![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Closed 15 months ago
#15636 closed defect (duplicate)
Crash waking Mac from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.4.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000207403ac0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, PIL._webp (total: 124)
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{
"uptime" : 2000000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 483559,
"osVersion" : {
"train" : "macOS 14.4.1",
"build" : "23E224",
"releaseType" : "User"
},
"captureTime" : "2024-07-19 10:36:33.4390 -0500",
"codeSigningMonitor" : 1,
"incident" : "DAB58396-878C-4367-8718-159A221F828F",
"pid" : 23322,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-07-18 11:51:41.6515 -0500",
"procStartAbsTime" : 48716523019572,
"procExitAbsTime" : 49392325403125,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"3A0898B3-BBDB-57AB-990B-31EFB916B62E","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "30A8010E-BBCF-7AA7-F854-CC551266B6A0",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 10,
"sleepWakeUUID" : "FBE905C4-E97D-43AB-B2A1-D463BADE145D",
"sip" : "enabled",
"vmRegionInfo" : "0x66a2ad25c378 is not in any region. Bytes after previous region: 7294685660025 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600020000000-600040000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x0000e6a2ad25c378","rawCodes":[1,253586364023672],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000e6a2ad25c378 -> 0x000066a2ad25c378 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":23322},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x66a2ad25c378 is not in any region. Bytes after previous region: 7294685660025 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600020000000-600040000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
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"faultingThread" : 0,
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System Profile:
Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports
Model: MacBookPro17,1, BootROM 10151.101.3, proc 8:4:4 processors, 16 GB, SMC
Thunderbolt Bus: MacBook Pro, Apple Inc.
Thunderbolt Bus: MacBook Pro, Apple Inc.
Boot Volume File System Type: apfs
Display: LG ULTRAFINE, 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition), Main, MirrorOff, Online
Graphics: Apple M1, Apple M1, Built-In
USB Device: USB31Bus
USB Device: 4-Port USB 2.0 Hub
USB Device: COLOR CALIBRATION SENSOR
USB Device: Keyboard Hub
USB Device: Apple Keyboard
USB Device: LG Monitor Controls
USB Device: USB31Bus
Memory Module: LPDDR4, Micron
AirPort: spairport_wireless_card_type_wifi (0x14E4, 0x4378), wl0: Jan 13 2024 03:06:59 version 18.20.440.9.7.8.167 FWID 01-7be24857
AirPort:
Network Service: Thunderbolt Ethernet, Ethernet, en5
Network Service: Wi-Fi, AirPort, en0
PCI Card: Apple 57762-A0, Ethernet Controller, Thunderbolt@3,0,0
Thunderbolt Device: Thunderbolt to Gigabit Ethernet Adapter, Apple Inc., 1, 5.5
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 7LIA fromDatabase pdb format mmcif
7lia title:
5-HT bound serotonin transporter reconstituted in lipid nanodisc in presence
of NaCl in outward facing conformation [more info...]
Chain information for 7lia #1
---
Chain | Description | UniProt
A | Sodium-dependent serotonin transporter | SC6A4_HUMAN 79-617
B | variable domain of 15B8 antibody Fab heavy chain |
C | variable domain of 15B8 antibody Fab light chain |
Non-standard residues in 7lia #1
---
CL — chloride ion
CLR — cholesterol
D10 — decane
HP6 — heptane
LNK — pentane
NA — sodium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
SRO — serotonin (3-(2-aminoethyl)-1H-indol-5-ol)
> select /B:20-137
913 atoms, 936 bonds, 118 residues, 1 model selected
> hide
> select hide
Expected an objects specifier or a keyword
> hide B
> hide chain:B
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sel cartoons
> select /C:21-130
830 atoms, 851 bonds, 110 residues, 1 model selected
> hide sel cartoons
> select /A:79-617
4305 atoms, 4444 bonds, 539 residues, 1 model selected
> color sel dark gray
> lighting simple
> lighting soft
> lighting full
> lighting soft
> open P31641 fromDatabase alphafold format mmcif
Summary of feedback from opening P31641 fetched from alphafold
---
note | Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Chain information for AlphaFold P31641 #2
---
Chain | Description | UniProt
A | Sodium- and chloride-dependent taurine transporter | SC6A6_HUMAN 1-620
Color AlphaFold P31641 by residue attribute pLDDT_score
> open 7LI7 fromDatabase pdb format mmcif
7li7 title:
apo serotonin transporter reconstituted in lipid nanodisc in presence of NaCl
in occluded conformation [more info...]
Chain information for 7li7 #3
---
Chain | Description | UniProt
A | Sodium-dependent serotonin transporter | SC6A4_HUMAN 79-615
B | variable domain of 15B8 antibody Fab heavy chain |
C | variable domain of 15B8 antibody Fab light chain |
Non-standard residues in 7li7 #3
---
CLR — cholesterol
D10 — decane
D12 — dodecane
HP6 — heptane
LNK — pentane
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> select #3/B:20-137
913 atoms, 936 bonds, 118 residues, 1 model selected
> hide sel cartoons
> select #3/C:21-130
830 atoms, 851 bonds, 110 residues, 1 model selected
> hide sel cartoons
> log metadata #3
Metadata for 7li7 #3
---
Title | apo serotonin transporter reconstituted in lipid nanodisc in presence of NaCl in occluded conformation
Citation | Yang, D., Gouaux, E. (2021). Illumination of serotonin transporter mechanism and role of the allosteric site. Sci Adv, 7, eabl3857-eabl3857. PMID: 34851672. DOI: 10.1126/sciadv.abl3857
Non-standard residues | CLR — cholesterol
D10 — decane
D12 — dodecane
HP6 — heptane
LNK — pentane
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
Sources (natural) | Mus musculus (mouse)
Mus musculus (mouse)
Gene source | Homo sapiens (human)
CryoEM Map | EMDB 23362 — open map
Experimental method | Electron microscopy
Resolution | 4.1Å
> log chains #3
Chain information for 7li7 #3
---
Chain | Description | UniProt
A | Sodium-dependent serotonin transporter | SC6A4_HUMAN 79-615
B | variable domain of 15B8 antibody Fab heavy chain |
C | variable domain of 15B8 antibody Fab light chain |
> color #2 #74bff9ff
> open 7LI8 fromDatabase pdb format mmcif
7li8 title:
apo serotonin transporter reconstituted in lipid nanodisc in presence of NaCl
in inward open conformation [more info...]
