1
1 model selected
Ungrouped to 17 regions
> select clear
> select #9.11
1 model selected
> select add #9.12
2 models selected
> select add #9.14
3 models selected
> select add #9.15
4 models selected
> select add #9.8
5 models selected
> select add #9.18
6 models selected
> select add #9.5
7 models selected
> select add #9.17
8 models selected
> select add #9.20
9 models selected
Deleted 9 regions
> select #9.7
1 model selected
> select add #9.3
2 models selected
> select add #9.21
3 models selected
> select add #9.16
4 models selected
> select add #9.10
5 models selected
> select add #9.19
6 models selected
> select add #9.9
7 models selected
> select add #9.4
8 models selected
> select clear
> select #9.2
1 model selected
> select #9.16
1 model selected
Deleted 1 regions
> select #9.2
1 model selected
> select add #9.10
2 models selected
> select add #9.19
3 models selected
> select add #9.9
4 models selected
> select add #9.4
5 models selected
> select add #9.7
6 models selected
> select add #9.3
7 models selected
> select add #9.21
8 models selected
Ungrouped to 92 regions, but did not show all surfaces, see Options
> select #9.70
1 model selected
> select add #9.76
2 models selected
> select add #9.33
3 models selected
Deleted 3 regions
> select add #9.41
1 model selected
> select add #9.12
2 models selected
> select add #9.8
3 models selected
> select add #9.44
4 models selected
> select add #9.50
5 models selected
> select subtract #9.44
4 models selected
> select add #9.44
5 models selected
Deleted 5 regions
> select #9.49
1 model selected
> select add #9.15
2 models selected
> select add #9.36
3 models selected
> select add #9.74
4 models selected
> select add #9.60
5 models selected
> select add #9.26
6 models selected
> select #9.31
1 model selected
> select add #9.42
2 models selected
> select add #9.11
3 models selected
> select add #9.18
4 models selected
> select add #9.51
5 models selected
> select add #9.54
6 models selected
Deleted 6 regions
> select #9.66
1 model selected
> select add #9.62
2 models selected
> select add #9.29
3 models selected
> select add #9.28
4 models selected
> select add #9.23
5 models selected
Deleted 5 regions
> select #9.59
1 model selected
> select #9.65
1 model selected
Deleted 1 regions
> select #9.57
1 model selected
Deleted 1 regions
> select #9.16
1 model selected
> select add #9.47
2 models selected
Deleted 2 regions
> select clear
> show #9.26 models
> show #9.36 models
Only showing 60 of 71 regions.
Showing 60 of 71 region surfaces
> select clear
> select #9.29
1 model selected
> select add #9.10
2 models selected
> select #9.2
1 model selected
> select #9.26
1 model selected
> select #9.59
1 model selected
Deleted 1 regions
> show #9.26 models
> show #9.29 models
> select #9.29
1 model selected
> select add #9.25
2 models selected
Deleted 2 regions
> select #9.51
1 model selected
> select add #9.26
2 models selected
> select add #9.74
3 models selected
Deleted 3 regions
> select clear
Drag select of 2633, 22 of 18068 triangles, 2767, 415 of 3452 triangles, 2632,
16 of 18012 triangles, 2646, 621 of 2008 triangles
> select add #9.73
5 models selected
> select subtract #9.7
4 models selected
> select subtract #9.73
3 models selected
> select subtract #9.53
2 models selected
Deleted 2 regions
> select clear
> select #9.18
1 model selected
> select add #9.11
2 models selected
Deleted 2 regions
> select #9.31
1 model selected
> select add #9.16
2 models selected
Deleted 2 regions
> select #9.12
1 model selected
> select add #9.33
2 models selected
Deleted 2 regions
> select #9.47
1 model selected
> select add #9.50
2 models selected
Deleted 2 regions
> select #9.43
1 model selected
> select add #9.1
2 models selected
> select add #9.46
3 models selected
> select add #9.4
4 models selected
> select add #9.63
5 models selected
> select add #9.22
6 models selected
> select add #9.2
7 models selected
> select add #9.3
8 models selected
Ungrouped to 192 regions, but did not show all surfaces, see Options
Only showing 60 of 239 regions.
Showing 60 of 239 region surfaces
Only showing 60 of 239 regions.
Showing 60 of 239 region surfaces
> select #9.10
1 model selected
> select #9.53
1 model selected
> show #9.10 models
> select #9.10
1 model selected
Deleted 1 regions
Smoothing and grouping, standard deviation 5 voxels
Showing 8 region surfaces
Got 8 regions after smoothing 5 voxels.
> select #9.4
1 model selected
Ungrouped to 28 regions
> select #9.20
1 model selected
> select add #9.17
2 models selected
> select clear
> select #9.17
1 model selected
> select #9.33
1 model selected
Deleted 1 regions
> select #9.17
1 model selected
> select #9.20
1 model selected
Showing 34 region surfaces
> select #9.17
1 model selected
> select add #9.20
2 models selected
Deleted 2 regions
> select #9.35
1 model selected
> select add #9.22
2 models selected
Deleted 2 regions
> select #9.21
1 model selected
> select #9.14
1 model selected
Deleted 1 regions
> select #9.29
1 model selected
Ungrouped to 23 regions
> select clear
> select #9.38
1 model selected
> select add #9.44
2 models selected
Deleted 2 regions
> select #9.37
1 model selected
> select add #9.50
2 models selected
Deleted 2 regions
> select #9.48
1 model selected
Deleted 1 regions
> select #9.31
1 model selected
Ungrouped to 5 regions
> select #9.37
1 model selected
Deleted 1 regions
> select #9.30
1 model selected
Deleted 1 regions
> select #9.35
1 model selected
> select add #9.33
2 models selected
> select add #9.32
3 models selected
> select subtract #9.32
2 models selected
Deleted 2 regions
> select #9.32
1 model selected
Ungrouped to 2 regions
> select clear
> select #9.31
1 model selected
Ungrouped to 5 regions
> select clear
> select #9.50
1 model selected
Deleted 1 regions
> select #9.26
1 model selected
> select #9.21
1 model selected
> select add #9.46
2 models selected
> select add #9.39
3 models selected
> select add #9.43
4 models selected
Ungrouped to 13 regions
> select clear
> select #9.59
1 model selected
Deleted 1 regions
> select #9.26
1 model selected
Ungrouped to 2 regions
> select #9.39
1 model selected
Ungrouped to 0 regions, but did not show their surfaces, see Options
> select #9.39
1 model selected
Ungrouped to 0 regions, but did not show their surfaces, see Options
> select clear
> select #9.39
1 model selected
> select clear
> select #9.49
1 model selected
Deleted 1 regions
> select #9.42
1 model selected
Deleted 1 regions
> select #9.40
1 model selected
Deleted 1 regions
Smoothing and grouping, standard deviation 6 voxels
Showing 8 region surfaces
Got 8 regions after smoothing 6 voxels.