Chain information for 7li8 #4
---
Chain | Description | UniProt
A | Sodium-dependent serotonin transporter | SC6A4_HUMAN 79-617
B | variable domain of 15B8 antibody Fab heavy chain |
C | variable domain of 15B8 antibody Fab light chain |
Non-standard residues in 7li8 #4
---
D10 — decane
D12 — dodecane
HP6 — heptane
LNK — pentane
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
R16 — hexadecane
> select #4/B:20-137
912 atoms, 935 bonds, 118 residues, 1 model selected
> hide sel cartoons
> select #4/C:21-130
829 atoms, 850 bonds, 110 residues, 1 model selected
> hide sel cartoons
> ui tool show Matchmaker
> matchmaker #2-4 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7lia, chain A (#1) with AlphaFold P31641, chain A (#2), sequence
alignment score = 1611
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7lia #1/A, AlphaFold P31641
#2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 450 pruned atom pairs is 1.068 angstroms; (across all 535 pairs:
1.634)
Matchmaker 7lia, chain A (#1) with 7li7, chain A (#3), sequence alignment
score = 2707.1
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: 7lia #1/A, 7li7 #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 460 pruned atom pairs is 0.987 angstroms; (across all 537 pairs:
1.539)
Matchmaker 7lia, chain A (#1) with 7li8, chain A (#4), sequence alignment
score = 2614.1
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: 7lia #1/A, 7li8 #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 374 pruned atom pairs is 1.125 angstroms; (across all 539 pairs:
4.435)
> select :D10
70 atoms, 63 bonds, 7 residues, 3 models selected
> hide sel atoms
> select :D12
72 atoms, 66 bonds, 6 residues, 2 models selected
> hide sel atoms
> select :HP6
168 atoms, 144 bonds, 24 residues, 3 models selected
> hide sel atoms
> select :LNK
15 atoms, 12 bonds, 3 residues, 3 models selected
> hide sel atoms
> select :NAG
84 atoms, 87 bonds, 6 residues, 3 models selected
> hide sel atoms
> select :R16
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select :CLR
56 atoms, 62 bonds, 2 residues, 2 models selected
> hide sel atoms
> select all
23566 atoms, 24243 bonds, 6 pseudobonds, 2973 residues, 5 models selected
> hide sel atoms
> select subtract #1
17287 atoms, 17796 bonds, 2179 residues, 3 models selected
> select subtract #3
11110 atoms, 11441 bonds, 1401 residues, 2 models selected
> select subtract #4
4929 atoms, 5086 bonds, 620 residues, 1 model selected
> select /A:401
23 atoms, 19 bonds, 4 residues, 4 models selected
> select 2/A:401
Expected an objects specifier or a keyword
> select #2/A:401
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select #1/A:437
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> select up
274 atoms, 279 bonds, 36 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
274 atoms, 279 bonds, 36 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
274 atoms, 279 bonds, 36 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
274 atoms, 279 bonds, 36 residues, 1 model selected
> select #3/A:437,show sel atoms,color sel red
Expected a keyword
> select #3/A:437
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> select #4/A:437
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> select #2/A:401
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> select #1/A:284
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel magenta
> select #2/A:249
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel magenta
> select #3/A:284
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel magenta
> select #4/A:284
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel magenta
> select :NA
2 atoms, 2 residues, 1 model selected
> show sel atoms
> color sel lime
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #!1 models
> hide #3 models
> hide #4 models
> show #!1 models
> select #1/A:437
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel hot pink
> color sel yellow
> select #1/A:284
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel yellow
> select #2/A:249
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:401
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/A:249
15 atoms, 13 bonds, 2 residues, 1 model selected
> color sel magenta
> show #3 models
> select #3
6177 atoms, 6355 bonds, 778 residues, 1 model selected
> color sel light gray
> select ~sel & ##selected
Nothing selected
> select #4
6181 atoms, 6355 bonds, 781 residues, 1 model selected
> color #1-3 dim gray
> select #4
6181 atoms, 6355 bonds, 781 residues, 1 model selected
> show #4 models
> color sel dim gray
> log metadata #4
Metadata for 7li8 #4
---
Title | apo serotonin transporter reconstituted in lipid nanodisc in presence of NaCl in inward open conformation
Citation | Yang, D., Gouaux, E. (2021). Illumination of serotonin transporter mechanism and role of the allosteric site. Sci Adv, 7, eabl3857-eabl3857. PMID: 34851672. DOI: 10.1126/sciadv.abl3857
Non-standard residues | D10 — decane
D12 — dodecane
HP6 — heptane
LNK — pentane
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
R16 — hexadecane
Source (natural) | Mus musculus (mouse)
Gene source | Homo sapiens (human)
CryoEM Map | EMDB 23363 — open map
Experimental method | Electron microscopy
Resolution | 3.9Å
> log chains #4
Chain information for 7li8 #4
---
Chain | Description | UniProt
A | Sodium-dependent serotonin transporter | SC6A4_HUMAN 79-617
B | variable domain of 15B8 antibody Fab heavy chain |
C | variable domain of 15B8 antibody Fab light chain |
> select clear
> select #1
6279 atoms, 6447 bonds, 6 pseudobonds, 794 residues, 2 models selected
> color (#!1 & sel) light gray
> select clear
> select #3
6177 atoms, 6355 bonds, 778 residues, 1 model selected
> color sel gray
> select #1
6279 atoms, 6447 bonds, 6 pseudobonds, 794 residues, 2 models selected
> color (#!1 & sel) black
> set bgColor white
> select #2
4929 atoms, 5086 bonds, 620 residues, 1 model selected
> select #3
6177 atoms, 6355 bonds, 778 residues, 1 model selected
> color sel dim gray
> select #4
6181 atoms, 6355 bonds, 781 residues, 1 model selected
> color sel dark gray
> select #1
6279 atoms, 6447 bonds, 6 pseudobonds, 794 residues, 2 models selected
> color (#!1 & sel) dim gray
> select #3
6177 atoms, 6355 bonds, 778 residues, 1 model selected
> color sel dark gray
> select #4
6181 atoms, 6355 bonds, 781 residues, 1 model selected
> color sel gray
> color sel light gray
> select clear
> hide #2 models
> select #1
6279 atoms, 6447 bonds, 6 pseudobonds, 794 residues, 2 models selected
> color (#!1 & sel) blue
> select #3
6177 atoms, 6355 bonds, 778 residues, 1 model selected
> color sel orange
> select #4
6181 atoms, 6355 bonds, 781 residues, 1 model selected
> color sel forest green
> select clear
> lighting simple
> lighting soft
> lighting full
> lighting soft