> select #9.2
1 model selected
Ungrouped to 5 regions
Ungrouped to 30 regions
> select #9.39
1 model selected
> select add #9.16
2 models selected
> select add #9.2
3 models selected
> select add #9.36
4 models selected
> select add #9.14
5 models selected
> select subtract #9.2
4 models selected
> select add #9.26
5 models selected
Deleted 5 regions
> select #9.30
1 model selected
Deleted 1 regions
> select #9.38
1 model selected
Deleted 1 regions
> select #9.40
1 model selected
> select add #9.24
2 models selected
Deleted 2 regions
> select #9.15
1 model selected
> select add #9.11
2 models selected
> select add #9.17
3 models selected
Deleted 3 regions
> select #9.37
1 model selected
Ungrouped to 22 regions
> select clear
> select #9.11
1 model selected
> select add #9.38
2 models selected
Deleted 2 regions
> select #9.17
1 model selected
> select add #9.26
2 models selected
> select add #9.46
3 models selected
> select subtract #9.26
2 models selected
Deleted 2 regions
> select #9.26
1 model selected
Ungrouped to 6 regions
> select clear
> select #9.37
1 model selected
> select clear
> select #9.37
1 model selected
Ungrouped to 0 regions
> select clear
> select #9.37
1 model selected
Ungrouped to 0 regions
Ungrouped to 46 regions, but did not show all surfaces, see Options
Smoothing and grouping, standard deviation 6 voxels
Showing 8 region surfaces
Got 8 regions after smoothing 6 voxels.
> select #9.2
1 model selected
> select add #9.6
2 models selected
Ungrouped to 88 regions, but did not show all surfaces, see Options
> select #9.16
1 model selected
Ungrouped to 6 regions, but did not show their surfaces, see Options
Only showing 60 of 99 regions.
Showing 60 of 99 region surfaces
> select #9.65
1 model selected
Ungrouped to 0 regions, but did not show their surfaces, see Options
Ungrouped to 3 regions, but did not show all surfaces, see Options
Only showing 60 of 101 regions.
Showing 60 of 101 region surfaces
> select clear
Smoothing and grouping, standard deviation 6 voxels
Showing 8 region surfaces
Got 8 regions after smoothing 6 voxels.
> select #9.8
1 model selected
> select add #9.5
2 models selected
> select add #9.3
3 models selected
> select add #9.7
4 models selected
> select add #9.1
5 models selected
> select add #9.4
6 models selected
Ungrouped to 153 regions, but did not show all surfaces, see Options
Only showing 60 of 155 regions.
Showing 60 of 155 region surfaces
> select #9.58
1 model selected
> select add #9.68
2 models selected
Only showing 60 of 155 regions.
Showing 60 of 155 region surfaces
> select clear
Smoothing and grouping, standard deviation 7 voxels
Showing 8 region surfaces
Got 8 regions after smoothing 7 voxels.
> select #9.8
1 model selected
> select add #9.4
2 models selected
> hide #9.2 models
> show #9.2 models
> hide #9.2 models
> hide #9.6 models
> hide #9.1 models
> hide #9.3 models
> select clear
> select #9.8
1 model selected
> select add #9.4
2 models selected
> select add #9.5
3 models selected
> hide #9.7 models
Ungrouped to 92 regions, but did not show all surfaces, see Options
Only showing 60 of 97 regions.
Showing 60 of 97 region surfaces
> select #9.82
1 model selected
> select add #9.55
2 models selected
Deleted 2 regions
> select #9.32
1 model selected
> select add #9.14
2 models selected
> select add #9.62
3 models selected
Deleted 3 regions
Drag select of 2465, 6 of 3988 triangles, 2510, 5 of 1952 triangles
> select subtract #9.77
1 model selected
> select clear
> select #9.79
1 model selected
> select add #9.77
2 models selected
Deleted 2 regions
> select #9.38
1 model selected
Deleted 1 regions
> select #9.37
1 model selected
Deleted 1 regions
> select #9.66
1 model selected
> select add #9.4
2 models selected
> select add #9.33
3 models selected
Ungrouped to 67 regions, but did not show all surfaces, see Options
Only showing 60 of 152 regions.
Showing 60 of 152 region surfaces
> select #9.3
1 model selected
> select #9.78
1 model selected
Deleted 1 regions
> select #9.71
1 model selected
> select clear
> select #9.71
1 model selected
Ungrouped to 6 regions, but did not show all surfaces, see Options
Only showing 60 of 156 regions.
Showing 60 of 156 region surfaces
Only showing 60 of 156 regions.
Showing 60 of 156 region surfaces
> select clear
Only showing 60 of 156 regions.
Showing 60 of 156 region surfaces
Only showing 60 of 156 regions.
Showing 60 of 156 region surfaces
Only showing 60 of 156 regions.
Showing 60 of 156 region surfaces
Only showing 60 of 156 regions.
Showing 60 of 156 region surfaces
Only showing 60 of 156 regions.
Showing 60 of 156 region surfaces
Smoothing and grouping, standard deviation 8 voxels
Showing 8 region surfaces
Got 8 regions after smoothing 8 voxels.
Ungrouped to 152 regions, but did not show all surfaces, see Options
Smoothing and grouping, standard deviation 8 voxels
Showing 8 region surfaces
Got 8 regions after smoothing 8 voxels.
Drag select of 2847, 64 of 36768 triangles
Ungrouped to 56 regions
> select #9.31
1 model selected
> select add #9.11
2 models selected
Deleted 2 regions
> select #9.56
1 model selected
> select add #9.57
2 models selected
Deleted 2 regions
> select #9.25
1 model selected
Deleted 1 regions
> select #9.48
1 model selected
> select add #9.44
2 models selected
Deleted 2 regions
> select #9.42
1 model selected
> select add #9.49
2 models selected
Deleted 2 regions
> select #9.63
1 model selected
Deleted 1 regions
> select #9.23
1 model selected
Deleted 1 regions
> select #9.59
1 model selected
> select #9.17
1 model selected
Deleted 1 regions
> select #9.51
1 model selected
Deleted 1 regions
> select #9.52
1 model selected
Deleted 1 regions
> select #9.33
1 model selected
> select add #9.47
2 models selected
> select add #9.27
3 models selected
> select add #9.50
4 models selected
> select subtract #9.47
3 models selected
Deleted 3 regions
Smoothing and grouping, standard deviation 9 voxels
Showing 8 region surfaces
Got 8 regions after smoothing 9 voxels.
> select #9.5
1 model selected
> select add #9.8
2 models selected
> select add #9.3
3 models selected
> select add #9.7
4 models selected
> select add #9.1
5 models selected
Ungrouped to 130 regions
> select clear
> select #9.102
1 model selected
> select add #9.105
2 models selected
> select add #9.133
3 models selected
> select add #9.93
4 models selected
> select add #9.121
5 models selected
Deleted 5 regions
> select #9.64
1 model selected
> select add #9.54
2 models selected
> select add #9.61
3 models selected
> select add #9.124
4 models selected
> select add #9.123
5 models selected
Deleted 5 regions
> select #9.119
1 model selected
Deleted 1 regions
> select #9.109
1 model selected
> select add #9.87
2 models selected
Deleted 2 regions
> select #9.118
1 model selected
Deleted 1 regions
> select #9.94
1 model selected
Deleted 1 regions
> select clear
> select #9.128
1 model selected
Deleted 1 regions
> select #9.116
1 model selected
Ungrouped to 2 regions
Ungrouped to 0 regions
> select #9.1
1 model selected
Deleted 1 regions
> select #9.3
1 model selected
Ungrouped to 0 regions
Ungrouped to 39 regions
Smoothing and grouping, standard deviation 8 voxels
Showing 8 region surfaces
Got 8 regions after smoothing 8 voxels.
> select #9.1
1 model selected
Ungrouped to 39 regions
> select clear
> select #9.21
1 model selected
Deleted 1 regions
> select clear
> select #9.14
1 model selected
Ungrouped to 6 regions
> select clear
> select #9.48
1 model selected
Ungrouped to 0 regions
> select #9.48
1 model selected
> select clear
Smoothing and grouping, standard deviation 9 voxels
Showing 8 region surfaces
Got 8 regions after smoothing 9 voxels.
> select #9.1
1 model selected
Ungrouped to 42 regions
> select clear
> select #9.34
1 model selected
Ungrouped to 10 regions
> select clear
> select #9.51
1 model selected
Deleted 1 regions
> select clear
Smoothing and grouping, standard deviation 10 voxels
Showing 8 region surfaces
Got 8 regions after smoothing 10 voxels.
> select #9.3
1 model selected
> select add #9.10
2 models selected
Ungrouped to 78 regions
> select clear
> select #9.69
1 model selected
Ungrouped to 10 regions
> select clear
> select #9.10
1 model selected
> select #9.29
1 model selected
Ungrouped to 5 regions
> select clear
> select #9.69
1 model selected
Deleted 1 regions
Smoothing and grouping, standard deviation 11 voxels
Showing 8 region surfaces
Got 8 regions after smoothing 11 voxels.
> select #9.3
1 model selected
Ungrouped to 56 regions
> select #9.13
1 model selected
Deleted 1 regions
> select #9.59
1 model selected
> select #9.54
1 model selected
Deleted 1 regions
> select #9.16
1 model selected
Ungrouped to 6 regions
> select clear
> select #9.67
1 model selected
> select add #9.13
2 models selected
Deleted 2 regions
> select clear
> select #9.42
1 model selected
Deleted 1 regions
> select #9.21
1 model selected
> select clear
> select #9.23
1 model selected
Deleted 1 regions
Smoothing and grouping, standard deviation 12 voxels
Showing 8 region surfaces
Got 8 regions after smoothing 12 voxels.
> select #9.4
1 model selected
> select add #9.9
2 models selected
> select add #9.13
3 models selected
Ungrouped to 34 regions
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right select
> select #9.19
1 model selected
Drag select of 2634, 12 of 18068 triangles
> select add #9.36
3 models selected
> select add #9.29
4 models selected
> select subtract #9.32
3 models selected
Deleted 3 regions
> select #9.11
1 model selected
Deleted 1 regions
> select #9.33
1 model selected
Deleted 1 regions
> save /Users/goncalvesgm/Desktop/ChimeraX-figures/CRD-talk-
> moviesandfigs/trying-to-make-NE.seg models #9
> select #9.17
1 model selected
> select add #9.30
2 models selected
> select add #9.37
3 models selected
Deleted 3 regions
> select #9.32
1 model selected
Ungrouped to 22 regions
> select clear
> select #9.45
1 model selected
> select add #9.11
2 models selected
> select add #9.34
3 models selected
> select subtract #9.34
2 models selected
Deleted 2 regions
> select #9.48
1 model selected
> select add #9.37
2 models selected
Deleted 2 regions
> select #9.19
1 model selected
> select #9.19
1 model selected
> select clear
> select #9.19
1 model selected
Deleted 1 regions
> select #9.28
1 model selected
Showing 47 region surfaces
Grouped 1 regions
> select clear
Smoothing and grouping, standard deviation 13 voxels
Showing 8 region surfaces
Got 8 regions after smoothing 13 voxels.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10-rc2025.06.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1079, in OpenSegmentation
segfile.show_open_dialog(self.session, dir)
File
"/Applications/ChimeraX-1.10-rc2025.06.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 145, in show_open_dialog
show_open_file_dialog(session, format_name = 'Segmentation',
TypeError: show_open_file_dialog() got an unexpected keyword argument
'format_name'
TypeError: show_open_file_dialog() got an unexpected keyword argument
'format_name'
File
"/Applications/ChimeraX-1.10-rc2025.06.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 145, in show_open_dialog
show_open_file_dialog(session, format_name = 'Segmentation',
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10-rc2025.06.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segment_dialog.py", line 1079, in OpenSegmentation
segfile.show_open_dialog(self.session, dir)
File
"/Applications/ChimeraX-1.10-rc2025.06.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 145, in show_open_dialog
show_open_file_dialog(session, format_name = 'Segmentation',
TypeError: show_open_file_dialog() got an unexpected keyword argument
'format_name'
TypeError: show_open_file_dialog() got an unexpected keyword argument
'format_name'
File
"/Applications/ChimeraX-1.10-rc2025.06.02.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/segger/segfile.py", line 145, in show_open_dialog
show_open_file_dialog(session, format_name = 'Segmentation',
See log for complete Python traceback.