> select NA
Expected an objects specifier or a keyword
> log metadata #1
Metadata for 7lia #1
---
Title | 5-HT bound serotonin transporter reconstituted in lipid nanodisc in presence of NaCl in outward facing conformation
Citation | Yang, D., Gouaux, E. (2021). Illumination of serotonin transporter mechanism and role of the allosteric site. Sci Adv, 7, eabl3857-eabl3857. PMID: 34851672. DOI: 10.1126/sciadv.abl3857
Non-standard residues | CL — chloride ion
CLR — cholesterol
D10 — decane
HP6 — heptane
LNK — pentane
NA — sodium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
SRO — serotonin (3-(2-aminoethyl)-1H-indol-5-ol)
Source (natural) | Mus musculus (mouse)
Gene source | Homo sapiens (human)
CryoEM Map | EMDB 23365 — open map
Experimental method | Electron microscopy
Resolution | 3.3Å
> log chains #1
Chain information for 7lia #1
---
Chain | Description | UniProt
A | Sodium-dependent serotonin transporter | SC6A4_HUMAN 79-617
B | variable domain of 15B8 antibody Fab heavy chain |
C | variable domain of 15B8 antibody Fab light chain |
> select :NA
2 atoms, 2 residues, 1 model selected
> color sel lime
> color sel yellow
> sle clear
Unknown command: sle clear
> select clear
> ui mousemode right distance
No visible atoms, bonds, or surfaces selected
> ui tool show "Side View"
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> set bgColor gray
> set bgColor white
> hide #!1 models
> hide #4 models
> select /A:284,437
62 atoms, 54 bonds, 8 residues, 4 models selected
> hbonds sel & #3 reveal true
19 hydrogen bonds found
> show #4 models
> show #!1 models
> hbonds sel & #3-4#!1 reveal true
47 hydrogen bonds found
> hide #4 models
> show #4 models
> ~hbonds
> select ~sel & ##selected
23504 atoms, 24189 bonds, 6 pseudobonds, 2965 residues, 5 models selected
> select ~sel & ##selected
62 atoms, 54 bonds, 8 residues, 4 models selected
> select #3/A:284,437
15 atoms, 13 bonds, 2 residues, 1 model selected
> hbonds sel reveal true
19 hydrogen bonds found
> ~hbonds
> hide #4 models
> hide #!1 models
> hbonds sel reveal true
19 hydrogen bonds found
> hide #3 models
> show #4 models
> select #4/A:284,437
15 atoms, 13 bonds, 2 residues, 1 model selected
> hbonds sel reveal true
13 hydrogen bonds found
> select #4/A:433
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #4/A:284
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #4/A:437
15 atoms, 13 bonds, 2 residues, 1 model selected
> hide #4 models
> show #!1 models
> select add #1/A:437
23 atoms, 20 bonds, 3 residues, 2 models selected
> select add #1/A:284
30 atoms, 26 bonds, 4 residues, 2 models selected
> hbonds sel & #!1 reveal true
16 hydrogen bonds found
> select add #1/A:904@NA
31 atoms, 26 bonds, 5 residues, 2 models selected
> hbonds sel & #!1 reveal true
16 hydrogen bonds found
> color sel & #!1 byhetero
> ui mousemode right translate
> color sel & #!1 byhetero
> undo
> show #3 models
> show #4 models
> hide #4 models
> hide #!1 models
> select add #3/A:437
8 atoms, 8 bonds, 1 residue, 1 model selected
> select add #3/A:284
15 atoms, 13 bonds, 2 residues, 1 model selected
> hbonds sel reveal true
19 hydrogen bonds found
> show #4 models
> show #!1 models
> hide #5 models
> show #2 models
> hide #2 models
> hide #!1 models
> hide #4 models
> show #4 models
> show #!1 models
> hide #3 models
> show #2 models
> show #3 models
> hide #3 models
> show #3 models
> hide #!1 models
> hide #4 models
> show #!1 models
> log metadata #3
Metadata for 7li7 #3
---
Title | apo serotonin transporter reconstituted in lipid nanodisc in presence of NaCl in occluded conformation
Citation | Yang, D., Gouaux, E. (2021). Illumination of serotonin transporter mechanism and role of the allosteric site. Sci Adv, 7, eabl3857-eabl3857. PMID: 34851672. DOI: 10.1126/sciadv.abl3857
Non-standard residues | CLR — cholesterol
D10 — decane
D12 — dodecane
HP6 — heptane
LNK — pentane
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
Sources (natural) | Mus musculus (mouse)
Mus musculus (mouse)
Gene source | Homo sapiens (human)
CryoEM Map | EMDB 23362 — open map
Experimental method | Electron microscopy
Resolution | 4.1Å
> log chains #3
Chain information for 7li7 #3
---
Chain | Description | UniProt
A | Sodium-dependent serotonin transporter | SC6A4_HUMAN 79-615
B | variable domain of 15B8 antibody Fab heavy chain |
C | variable domain of 15B8 antibody Fab light chain |
> log metadata #1
Metadata for 7lia #1
---
Title | 5-HT bound serotonin transporter reconstituted in lipid nanodisc in presence of NaCl in outward facing conformation
Citation | Yang, D., Gouaux, E. (2021). Illumination of serotonin transporter mechanism and role of the allosteric site. Sci Adv, 7, eabl3857-eabl3857. PMID: 34851672. DOI: 10.1126/sciadv.abl3857
Non-standard residues | CL — chloride ion
CLR — cholesterol
D10 — decane
HP6 — heptane
LNK — pentane
NA — sodium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
SRO — serotonin (3-(2-aminoethyl)-1H-indol-5-ol)
Source (natural) | Mus musculus (mouse)
Gene source | Homo sapiens (human)
CryoEM Map | EMDB 23365 — open map
Experimental method | Electron microscopy
Resolution | 3.3Å
> log chains #1
Chain information for 7lia #1
---
Chain | Description | UniProt
A | Sodium-dependent serotonin transporter | SC6A4_HUMAN 79-617
B | variable domain of 15B8 antibody Fab heavy chain |
C | variable domain of 15B8 antibody Fab light chain |
> log metadata #4
Metadata for 7li8 #4
---
Title | apo serotonin transporter reconstituted in lipid nanodisc in presence of NaCl in inward open conformation
Citation | Yang, D., Gouaux, E. (2021). Illumination of serotonin transporter mechanism and role of the allosteric site. Sci Adv, 7, eabl3857-eabl3857. PMID: 34851672. DOI: 10.1126/sciadv.abl3857
Non-standard residues | D10 — decane
D12 — dodecane
HP6 — heptane
LNK — pentane
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
R16 — hexadecane
Source (natural) | Mus musculus (mouse)
Gene source | Homo sapiens (human)
CryoEM Map | EMDB 23363 — open map
Experimental method | Electron microscopy
Resolution | 3.9Å
> log chains #4
Chain information for 7li8 #4
---
Chain | Description | UniProt
A | Sodium-dependent serotonin transporter | SC6A4_HUMAN 79-617
B | variable domain of 15B8 antibody Fab heavy chain |
C | variable domain of 15B8 antibody Fab light chain |
> hide #2 models
> show #4 models
> hbonds sel reveal true
19 hydrogen bonds found
> lighting simple
> select #4/A:433
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> label sel attribute name
> undo
> redo
> ~label sel residues
> select #1/A:284,437
15 atoms, 13 bonds, 2 residues, 1 model selected
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> ~label sel residues
> select N2
1 atom, 1 residue, 1 model selected
> view sel
No displayed objects specified.