> open /Users/goncalvesgm/Desktop/ChimeraX-figures/CRD-talk-
> moviesandfigs/trying-to-make-NE.seg
Summary of feedback from opening /Users/goncalvesgm/Desktop/ChimeraX-
figures/CRD-talk-moviesandfigs/trying-to-make-NE.seg
---
notes | Volume data not found
Showing 34 region surfaces
Opened trying-to-make-NE.seg
Showing trying-to-make-NE.seg - 34 regions, 34 surfaces
> select #9.25
1 model selected
> select add #9.13
2 models selected
> select subtract #9.13
1 model selected
Deleted 1 regions
> select #9.28
1 model selected
> select add #9.31
2 models selected
Deleted 2 regions
> select #9.19
1 model selected
> select clear
> select #9.13
1 model selected
Ungrouped to 6 regions
> select clear
> select #9.28
1 model selected
Deleted 1 regions
> select #9.31
1 model selected
> select add #9.27
2 models selected
Deleted 2 regions
> select #9.19
1 model selected
Ungrouped to 0 regions
> select #9.15
1 model selected
Ungrouped to 3 regions
> select #9.13
1 model selected
Ungrouped to 0 regions
> select clear
> select #9.8
1 model selected
Ungrouped to 22 regions
> select #9.41
1 model selected
> select #9.40
1 model selected
> select add #9.48
2 models selected
Deleted 2 regions
> select #9.41
1 model selected
Deleted 1 regions
> select #9.44
1 model selected
Deleted 1 regions
> select #9.51
1 model selected
Ungrouped to 6 regions
Ungrouped to 0 regions
> select clear
> select #9.48
1 model selected
> select clear
Ungrouped to 54 regions
> select #9.9
1 model selected
Ungrouped to 10 regions
> select #9.117
1 model selected
Deleted 1 regions
> select #9.15
1 model selected
Deleted 1 regions
> select #9.13
1 model selected
Ungrouped to 0 regions
> select #9.13
1 model selected
> select #9.27
1 model selected
Deleted 1 regions
> select #9.37
1 model selected
> select #9.35
1 model selected
Deleted 1 regions
Segmentation map not opened
> select clear
Segmentation map not opened
> select clear
Segmentation map not opened
Drag select of 2822, 8723 of 39380 triangles, 2199, 591 of 3984 triangles,
2572, 2680 of 3064 triangles, 2556, 2695, 2471, 2517, 731, 1239 of 1396
triangles, 1028, 1237 of 1316 triangles, 2304, 912 of 1236 triangles, 1709,
2503, 664, 1579, 1447, 2036, 1845, 845, 884 of 1268 triangles, 1255, 1328,
1150 of 1176 triangles, 1330, 1717 of 1760 triangles, 1480, 554, 619, 802,
913, 129 of 136 triangles, 1088, 74 of 1004 triangles, 2159, 2168, 2187, 124
of 1176 triangles, 2190, 3018 of 3428 triangles, 2203, 1605 of 3024 triangles,
2285, 2302, 2303, 1186 of 1384 triangles, 2329, 2391, 627, 16 of 1136
triangles, 741, 425 of 1884 triangles, 857, 444 of 844 triangles, 1536, 689 of
2356 triangles, 1711, 337 of 612 triangles, 1712, 218 of 600 triangles, 1713,
318 of 876 triangles, 1909
Grouped 45 regions
> select #9.1
1 model selected
Ungrouped to 45 regions
> select #9.26
1 model selected
Ungrouped to 30 regions
> select #9.142
1 model selected
Ungrouped to 23 regions
> select #9.26
1 model selected
> select add #9.152
2 models selected
> select add #9.149
3 models selected
> select add #9.166
4 models selected
> select add #9.154
5 models selected
> select add #9.132
6 models selected
> select add #9.137
7 models selected
Deleted 7 regions
> select #9.141
1 model selected
> select add #9.121
2 models selected
> select add #9.140
3 models selected
> select subtract #9.141
2 models selected
> select clear
> select #9.121
1 model selected
Deleted 1 regions
> select #9.140
1 model selected
> select add #9.141
2 models selected
Ungrouped to 6 regions
> select clear
> select #9.26
1 model selected
> select add #9.137
2 models selected
Deleted 2 regions
> select #9.121
1 model selected
Deleted 1 regions
> select #9.157
1 model selected
Deleted 1 regions
> select #9.131
1 model selected
> select add #9.134
2 models selected
> select subtract #9.134
1 model selected
> select add #9.122
2 models selected
Deleted 2 regions
Select one or more regions to delete
> select #9.163
1 model selected
Ungrouped to 3 regions
Ungrouped to 0 regions
> select clear
> select #9.121
1 model selected
Ungrouped to 0 regions
> select #9.121
1 model selected
Ungrouped to 0 regions
Drag select of 2858, 25963 of 38728 triangles, 2856, 7370 of 31300 triangles,
2616, 1650, 560, 565, 672, 673, 1537, 1652, 1771, 1823, 1712, 741, 2391, 2036,
1255, 2695, 1028, 1480, 2190, 664, 1536, 1328, 845, 2471, 1713, 802, 554, 627,
1711, 2302, 2285, 731, 2159, 2517, 2168, 1579, 1330, 857, 1447, 2503, 619,
2203, 2187, 2556, 2572, 1088, 2329, 2199, 2304, 1845, 1909, 2303, 913, 1709,
718, 767, 1013, 341 of 344 triangles, 1272, 1417, 1627, 1636, 1688, 1691,