> show sel atoms
> view sel
> undo
> style sel stick
Changed 1 atom style
> show sel atoms
> select #1/A:208@ND2
1 atom, 1 residue, 1 model selected
> select #1/A:208
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> undo
> select clear
> select #1/A:208@ND2
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select down
Nothing selected
> toolshed show
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" sticks
Using preset: Initial Styles / Sticks
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" cartoon
Using preset: Initial Styles / Cartoon
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "space-filling (chain colors)"
Using preset: Initial Styles / Space-Filling (Chain Colors)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "initial styles" "space-filling (single color)"
Using preset: Initial Styles / Space-Filling (Single Color)
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 23147 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "molecular surfaces" "atomic coloring (transparent)"
Using preset: Molecular Surfaces / Atomic Coloring (Transparent)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> preset "molecular surfaces" "chain id coloring (opaque)"
Using preset: Molecular Surfaces / Chain ID Coloring (Opaque)
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color bychain targ s trans 0
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> undo
> select #1
6279 atoms, 6447 bonds, 6 pseudobonds, 794 residues, 2 models selected
> color (#!1 & sel) cornflower blue
> select #3
6177 atoms, 6355 bonds, 6 pseudobonds, 778 residues, 2 models selected
> color (#!3 & sel) orange
> select #4
6181 atoms, 6355 bonds, 781 residues, 1 model selected
> color (#!4 & sel) forest green
> select #2
4929 atoms, 5086 bonds, 620 residues, 1 model selected
> color #1,3-4 cyan
> show #!2 models
> color (#!2 & sel) cyan
> select #1
6279 atoms, 6447 bonds, 6 pseudobonds, 794 residues, 2 models selected
> color (#!1 & sel) blue
> set bgColor white
> log metadata #1
Metadata for 7lia #1
---
Title | 5-HT bound serotonin transporter reconstituted in lipid nanodisc in presence of NaCl in outward facing conformation
Citation | Yang, D., Gouaux, E. (2021). Illumination of serotonin transporter mechanism and role of the allosteric site. Sci Adv, 7, eabl3857-eabl3857. PMID: 34851672. DOI: 10.1126/sciadv.abl3857
Non-standard residues | CL — chloride ion
CLR — cholesterol
D10 — decane
HP6 — heptane
LNK — pentane
NA — sodium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
SRO — serotonin (3-(2-aminoethyl)-1H-indol-5-ol)
Source (natural) | Mus musculus (mouse)
Gene source | Homo sapiens (human)
CryoEM Map | EMDB 23365 — open map
Experimental method | Electron microscopy
Resolution | 3.3Å
> log chains #1
Chain information for 7lia #1
---
Chain | Description | UniProt
A | Sodium-dependent serotonin transporter | SC6A4_HUMAN 79-617
B | variable domain of 15B8 antibody Fab heavy chain |
C | variable domain of 15B8 antibody Fab light chain |
> select :CLR
56 atoms, 62 bonds, 2 residues, 2 models selected
> hide sel atoms
> select :D10
70 atoms, 63 bonds, 7 residues, 3 models selected
> hide sel atoms
> select :HP6
168 atoms, 144 bonds, 24 residues, 3 models selected
> hide sel atoms
> select :LNK
15 atoms, 12 bonds, 3 residues, 3 models selected
> hide sel atoms
> select :NAG
84 atoms, 87 bonds, 6 residues, 3 models selected
> hide sel atoms
> log metadata #3
Metadata for 7li7 #3
---
Title | apo serotonin transporter reconstituted in lipid nanodisc in presence of NaCl in occluded conformation
Citation | Yang, D., Gouaux, E. (2021). Illumination of serotonin transporter mechanism and role of the allosteric site. Sci Adv, 7, eabl3857-eabl3857. PMID: 34851672. DOI: 10.1126/sciadv.abl3857
Non-standard residues | CLR — cholesterol
D10 — decane
D12 — dodecane
HP6 — heptane
LNK — pentane
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
Sources (natural) | Mus musculus (mouse)
Mus musculus (mouse)
Gene source | Homo sapiens (human)
CryoEM Map | EMDB 23362 — open map
Experimental method | Electron microscopy
Resolution | 4.1Å
> log chains #3
Chain information for 7li7 #3
---
Chain | Description | UniProt
A | Sodium-dependent serotonin transporter | SC6A4_HUMAN 79-615
B | variable domain of 15B8 antibody Fab heavy chain |
C | variable domain of 15B8 antibody Fab light chain |
> select :CLR
56 atoms, 62 bonds, 2 residues, 2 models selected
> hide sel atoms
> select :D10
70 atoms, 63 bonds, 7 residues, 3 models selected
> hide sel atoms
> select :D12
72 atoms, 66 bonds, 6 residues, 2 models selected
> hide sel atoms
> select :HP6
168 atoms, 144 bonds, 24 residues, 3 models selected
> hide sel atoms
> select :LNK
15 atoms, 12 bonds, 3 residues, 3 models selected
> hide sel atoms
> select :NAG
84 atoms, 87 bonds, 6 residues, 3 models selected
> hide sel atoms
> select all
23566 atoms, 24243 bonds, 25 pseudobonds, 2973 residues, 6 models selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> style sel stick
Changed 23566 atom styles
> select #1/A:284,437
15 atoms, 13 bonds, 2 residues, 1 model selected
> show sel atoms
> select #3/A:284,437
15 atoms, 13 bonds, 2 pseudobonds, 2 residues, 2 models selected
> style sel stick
Changed 15 atom styles
> select #4/A:284,437
15 atoms, 13 bonds, 2 residues, 1 model selected
> style sel stick
Changed 15 atom styles
> select #2/A:294,401
13 atoms, 11 bonds, 2 residues, 1 model selected
> style sel stick
Changed 13 atom styles
> select #2/A:249,401
15 atoms, 13 bonds, 2 residues, 1 model selected
> style sel stick
Changed 15 atom styles
> select ~sel & ##selected
4914 atoms, 5073 bonds, 618 residues, 1 model selected
> select #2/A:294
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #1/A:249
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/A:284
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:437
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/A:284
15 atoms, 13 bonds, 2 residues, 2 models selected
> log metadata #1
Metadata for 7lia #1
---
Title | 5-HT bound serotonin transporter reconstituted in lipid nanodisc in presence of NaCl in outward facing conformation
Citation | Yang, D., Gouaux, E. (2021). Illumination of serotonin transporter mechanism and role of the allosteric site. Sci Adv, 7, eabl3857-eabl3857. PMID: 34851672. DOI: 10.1126/sciadv.abl3857
Non-standard residues | CL — chloride ion
CLR — cholesterol
D10 — decane
HP6 — heptane
LNK — pentane
NA — sodium ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
SRO — serotonin (3-(2-aminoethyl)-1H-indol-5-ol)
Source (natural) | Mus musculus (mouse)
Gene source | Homo sapiens (human)
CryoEM Map | EMDB 23365 — open map
Experimental method | Electron microscopy
Resolution | 3.3Å
> log chains #1
Chain information for 7lia #1
---
Chain | Description | UniProt
A | Sodium-dependent serotonin transporter | SC6A4_HUMAN 79-617
B | variable domain of 15B8 antibody Fab heavy chain |
C | variable domain of 15B8 antibody Fab light chain |
> select :NA
2 atoms, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 2 atom styles
> select add #4
6183 atoms, 6355 bonds, 783 residues, 2 models selected
> select subtract #4
2 atoms, 2 residues, 4 models selected
> select add #4
6183 atoms, 6355 bonds, 783 residues, 2 models selected
> select subtract #4
2 atoms, 2 residues, 4 models selected
> hide #!2 models
> select /A:284,437
62 atoms, 54 bonds, 3 pseudobonds, 8 residues, 5 models selected
> style sel & #!1,3-4 stick
Changed 45 atom styles
> show sel & #!1,3-4 atoms
> show #!2 models
> hide #!1 models
> hide #!3 models
> hide #!4 models
> select /A:249,401
42 atoms, 34 bonds, 8 residues, 4 models selected
> style sel & #!2 stick
Changed 15 atom styles
> show sel & #!2 atoms
> show #!1 models
> show #!3 models
> show #!4 models
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting soft
> lighting simple
> save
Missing or invalid "fileName" argument: Expected a file name
> save TauT and SERT 7LIA LI7 LI8
Cannot determine format for 'TauT'
> save "/Users/michaelallen/Desktop/TauT SERT 7LIA 7LI7 7LI8.cxs"
> close
> open P31641 fromDatabase alphafold format mmcif
Chain information for AlphaFold P31641 #1
---
Chain | Description | UniProt
A | Sodium- and chloride-dependent taurine transporter | SC6A6_HUMAN 1-620
Color AlphaFold P31641 by residue attribute pLDDT_score
Associated AlphaFold P31641 chain A to AlphaFold P31641, chain A with 0
mismatches
> select all
4929 atoms, 5086 bonds, 620 residues, 1 model selected
> color sel gray
> lighting soft
> select /A:249,401
15 atoms, 13 bonds, 2 residues, 1 model selected
> style sel stick
Changed 15 atom styles
> show sel atoms
> hbonds sel reveal true
6 hydrogen bonds found
> color sel magenta
> select /A:249
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
88 atoms, 89 bonds, 11 residues, 1 model selected
> select up
4929 atoms, 5086 bonds, 620 residues, 1 model selected
> select add /A:265
96 atoms, 96 bonds, 12 residues, 1 model selected
> select up
199 atoms, 202 bonds, 25 residues, 1 model selected
> select add /A:250
204 atoms, 206 bonds, 26 residues, 1 model selected
> select add /A:251
211 atoms, 212 bonds, 27 residues, 1 model selected
> color sel cornflower blue
> select /A:249
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel magenta
> select /A:401
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
258 atoms, 264 bonds, 32 residues, 1 model selected
> color sel forest green
> ui tool show "Color Actions"
> color sel #000000ff
> color sel #ffffffff
> color sel #000000ff
> color sel #ffffffff
> color sel #000000ff
> color sel #469b76ff
> color sel #3170adff
> color sel #6eb2e4ff
> color sel #eee561ff
> color sel #dba237ff
> color sel #c76526ff
> color sel #c07da5ff
> color sel #ffffffff
> color sel #000000ff
> color sel #ffffffff
> color sel #000000ff
> color sel #469b76ff
> color sel #3170adff
> color sel #6eb2e4ff
> color sel #eee561ff
> color sel #dba237ff
> color sel #c76526ff
> color sel #c07da5ff
> color sel #678cf5ff
> color sel #6e5de7ff
> color sel #515050ff
> color sel #6e5de7ff
> color sel #cb377bff
> color sel #ec6a2cff
> color sel #f3b341ff
> color sel #c07da5ff
> color sel #678cf5ff
> color sel #6e5de7ff
> color sel #cb377bff
> color sel #ec6a2cff
> color sel #f3b341ff
> color sel #ddddddff
> color sel #2d257fff
> color sel #45733fff
> color sel #6fa69aff
> color sel #a0c9e8ff
> color sel #dace87ff
> color sel #b66e77ff
> color sel #954f93ff
> color sel #742f53ff
> color sel #f3b341ff
> color sel #ddddddff
> color sel #bbbbbbff
> color sel #ddddddff
> color sel #5075a5ff
> color sel #43863eff
> color sel #80c9eaff
> color sel #c9bc58ff
> color sel #dd6e79ff
> color sel #9d3c75ff
> color sel #bbbbbbff
> color sel #5075a5ff
> color sel #43863eff
> color sel #80c9eaff
> color sel #c9bc58ff
> color sel #dd6e79ff
> color sel #9d3c75ff
> color sel #954f93ff
> color sel #6e5de7ff
> color sel #cb377bff
> color sel #ec6a2cff
> select /A:249,401
15 atoms, 13 bonds, 2 pseudobonds, 2 residues, 2 models selected
> select /A:249,265
15 atoms, 13 bonds, 2 residues, 1 model selected
> select up
199 atoms, 202 bonds, 25 residues, 1 model selected
> select add /A:251
206 atoms, 208 bonds, 26 residues, 1 model selected