2069, 2348, 2362, 6 of 1232 triangles, 2377, 2423, 2425, 2483, 2504, 2548,
2561, 2691, 2666 of 2668 triangles, 2729, 2749, 1849 of 2416 triangles, 285,
292, 529, 536, 537, 834, 891, 955, 1073, 2160, 603 of 1104 triangles, 2174,
2182, 2189, 3407 of 3700 triangles, 2216, 2242, 2525, 1229, 1234, 1373, 538,
726, 777
Grouped 100 regions
> ui mousemode right clip
> ui mousemode right select
Drag select of 2863, 14727 of 28652 triangles, 1288, 365, 569, 583, 643, 681,
750, 823, 871, 929, 1039, 1102, 1291, 1296, 1349, 1468, 1542, 1543, 1605,
1658, 1667, 1717, 1728, 1729, 1730, 1731, 1777, 1780, 1829, 1858, 1921, 2042,
2090, 2167, 2176, 2178, 2186, 2188, 2210, 2213, 2342, 2352, 2354, 2358, 2366,
2400, 2448, 2531, 2564, 2567, 2607, 2613, 2614, 2771, 2772, 2866, 54236 of
121292 triangles
Grouped 57 regions
Drag select of 2867, 28802 of 174232 triangles
Ungrouped to 57 regions
Ungrouped to 212 regions
Ungrouped to 201 regions
Ungrouped to 92 regions
> select #9.180
1 model selected
> select add #9.161
2 models selected
> select add #9.101
3 models selected
Deleted 3 regions
> select #9.176
1 model selected
> select add #9.195
2 models selected
> select subtract #9.195
1 model selected
Deleted 1 regions
> select #9.104
1 model selected
Deleted 1 regions
> select #9.100
1 model selected
Deleted 1 regions
> select #9.195
1 model selected
> select add #9.197
2 models selected
Ungrouped to 27 regions
> select clear
> select #9.494
1 model selected
> select add #9.180
2 models selected
Deleted 2 regions
> select #9.387
1 model selected
Ungrouped to 0 regions
> select #9.387
1 model selected
Deleted 1 regions
> select #9.408
1 model selected
> select add #9.10
2 models selected
> select add #9.100
3 models selected
> select add #9.45
4 models selected
Deleted 4 regions
> select #9.484
1 model selected
Deleted 1 regions
> select add #9.39
1 model selected
> select add #9.493
2 models selected
> select subtract #9.493
1 model selected
Deleted 1 regions
> select #9.104
1 model selected
Deleted 1 regions
> select #9.16
1 model selected
Deleted 1 regions
> select #9.230
1 model selected
Deleted 1 regions
> select #9.364
1 model selected
> select add #9.471
2 models selected
Ungrouped to 10 regions
> select #9.195
1 model selected
> select add #9.364
2 models selected
Deleted 2 regions
> select #9.11
1 model selected
> select add #9.5
2 models selected
Deleted 2 regions
> select #9.178
1 model selected
> select clear
> select #9.178
1 model selected
Ungrouped to 5 regions
> select #9.387
1 model selected
Deleted 1 regions
Drag select of 2860, 2861, 929, 1728, 1349, 1543, 1658, 583, 1667, 1731, 1102,
871, 1730, 1291, 643, 1717, 1296, 1729, 823, 750, 1858, 1039, 1468, 2090,
1780, 681, 569, 1542, 1605, 1921, 2042, 461, 466, 499, 1606, 1670, 1671, 1734,
1922, 1350, 1396, 1487, 1289, 1524, 1602, 309, 316, 747, 863, 914, 986, 1083,
1263, 1277, 1281, 1457, 1538, 1590, 1594, 1642, 1645, 1654, 1719, 1460, 1601,
1044, 465, 1007, 320, 369, 464, 500, 680, 712, 819, 821, 1106, 1212, 370, 752,
1672, 1890, 584, 640, 824, 1006, 457, 498, 279, 319, 1143, 1347, 1485, 1603,
1662, 575, 636, 677, 678, 748, 870, 372, 644, 460, 462, 463, 576, 578, 581,
586, 638, 642, 684, 1417, 741, 2036, 1255, 1028, 1480, 1328, 1229, 536, 1650,
1537, 731, 673, 538, 292, 913, 1712, 718, 1073, 1013, 1272, 1536, 285, 627,
672, 1691, 1330, 857, 537, 619, 529, 1234, 1909, 2069, 1709, 1373, 1771, 834,
845, 560, 1823, 1688, 565, 1579, 1636, 891, 1652, 777, 1713, 554, 802, 1711,
1447, 955, 1088, 726, 1627, 1845, 664, 364, 456, 579, 1607, 1668, 1732, 582,
639, 682, 683, 710, 751, 513, 652, 271, 308, 1456, 1541, 1597, 1193, 1335,
401, 527, 760, 884, 1664, 1725, 1511, 1535, 1583, 415, 418, 422, 539, 544,
546, 547, 614, 615, 663, 1516, 1715, 1767, 1435, 1572, 1635, 1703, 927, 1292,
671, 702, 706, 805, 808, 1085, 354, 488, 559, 624, 438, 563, 339, 481, 531,
609, 384, 470, 567, 626, 707, 814, 866, 867, 1094, 429, 982, 389, 391, 393,
518, 523, 601, 653, 327, 597, 348, 733, 1498, 1534, 1568, 355, 437, 562, 300,
342, 413, 483, 431, 434, 489, 525, 608, 690, 763, 831, 832, 1063, 371, 467,
468, 444, 493, 366, 637, 548, 622, 668, 670, 705, 736, 1237, 1531, 1559, 1563,
662, 699, 786, 790, 1080, 1188, 1643, 1876, 399, 1593, 1653, 1655, 1720, 1774,
1914, 1576, 1641, 1704, 1598, 1723, 441, 1136, 1340, 1482, 1591, 1651, 1175,
1320, 553, 738, 800, 1497, 1692, 1693, 1748, 492, 630, 1418, 1529, 1557, 1659,
1617, 1684, 448, 450, 454, 564, 566, 633, 676, 1584, 1647, 1648, 1708, 1907,
344, 616, 477, 603, 658, 691, 693, 770, 771, 1071, 1562, 1624, 1628, 1689,