> select add /A:250
211 atoms, 212 bonds, 27 residues, 1 model selected
> color sel #678cf5ff
> select /A:249
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add /A:401
15 atoms, 13 bonds, 2 residues, 1 model selected
> color sel #cb377bff
> color sel magenta
> save "/Users/michaelallen/Desktop/TauT T249 D401 Colored.cxs"
> close
> open "/Users/michaelallen/Desktop/TauT T249 D401 Colored.cxs" format session
opened ChimeraX session
> select all
4929 atoms, 5086 bonds, 6 pseudobonds, 620 residues, 2 models selected
> rainbow sel
> undo
> select /A:48
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /A:72
20 atoms, 19 bonds, 2 residues, 1 model selected
> select up
153 atoms, 157 bonds, 19 residues, 1 model selected
> color sel #f3b341ff
> select /A:289
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /A:314
15 atoms, 13 bonds, 2 residues, 1 model selected
> select up
158 atoms, 161 bonds, 21 residues, 1 model selected
> color sel #cb377bff
> select add /A:302
170 atoms, 173 bonds, 22 residues, 1 model selected
> select add /A:303
175 atoms, 177 bonds, 23 residues, 1 model selected
> select add /A:304
183 atoms, 184 bonds, 24 residues, 1 model selected
> select add /A:305
189 atoms, 189 bonds, 25 residues, 1 model selected
> select add /A:306
197 atoms, 196 bonds, 26 residues, 1 model selected
> select add /A:307
201 atoms, 199 bonds, 27 residues, 1 model selected
> color sel #ec6a2cff
> color sel #cb377bff
> select /A:66
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add /A:65
25 atoms, 25 bonds, 2 residues, 1 model selected
> select add /A:64
32 atoms, 31 bonds, 3 residues, 1 model selected
> select add /A:63
40 atoms, 38 bonds, 4 residues, 1 model selected
> select add /A:62
44 atoms, 41 bonds, 5 residues, 1 model selected
> select add /A:61
52 atoms, 48 bonds, 6 residues, 1 model selected
> select add /A:60
56 atoms, 51 bonds, 7 residues, 1 model selected
> select add /A:59
63 atoms, 57 bonds, 8 residues, 1 model selected
> color sel #f3b341ff
> save "/Users/michaelallen/Desktop/TauT T249 D401 Colored.cxs"
> ui tool show "Side View"
> clip y
Expected a keyword
> clip axis y
> ~clip
> lighting full
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> save "/Users/michaelallen/Desktop/Image Attempt TauT.tif" width 1921 height
> 1886 supersample 3
> selc lear
Unknown command: selc lear
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> select /A:390
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:64
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:64
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> lighting flat
> undo
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> save "/Users/michaelallen/Desktop/Image Attempt TauT.tif" width 1921 height
> 1886 supersample 4
> save
Missing or invalid "fileName" argument: Expected a file name
> close
> open "/Users/michaelallen/Desktop/TauT SERT 7LIA 7LI7 7LI8.cxs" format
> session
opened ChimeraX session
> close]
Unknown command: close]
> close
> open "/Users/michaelallen/Desktop/TauT T249 D401 Colored.cxs" format session
opened ChimeraX session
> close
> open "/Users/michaelallen/Desktop/TauT SERT 7LIA 7LI7 7LI8.cxs" format
> session
opened ChimeraX session
> hide #!2 models
> show #!2 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> log metadata #3
No models had metadata
> log chains #3
Chain information for 7li7 #3
---
Chain | Description | UniProt
A | Sodium-dependent serotonin transporter | SC6A4_HUMAN 79-615
B | variable domain of 15B8 antibody Fab heavy chain |
C | variable domain of 15B8 antibody Fab light chain |
> log metadata #3
No models had metadata
> log chains #3
Chain information for 7li7 #3
---
Chain | Description | UniProt
A | Sodium-dependent serotonin transporter | SC6A4_HUMAN 79-615
B | variable domain of 15B8 antibody Fab heavy chain |
C | variable domain of 15B8 antibody Fab light chain |
> hide #!3 models
> show #!3 models
> select #3/A:T268,T437
Nothing selected
> hide #!3 models
> log metadata #1
No models had metadata
> log chains #1
Chain information for 7lia #1
---
Chain | Description | UniProt
A | Sodium-dependent serotonin transporter | SC6A4_HUMAN 79-617
B | variable domain of 15B8 antibody Fab heavy chain |
C | variable domain of 15B8 antibody Fab light chain |
> select #1/A:79-617
4305 atoms, 4444 bonds, 539 residues, 1 model selected
> hide sel atoms
> undo
> hide sel cartoons
> select #1/A:437@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/A:437@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/A:437@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/A:284@O
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #1/A:284@C
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> select #1/A:284@N
1 atom, 1 residue, 1 model selected
> select add #1/A:284@C
2 atoms, 1 residue, 2 models selected
> hide sel atoms
> select add #1/A:284@CG2
3 atoms, 1 residue, 2 models selected
> select add #1/A:284@OG1
4 atoms, 1 residue, 2 models selected
> select add #1/A:284@CA
5 atoms, 1 residue, 2 models selected
> hide sel atoms
> select add #1/A:284@CB
6 atoms, 1 residue, 2 models selected
> hide sel atoms
> log metadata #2
No models had metadata
> log chains #2
Chain information for AlphaFold P31641 #2
---
Chain | Description | UniProt
A | Sodium- and chloride-dependent taurine transporter | SC6A6_HUMAN 1-620
> select #2/A:1-620
4929 atoms, 5086 bonds, 620 residues, 1 model selected
> select #2/A:1-620
4929 atoms, 5086 bonds, 620 residues, 1 model selected
> color (#!2 & sel) dark gray
> lighting soft
> select clear
> ui tool show "Model Loops"
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select