1743, 1899, 561, 625, 809, 994, 1556, 1686, 1269, 1508, 1585, 1571, 1757, 360,
447, 451, 494, 997, 742, 1459, 1465, 1660, 1666, 1714, 1724, 2192, 2376, 2386,
2436, 2495, 2546, 2568, 2602, 2711, 2736, 2773, 333, 390, 392, 475, 945, 1661,
1778, 1619, 1739, 329, 501, 505, 506, 521, 590, 598, 647, 650, 715, 717, 754,
826, 827, 878, 1014, 1053, 1123, 1162, 1217, 1222, 1307, 1407, 1548, 1625,
1676, 2166, 2171, 2209, 2218, 2269, 2281, 2282, 2308, 2312, 2316, 2332, 2538,
2542, 2549, 2552, 2559, 2571, 2596, 2686, 351, 421, 424, 1282, 315, 317, 573,
585, 588, 872, 926, 998, 1104, 2165, 2172, 2175, 2183, 2197, 2356, 2422, 2536,
1526, 1527, 1614, 1675, 1680, 1681, 1737, 1808, 1892, 1290, 1540, 1596, 1599
Grouped 489 regions
> select #9.1
1 model selected
Ungrouped to 489 regions
> select #9.485
1 model selected
> select add #9.203
2 models selected
> select add #9.261
3 models selected
> select add #9.59
4 models selected
Deleted 4 regions
> select add #9.236
1 model selected
> select add #9.250
2 models selected
> select add #9.246
3 models selected
> select add #9.338
4 models selected
> select add #9.22
5 models selected
> select add #9.419
6 models selected
> select add #9.70
7 models selected
> select add #9.172
8 models selected
> select add #9.237
9 models selected
> select add #9.114
10 models selected
Deleted 10 regions
> select #9.52
1 model selected
> select add #9.169
2 models selected
> select add #9.283
3 models selected
> select add #9.159
4 models selected
Deleted 4 regions
Drag select of 364, 1485, 1686, 370, 1028, 1591, 1681, 1892, 271, 2559, 1650,
1593, 431, 1537, 1014, 1641, 914, 292, 1053, 1498, 1143, 300, 1737, 413, 1563,
1712, 1527, 929, 1720, 348, 1594, 1672, 1614, 1536, 1576, 1603, 1658, 355,
1123, 285, 1642, 1725, 1717, 1526, 316, 1619, 1858, 309, 597, 1562, 1606,
1723, 1645, 1732, 351, 1692, 1524, 1660, 2552, 1590, 2736, 1704, 1516, 1511,
1823, 1876, 2549, 327, 1579, 1664, 1748, 1080, 1460, 1724, 339, 1542, 1085,
994, 315, 421, 1540, 1568, 360, 1106, 945, 429, 1572, 1652, 870, 392, 1584,
320, 1667, 366, 1585, 1102, 1731, 1624, 1730, 1671, 2568, 329, 1703, 1655,
1729, 1693, 1743, 1715, 955, 344, 1559, 1104, 1739, 1541, 1684, 863, 1899,
1709, 1556, 1680, 2602, 1643, 1728, 1531, 1497, 1480, 1670, 1543, 1651, 1625,
867, 2861, 30627 of 30688 triangles, 866, 342, 1808, 1659, 1006, 1039, 1535,
384, 418, 1780, 1617, 279, 997, 1767, 389, 1548, 878, 1596, 998, 1628, 1778,
415, 1456, 1601, 424, 1648, 1073, 1013, 372, 371, 2773, 871, 1691, 1647, 1136,
1662, 1675, 1063, 1557, 2860, 1757, 1435, 1676, 1708, 422, 354, 1605, 2571,
1635, 1071, 1890, 391, 308, 1534, 1529, 1661, 390, 1602, 1771, 1666, 1734,
399, 1688, 1774, 1487, 1653, 1538, 393, 1007, 333, 1508, 2711, 317, 1636, 891,
1597, 369, 1598, 1482, 2546, 1599, 986, 1583, 1083, 1713, 1571, 1719, 401,
1711, 1714, 1689, 1607, 1094, 2596, 1088, 319, 1668, 1845, 1627, 2686, 1654,
2282, 1914, 475, 1255, 821, 2197, 736, 680, 630, 751, 1328, 1229, 583, 608,
652, 731, 498, 1922, 2281, 463, 468, 1320, 564, 523, 581, 642, 590, 718, 2376,
563, 678, 693, 2386, 1281, 567, 1162, 559, 2312, 506, 662, 742, 2269, 1217,
1175, 1296, 1330, 2316, 544, 609, 619, 603, 2090, 663, 1907, 1909, 466, 598,
444, 493, 2171, 531, 465, 717, 834, 1335, 1282, 565, 640, 636, 578, 647, 1290,
832, 738, 650, 553, 586, 625, 1350, 614, 824, 2183, 705, 573, 441, 579, 777,
539, 554, 677, 1222, 501, 658, 691, 456, 584, 715, 670, 747, 790, 2332, 827,
637, 750, 1277, 683, 561, 548, 726, 450, 624, 763, 477, 527, 616, 454, 664,
682, 1417, 467, 741, 1340, 676, 566, 2036, 814, 536, 500, 1291, 447, 643, 494,
448, 492, 707, 2308, 488, 2172, 2175, 585, 673, 575, 538, 1289, 690, 1347,
684, 770, 668, 461, 546, 2218, 462, 1349, 1272, 2166, 800, 627, 464, 562, 672,
826, 489, 633, 857, 712, 537, 2542, 529, 653, 1396, 1234, 681, 1237, 451,
2536, 460, 2069, 1263, 505, 638, 752, 1373, 786, 622, 499, 2165, 845, 582,
671, 560, 831, 438, 483, 518, 706, 481, 819, 513, 601, 457, 626, 2356, 639,
808, 569, 2422, 437, 1921, 702, 2192, 470, 434, 699, 525, 2209, 576, 644,
2538, 1269, 521, 1307, 733, 2495, 771, 710, 588, 823, 1292, 748, 615, 754,
760, 547, 1193, 1418, 2042, 805
Grouped 471 regions
Map not found - please associate a map first
Please select a map from which density will be taken
> select #9.1
1 model selected
Please select a map from which density will be taken
> select clear
Map not found - please associate a map first
> save /Users/goncalvesgm/Desktop/ChimeraX-figures/CRD-talk-
> moviesandfigs/trying-to-make-NE.seg models #9
Saving 1 regions to mrc file...