> #2/A:2-18,20-21,30-34,37-42,47-58,61-73,77-105,111-116,118-120,122-152,174-178,180-185,194-203,218-235,239-249,252-265,270-278,282-286,288-301,308-314,322-355,359-361,363-364,368-379,384-415,419-422,427-446,451-462,465-496,499-525,540-554,556-567,572-580,587-593,600-604
3615 atoms, 3693 bonds, 449 residues, 1 model selected
> select clear
> select
> #2/A:2-18,20-21,30-34,37-42,47-58,61-73,77-105,111-116,118-120,122-152,174-178,180-185,194-203,218-235,239-249,252-265,270-278,282-286,288-301,308-314,322-355,359-361,363-364,368-379,384-415,419-422,427-446,451-462,465-496,499-525,540-554,556-567,572-580,587-593,600-604
3615 atoms, 3693 bonds, 449 residues, 1 model selected
> select #2/A:1-2
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/A:1-27
208 atoms, 212 bonds, 27 residues, 1 model selected
> select #2/A:27-28
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #2/A:27-31
38 atoms, 38 bonds, 5 residues, 1 model selected
> select #2/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:1-42
329 atoms, 336 bonds, 42 residues, 1 model selected
> select #2/A:1-42
329 atoms, 336 bonds, 42 residues, 1 model selected
> select #2/A:1-47
373 atoms, 382 bonds, 47 residues, 1 model selected
> select #2/A:1-47
373 atoms, 382 bonds, 47 residues, 1 model selected
> select #2/A:1-47
373 atoms, 382 bonds, 47 residues, 1 model selected
> select #2/A:46
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:1-46
364 atoms, 373 bonds, 46 residues, 1 model selected
> open P31641 fromDatabase uniprot format uniprot
Summary of feedback from opening P31641 fetched from uniprot
---
notes | Fetching compressed P31641 UniProt info from https://www.uniprot.org/uniprot/P31641.xml
Alignment identifier is P31641
Associated AlphaFold P31641 chain A to P31641 with 0 mismatches
Opened UniProt P31641
> select #2/A:1-19,26-42
290 atoms, 294 bonds, 36 residues, 1 model selected
> select #2/A
4929 atoms, 5086 bonds, 620 residues, 1 model selected
> select #2/A:1-19,26-42
290 atoms, 294 bonds, 36 residues, 1 model selected
> select #2/A:163,179,190
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #2/A:322
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/A:1-42
329 atoms, 336 bonds, 42 residues, 1 model selected
> select #2/A:28,272,509,538-540
44 atoms, 42 bonds, 6 residues, 1 model selected
> select #2/A:17-18,78,399
25 atoms, 22 bonds, 4 residues, 1 model selected
> select #2/A:201-620
3320 atoms, 3420 bonds, 420 residues, 1 model selected
> select #2/A:1-49,143-217,564-620
1470 atoms, 1513 bonds, 181 residues, 1 model selected
> select
> #2/A:50-70,78-97,122-142,218-236,245-262,298-315,327-348,381-400,430-448,465-485,506-525,545-563
1866 atoms, 1920 bonds, 238 residues, 1 model selected
> select down
1866 atoms, 1920 bonds, 238 residues, 2 models selected
> select down
1866 atoms, 1920 bonds, 238 residues, 2 models selected
> select down
1866 atoms, 1920 bonds, 238 residues, 2 models selected
> select
> #2/A:2-18,20-21,30-34,37-42,47-58,61-73,77-105,111-116,118-120,122-152,174-178,180-185,194-203,218-235,239-249,252-265,270-278,282-286,288-301,308-314,322-355,359-361,363-364,368-379,384-415,419-422,427-446,451-462,465-496,499-525,540-554,556-567,572-580,587-593,600-604
3615 atoms, 3693 bonds, 449 residues, 1 model selected
> ui tool show Matchmaker
> select #2/A:50-70
164 atoms, 170 bonds, 21 residues, 1 model selected
> select #2/A:50-70
164 atoms, 170 bonds, 21 residues, 1 model selected
> select #2/A:545-563
139 atoms, 141 bonds, 19 residues, 1 model selected
> select #2/A:545-563
139 atoms, 141 bonds, 19 residues, 1 model selected
> select #2/A:506-525
155 atoms, 160 bonds, 20 residues, 1 model selected
> select #2/A:465-485
169 atoms, 176 bonds, 21 residues, 1 model selected
> select #2/A:430-448
145 atoms, 147 bonds, 19 residues, 1 model selected
> select #2/A:381-400
166 atoms, 172 bonds, 20 residues, 1 model selected
> select #2/A:327-348
158 atoms, 160 bonds, 22 residues, 1 model selected
> select #2/A:298-315
135 atoms, 138 bonds, 18 residues, 1 model selected
> select #2/A:298-315
135 atoms, 138 bonds, 18 residues, 1 model selected
> select #2/A:245-262
144 atoms, 148 bonds, 18 residues, 1 model selected
> select #2/A:122-142
160 atoms, 162 bonds, 21 residues, 1 model selected
> select #2/A:545-563
139 atoms, 141 bonds, 19 residues, 1 model selected
> select #2/A:506-525
155 atoms, 160 bonds, 20 residues, 1 model selected
> select #2/A:545-563
139 atoms, 141 bonds, 19 residues, 1 model selected
> select all
23566 atoms, 24243 bonds, 25 pseudobonds, 2973 residues, 6 models selected
> hide #!1 models
> select subtract #1
17287 atoms, 17796 bonds, 16 pseudobonds, 2179 residues, 14 models selected
> select subtract #3
11110 atoms, 11441 bonds, 1401 residues, 9 models selected
> select subtract #4
4929 atoms, 5086 bonds, 620 residues, 5 models selected
> hide sel atoms
> hide sel cartoons
> select #2/A:50-70
164 atoms, 170 bonds, 21 residues, 1 model selected
> select #2/A:78-97
166 atoms, 174 bonds, 20 residues, 1 model selected
> select #2/A:122-142
160 atoms, 162 bonds, 21 residues, 1 model selected
> select #2/A:218-236
165 atoms, 172 bonds, 19 residues, 1 model selected
> select #2/A:245-262
144 atoms, 148 bonds, 18 residues, 1 model selected
> show sel cartoons
> select #2/A:298-315
135 atoms, 138 bonds, 18 residues, 1 model selected
> select #2/A:327-348
158 atoms, 160 bonds, 22 residues, 1 model selected
> select #2/A:381-400
166 atoms, 172 bonds, 20 residues, 1 model selected
> show sel cartoons
> show #!1 models
> select #2/A:249
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide #!1 models
> select #2/A:327-348
158 atoms, 160 bonds, 22 residues, 1 model selected
> select #2/A:381-400
166 atoms, 172 bonds, 20 residues, 1 model selected
> select
> #2/A:2-18,20-21,30-34,37-42,47-58,61-73,77-105,111-116,118-120,122-152,174-178,180-185,194-203,218-235,239-249,252-265,270-278,282-286,288-301,308-314,322-355,359-361,363-364,368-379,384-415,419-422,427-446,451-462,465-496,499-525,540-554,556-567,572-580,587-593,600-604
3615 atoms, 3693 bonds, 449 residues, 1 model selected
> select #2/A:430-448
145 atoms, 147 bonds, 19 residues, 1 model selected
> select #2/A:381-400
166 atoms, 172 bonds, 20 residues, 1 model selected
> select #2/A:381-400
166 atoms, 172 bonds, 20 residues, 1 model selected
> select #2/A:381-415
281 atoms, 288 bonds, 35 residues, 1 model selected
> show sel cartoons
Cannot rename transmembrane region region
> select #2/A:327-348
158 atoms, 160 bonds, 22 residues, 1 model selected
> select #2/A:298-315
135 atoms, 138 bonds, 18 residues, 1 model selected
> select #2/A:245-262
144 atoms, 148 bonds, 18 residues, 1 model selected
> select #2/A:245-265
167 atoms, 171 bonds, 21 residues, 1 model selected
> select #2/A:239-265
211 atoms, 215 bonds, 27 residues, 1 model selected
> show sel cartoons
> show #!1 models
> select #2/A:50-70
164 atoms, 170 bonds, 21 residues, 1 model selected
> show sel cartoons
> select #2/A:298-315
135 atoms, 138 bonds, 18 residues, 1 model selected
> show sel cartoons
> select #2/A:401
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:249
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #2/A:401
15 atoms, 13 bonds, 2 residues, 2 models selected
> show sel atoms
> select #2/A:249
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/A:249
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color (#!2 & sel) #ff9300ff
> color (#!2 & sel) #dba237ff
> color (#!2 & sel) #c76526ff
> select #2/A:401
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!2 & sel) #eee561ff
> select add #1/A:904@NA
9 atoms, 7 bonds, 2 residues, 3 models selected
> select subtract #1/A:904@NA
8 atoms, 7 bonds, 1 residue, 2 models selected
> select add #1/A:904@NA
9 atoms, 7 bonds, 2 residues, 3 models selected
> select add #1/A:903@NA
10 atoms, 7 bonds, 3 residues, 3 models selected
> color (#!1-2 & sel) #3170adff
> select subtract #2/A:401
2 atoms, 2 residues, 2 models selected
> color sel #5075a5ff
> color sel #2d257fff
> color sel #a0c9e8ff
> color sel #f3b341ff
> color sel #ff9300ff
> color sel #dba237ff
> color sel #eee561ff
> color #1 #dba237ff
> color #1 #6eb2e4ff
> undo
> select #1/A:904@NA
1 atom, 1 residue, 1 model selected
> select add #1/A:903@NA
2 atoms, 2 residues, 1 model selected
> color #1 #eee561ff
> color #1 #dba237ff
> select #2/A:249
7 atoms, 6 bonds, 1 residue, 1 model selected
> color #1 #3170adff
> color #1 #469b76ff
> color #1 #3170adff
> sle clear
Unknown command: sle clear
> select clear
> select #2/A:249
7 atoms, 6 bonds, 1 residue, 1 model selected
> color #1 #469b76ff
> select add #1
6286 atoms, 6453 bonds, 6 pseudobonds, 795 residues, 4 models selected
> select clear
> select #2/A:249
7 atoms, 6 bonds, 1 residue, 1 model selected
> color #1 #3170adff
> select #2/A:50-70
164 atoms, 170 bonds, 21 residues, 1 model selected
> select #2/A:50-73
191 atoms, 198 bonds, 24 residues, 1 model selected
> select #2/A:47-73
216 atoms, 223 bonds, 27 residues, 1 model selected
> show sel cartoons
> select #2/A:298-315
135 atoms, 138 bonds, 18 residues, 1 model selected
> select #2/A:288-315
213 atoms, 219 bonds, 28 residues, 1 model selected
> show sel cartoons
> select #2/A:249
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!2 & sel) magenta
> select #2/A:401
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!2 & sel) cornflower blue
> select
> #2/A:2-18,20-21,30-34,37-42,47-58,61-73,77-105,111-116,118-120,122-152,174-178,180-185,194-203,218-235,239-249,252-265,270-278,282-286,288-301,308-314,322-355,359-361,363-364,368-379,384-415,419-422,427-446,451-462,465-496,499-525,540-554,556-567,572-580,587-593,600-604
3615 atoms, 3693 bonds, 449 residues, 1 model selected
> select
> #2/A:2-18,20-21,30-34,37-42,47-58,61-73,77-105,111-116,118-120,122-152,174-178,180-185,194-203,218-235,239-249,252-265,270-278,282-286,288-301,308-314,322-355,359-361,363-364,368-379,384-415,419-422,427-446,451-462,465-496,499-525,540-554,556-567,572-580,587-593,600-604
3615 atoms, 3693 bonds, 449 residues, 1 model selected
> select #2/A:47-48
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:47-58
88 atoms, 89 bonds, 12 residues, 1 model selected
> select #2/A:1-46
364 atoms, 373 bonds, 46 residues, 1 model selected
> select #2/A:47-58
88 atoms, 89 bonds, 12 residues, 1 model selected
===== Log before crash end =====
Log:
Startup Messages
---
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UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: MJ123LL/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.101.3
OS Loader Version: 10151.101.3
Software:
System Software Overview:
System Version: macOS 14.4.1 (23E224)
Kernel Version: Darwin 23.4.0
Time since boot: 104 days, 13 hours, 21 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
LG ULTRAFINE:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 3840 x 2160 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 15 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash waking Mac from sleep |
comment:2 by , 15 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Crash in _NSViewHierarchyDidChangeBackingProperties(). Possibly plugging in an external display. Likely Qt 6.6 bug.