Opened emdb14321_region_maybeNE.mrc as #16, grid size 121,121,44, pixel 13.8,
shown at step 1, values float32
Masked map emdb 14321, wrote emdb14321_region_maybeNE.mrc
> hide #!9 models
> vop resample #16 ongrid #15
Opened emdb14321_region_maybeNE.mrc resampled as #17, grid size 144,144,144,
pixel 13.8, shown at step 1, values float32
> volume #17 level 0.0746
> volume #17 level 0.01035
> volume #17 step 2
> volume #17 step 1
> gaussian help
Unknown command: gaussian help
> vop gaussian help
> volume gaussian help
Missing or invalid "volumes" argument: invalid density maps specifier
> vop gaussian #17 sd1
> volume gaussian #17 sd1
Expected a keyword
> vop gaussian #17 sd 1
Opened emdb14321_region_maybeNE.mrc resampled gaussian as #18, grid size
144,144,144, pixel 13.8, shown at step 1, values float32
> volume #18 level 0.08235
> vop gaussian #17 sd 2
Opened emdb14321_region_maybeNE.mrc resampled gaussian as #19, grid size
144,144,144, pixel 13.8, shown at step 1, values float32
> volume #19 level 0.07545
> vop gaussian #17 sd 5
Opened emdb14321_region_maybeNE.mrc resampled gaussian as #20, grid size
144,144,144, pixel 13.8, shown at step 1, values float32
> volume #20 level 0.07057
> volume #20 color #929292
> volume #20 color darkgrey
> lighting soft
> close #18-19
> save /Users/goncalvesgm/Desktop/ChimeraX-figures/CRD-talk-
> moviesandfigs/emdb14321_region_maybeNE.mrc models #17
> volume #20 level 0.07057
> volume #20 level 0.01345
> volume #20 step 2
> volume #20 level 0.2268
> volume #20 level 0.02984
> vop gaussian #20 sdev 41.4
Opened emdb14321_region_maybeNE.mrc resampled gaussian as #18, grid size
144,144,144, pixel 13.8, shown at step 1, values float32
> volume #18 level 0.04102
> volume #18 color silver
> volume #18 level 0.06526
> show #!1 models
> volume #18 level 0.03938
> volume #18 step 2
> volume #18 level 0.01688
> volume #18 color #c0c0c033
> volume #18 level 0.06301
> volume #18 step 1
> volume #18 level 0.108
> volume #18 level 0.1091
> show #!20 models
> hide #!18 models
> hide #!20 models
> show #!18 models
> show #!17 models
> hide #!18 models
> hide #!17 models
> show #!17 models
> show #!16 models
> hide #!17 models
> hide #!16 models
> show #!17 models
> close #16
> vop gaussian #17 sdev 20
Opened emdb14321_region_maybeNE.mrc gaussian as #16, grid size 144,144,144,
pixel 13.8, shown at step 1, values float32
> volume #16 level 0.2743
> volume #16 level 0.1282
> show #!17 models
> volume #16 level 0.1756
> hide #!17 models
> hide #!16 models
> show #!17 models
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right clip
> view
> surface close
> hide all cartoons
> surface dust #17 size 138
> show #1 cartoons
> lighting simple
> show #!2 models
> show #1-8:A0-J3 cartoons
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #1-8:K*-Q* c
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide all cartoons
> show #2 cartoons
> show #1-8 cartoons
> show #!8 models
> hide #!8 models
> show #!7 models
> show #!8 models
> ui mousemode right "clip rotate"
> view
> ui mousemode right select
> color #1-8/K0,K2,L0,L2,M0,M2,N0,N2,O0,O2,P0,P2,Q0,Q2,R0,R2,S0,S2 gold
> name frozen #1-8/K0,K2,L0,L2,M0,M2,N0,N2,O0,O2,P0,P2,Q0,Q2,R0,R2,S0,S2
> ycomplexes-outermost
Missing or invalid "objects" argument: invalid objects specifier
> name frozen ycomplexes-outermost
> #1-8/K0,K2,L0,L2,M0,M2,N0,N2,O0,O2,P0,P2,Q0,Q2,R0,R2,S0,S2
> name frozen ycomplexes-innermost
> #1-8/K1,K3,L1,L3,M1,M3,N1,N3,O1,O3,P1,P3,Q1,Q3,R1,R3,S1,S3
> ui mousemode right clip
> show #!4 models
> show #!5 models
> show #!6 models
> ui mousemode right "clip rotate"
> save /Users/goncalvesgm/Desktop/ChimeraX-figures/CRD-talk-
> moviesandfigs/npccartoon-lattice.cxs includeMaps true
> ui mousemode right clip
> name list
Y-complexes-all [2397856 atoms, 2449728 bonds, 8 models]
no-change-podDiff [1752984 atoms, 1789216 bonds, 8 models]
pododiff-high [454585 atoms, 464648 bonds, 9 models]
pododiff-low [1394248 atoms, 1422160 bonds, 8 models]
pododiff-mid [904720 atoms, 924688 bonds, 8 models]
ycomplexes-innermost [751072 atoms, 767872 bonds, 8 models]
ycomplexes-outermost [751072 atoms, 767872 bonds, 8 models]
> color ycomplexes-innermost purple
> color ycomplexes-outermost pink
> color ycomplexes-outermost magenta
> color ycomplexes-innermost pink
> color ycomplexes-innermost lightblue purple
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color ycomplexes-innermost slateblue
> color ycomplexes-outermost orchid
> select down
Nothing selected
> select down
Nothing selected
> name frozen ycomplexes-outermost
> #1-8/K1,K3,L1,L3,M1,M3,N1,N3,O1,O3,P1,P3,Q1,Q3,R1,R3,S1,S3,T1
> name frozen ycomplexes-innermost
> #1-8/K0,K2,L0,L2,M0,M2,N0,N2,O0,O2,P0,P2,Q0,Q2,R0,R2,S0,S2,T0
> color ycomplexes-innermost slateblue
> color ycomplexes-outermost orchid
> select #*/C0-C2
384312 atoms, 391920 bonds, 48264 residues, 8 models selected
> select #*/C5
Nothing selected
> select #*/C4
128104 atoms, 130640 bonds, 16088 residues, 8 models selected
> select #*/C2,C3
256208 atoms, 261280 bonds, 32176 residues, 8 models selected
> select #*/C0,C1
256208 atoms, 261280 bonds, 32176 residues, 8 models selected
> select #*/A0-A3
210176 atoms, 213984 bonds, 26176 residues, 8 models selected
> name frozen inner-ring-all #1-8/C0,C1,A0-A3,B*,D0-D3,F*
> color inner-ring-all yellow
> ui mousemode right select
> select clear
> name frozen TM-nups-all #1-8/E*,00-17
> color TM-nups-all dark orange
> name frozen TM-nups-all #1-8/E*,10-17
> color TM-nups-all dark orange
> color 00-04 light blue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> name frozen TM-nups-all #1-8/E*,10-17
> color TM-nups-all dark orange
> color #1-8/00-04 light blue
> show TM-nups c
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show TM-nups-all cartoons
> volume #17 color #99bfe54d
> volume #17 level 0.1483
> volume #17 level 0.05519
> volume #18 level 0.03657
> volume #18 color silver
> volume #18 level 0.1502
> view
> volume #17 level 0.07417
> name frozen FG-nups #1/H*,I*,J0-J3, U*
> color FG-nups yellow
> color inner-ring-all light green
> name frozen FG-nups #1-8/H*,I*,J0-J3, U*
> color FG-nups yellow
> name frozen cyt-nups-all #1-8/J4,W0,V0,00-04
> color cyt-nups-all light blue
> volume #17 color darkgrey
> volume #17 color silver
> volume #17 color darkgrey
> volume #17 color #929292
> volume #17 color darkgrey
> volume #17 color black
> volume #17 color darkgrey
> save /Users/goncalvesgm/Desktop/ChimeraX-figures/CRD-talk-
> moviesandfigs/npccartoon-lattice.cxs includeMaps true
> select #1/C0-C2
48039 atoms, 48990 bonds, 6033 residues, 1 model selected
> select #1/C2-C4
48039 atoms, 48990 bonds, 6033 residues, 1 model selected
> select #1-8/C2-C4
384312 atoms, 391920 bonds, 48264 residues, 8 models selected
> select #1-8/A4-A6
140640 atoms, 143328 bonds, 17424 residues, 8 models selected
> select #1-8/D4,D5
165808 atoms, 169088 bonds, 16 pseudobonds, 20992 residues, 16 models selected
> select #1-8/A4-A6,C2-C4,D4,D5
690760 atoms, 704336 bonds, 16 pseudobonds, 86680 residues, 16 models selected
> name frozen linkers-all #1-8/A4-A6,C2-C4,D4-D5
> color linkers-all cyan
> select clear
> view
> surface #1-8 resolution 50
808 Gaussian surfaces, threshold level 0.004 - 0.020
> lighting flat
> graphics silhouettes false
> surface close
> lighting simple
> lighting soft
> hide all cartoons
> surface ycomplexes-outermost resolution 50
152 Gaussian surfaces, threshold level 0.008 - 0.020
> lighting flat
> hide all surfaces
> surface hidePatches
> surface help
Expected an atoms specifier or a keyword
> surface close
> surface ycomplexes-innermost resolution 50
152 Gaussian surfaces, threshold level 0.008 - 0.020
> camera mono
> camera ortho
> surface close
> surface #1/K0 resolution 50
1 Gaussian surfaces, threshold level 0.014
> surface #1/K0,L0,M0,N0,O0,P0,Q0,R0,S0 resolution 50
9 Gaussian surfaces, threshold level 0.008 - 0.020
> cd /Users/goncalvesgm/Desktop/ChimeraX-figures/CRD-talk-moviesandfigs
Current working directory is: /Users/goncalvesgm/Desktop/ChimeraX-figures/CRD-
talk-moviesandfigs
> movie record
> wait 50
> surface #2/K0,L0,M0,N0,O0,P0,Q0,R0,S0 resolution 50
9 Gaussian surfaces, threshold level 0.008 - 0.020
> movie crossfade 50
> wait 50
> movie encode
Movie saved to /Users/goncalvesgm/Desktop/movie.mp4
> surface close
> movie record
> surface #1/K0,L0,M0,N0,O0,P0,Q0,R0,S0 resolution 50
9 Gaussian surfaces, threshold level 0.008 - 0.020
> movie crossfade 50
> surface #2/K0,L0,M0,N0,O0,P0,Q0,R0,S0 resolution 50
9 Gaussian surfaces, threshold level 0.008 - 0.020
> movie crossfade 50
> movie encode
movie crossfade cannot be used until one frame has been recorded.
> surface close
> movie record
> wait 50
> surface #1/K0,L0,M0,N0,O0,P0,Q0,R0,S0 resolution 50
9 Gaussian surfaces, threshold level 0.008 - 0.020
> movie crossfade 50
> wait50; surface #2/K0,L0,M0,N0,O0,P0,Q0,R0,S0 resolution 50; movie crossfade
> 50;movie encode
Unknown command: wait50; surface #2/K0,L0,M0,N0,O0,P0,Q0,R0,S0 resolution 50;
movie crossfade 50;movie encode
> surface close
> movie record
Already recording a movie
> movie reset
> surface close
> movie record
> wait 50
> surface #1/K0,L0,M0,N0,O0,P0,Q0,R0,S0 resolution 50
9 Gaussian surfaces, threshold level 0.008 - 0.020
> movie crossfade 50
> wait 50
> surface #2/K0,L0,M0,N0,O0,P0,Q0,R0,S0 resolution 50
9 Gaussian surfaces, threshold level 0.008 - 0.020
> movie crossfade 50
> movie encode
Movie saved to /Users/goncalvesgm/Desktop/movie.mp4
> surface close
> movie record
> wait 50
> surface #1/K0,L0,M0,N0,O0,P0,Q0,R0,S0 resolution 50
9 Gaussian surfaces, threshold level 0.008 - 0.020
> movie crossfade 50
> wait 50
> surface #2/K0,L0,M0,N0,O0,P0,Q0,R0,S0 resolution 50
9 Gaussian surfaces, threshold level 0.008 - 0.020
> movie crossfade 50
> movie encode
Movie saved to /Users/goncalvesgm/Desktop/movie.mp4
> surface close
> movie record
> wait 10
> surface #1/K0,L0,M0,N0,O0,P0,Q0,R0,S0 resolution 50
9 Gaussian surfaces, threshold level 0.008 - 0.020
> movie crossfade 10
> wait 25
> surface #2/K0,L0,M0,N0,O0,P0,Q0,R0,S0 resolution 50
9 Gaussian surfaces, threshold level 0.008 - 0.020
> movie crossfade 25
> movie encode
Movie saved to /Users/goncalvesgm/Desktop/movie.mp4
> surface close
> surface #1/K0,L0,M0,P0,R0,S0 resolution 50
6 Gaussian surfaces, threshold level 0.008 - 0.020
> surface #1/K0,L0,M0,P0,R0,S0 resolution 25
6 Gaussian surfaces, threshold level 0.014 - 0.021
> show #1/K0,L0,M0,P0,R0,S0 cartoons
> surface close
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10rc202505310246 (2025-05-31)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,1
Model Number: Z14V0015WLL/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: mBoot-18000.120.36
OS Loader Version: 11881.140.96.701.1
Software:
System Software Overview:
System Version: macOS 15.7.7 (24G720)
Kernel Version: Darwin 24.6.0
Time since boot: 21 days, 15 hours, 59 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL P2419H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.3.4
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10rc202505310246
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
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: 1.6.2
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: 2.2.1
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.1
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.8.2
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.1
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.13.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
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
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.3.5
pytest-cov: 6.1.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 26.4.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.13.2
tzdata: 2025.2
urllib3: 2.4.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
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