![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 weeks ago
Closed 5 weeks ago
#19006 closed defect (duplicate)
Crash on Mac waking 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-15.6.1-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.
suhas's comments: I stepped away from my laptop for a few mins and it went to sleep, and chimeraX crashed when i reopened my laptop.
Fatal Python error: Segmentation fault
Current thread 0x00000001f8dda0c0 (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.pdb_lib._load_libs, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree (total: 62)
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{
"uptime" : 550000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,12",
"coalitionID" : 22551,
"osVersion" : {
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"build" : "24G90",
"releaseType" : "User"
},
"captureTime" : "2025-10-01 13:35:31.4869 -0400",
"codeSigningMonitor" : 1,
"incident" : "57CA26B5-9683-4A8D-8F08-87A4DFDF2AA6",
"pid" : 85153,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-09-30 09:08:23.5320 -0400",
"procStartAbsTime" : 12330364558369,
"procExitAbsTime" : 13278368640360,
"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":"CFDC5ADD-BD23-54F7-ABE9-67DF663965BE","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "9F9E57F5-547E-D476-8C06-E64738D3D883",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["siriAssetIsNotReady","assetIsNotReady","notOptedIn"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "01F4A0AE-C30B-46F6-A555-EB915012A58F",
"sleepWakeUUID" : "D38D4C54-142E-48CC-A947-1DE863EAF5ED",
"sip" : "enabled",
"vmRegionInfo" : "0x141b7ba83448 is not in any region. Bytes after previous region: 21627234956361 Bytes before following region: 83444844972984\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000941b7ba83448","rawCodes":[1,162845759648840],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000941b7ba83448 -> 0x0000141b7ba83448 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":85153},
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> set bgColor white
> cd
> /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/3_no_templates
Current working directory is:
/Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/3_no_templates
> open
> /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/pdb_templates/9ut9_tas1r2_only.pdb
Chain information for 9ut9_tas1r2_only.pdb #1
---
Chain | Description
A | No description available
> open
> /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/3_no_templates/v1/boltz_results_v1/predictions/v1/v1_model_0.cif
Summary of feedback from opening
/Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/3_no_templates/v1/boltz_results_v1/predictions/v1/v1_model_0.cif
---
warning | Unable to fetch template for 'LIG1': will connect using distance criteria
v1_model_0.cif title:
. [more info...]
Chain information for v1_model_0.cif #2
---
Chain | Description
A | .
Non-standard residues in v1_model_0.cif #2
---
LIG1 — (LIG1)
No chain in structure corresponds to chain ID given in local score info (chain
'B')
> close #1
> open
> /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/pdb_templates/9utc_tas1r2_sucralose_only.pdb
Summary of feedback from opening
/Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/pdb_templates/9utc_tas1r2_sucralose_only.pdb
---
warnings | Start residue of secondary structure not found: HELIX 16 16 SER B 26 ARG B 30 1 5
Start residue of secondary structure not found: HELIX 17 17 SER B 66 LYS B 86
1 21
Start residue of secondary structure not found: HELIX 18 18 PRO B 106 PHE B
116 1 11
Start residue of secondary structure not found: HELIX 19 19 SER B 146 LEU B
161 1 16
Start residue of secondary structure not found: HELIX 20 20 SER B 189 PHE B
204 1 16
28 messages similar to the above omitted
Cannot find LINK/SSBOND residue CYS (24 )
Cannot find LINK/SSBOND residue CYS (62 )
Cannot find LINK/SSBOND residue CYS (236 )
Cannot find LINK/SSBOND residue CYS (370 )
Cannot find LINK/SSBOND residue CYS (410 )
4 messages similar to the above omitted
9utc_tas1r2_sucralose_only.pdb title:
The VFT domains of human sweet taste receptor TAS1R2 and TAS1R3 In the
sucralose-bound state [more info...]
Chain information for 9utc_tas1r2_sucralose_only.pdb #1
---
Chain | Description | UniProt
A | taste receptor type 1 member 2,taste receptor type 1 member 2,engineered red fluorescent protein MSCARLET3 | TS1R2_HUMAN 26-839
Non-standard residues in 9utc_tas1r2_sucralose_only.pdb #1
---
RRJ — 4-chloro-4-deoxy-α-D-galactopyranose
RRY — 1,6-dichloro-1,6-dideoxy-β-D-fructofuranose
> open
> /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/3_no_templates/v2/boltz_results_v2/predictions/v2/v2_model_0.cif
Summary of feedback from opening
/Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/3_no_templates/v2/boltz_results_v2/predictions/v2/v2_model_0.cif
---
warning | Unable to fetch template for 'LIG1': will connect using distance criteria
v2_model_0.cif title:
. [more info...]
Chain information for v2_model_0.cif #3
---
Chain | Description
A | .
Non-standard residues in v2_model_0.cif #3
---
LIG1 — (LIG1)
No chain in structure corresponds to chain ID given in local score info (chain
'B')
> mmaker #2 to #1 showAlignment t
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 9utc_tas1r2_sucralose_only.pdb, chain A (#1) with v1_model_0.cif,
chain A (#2), sequence alignment score = 2525.9
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: 9utc_tas1r2_sucralose_only.pdb
#1/A, v1_model_0.cif #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 457 pruned atom pairs is 0.980 angstroms; (across all 500 pairs:
1.282)
> mmaker #3 to #1 showAlignment t
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 9utc_tas1r2_sucralose_only.pdb, chain A (#1) with v2_model_0.cif,
chain A (#3), sequence alignment score = 2510.6
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: 9utc_tas1r2_sucralose_only.pdb
#1/A, v2_model_0.cif #3/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 398 pruned atom pairs is 1.043 angstroms; (across all 500 pairs:
1.769)
> hide #3 models
> view
> save
> /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/3_no_templates/results_representations.cxs
> rename #2 3_no_template_wt_aka_v1_model_0.cif
> rename #3 3_no_template_y103_aka_v2v2_model_0.cif
> rename #3 3_no_template_y103_aka_v2_model_0.cif
> mmaker #2 ro #1
> matchmaker #2 ro #1
Expected a keyword
> mmaker #2 to #1
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 9utc_tas1r2_sucralose_only.pdb, chain A (#1) with
3_no_template_wt_aka_v1_model_0.cif, chain A (#2), sequence alignment score =
2525.9
RMSD between 457 pruned atom pairs is 0.980 angstroms; (across all 500 pairs:
1.282)
> renumber #2/A seqStart 26
527 residues renumbered
> rmsd #2:40,65,67,71,103,142,143,165,277,278,302,303,306 to
> #1:40,65,67,71,103,142,143,165,277,278,302,303,306
RMSD between 103 atom pairs is 1.405
> save
> /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/3_no_templates/results_representations.cxs
> open
> /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/2_apo_templates/results_visualization.cxs
opened ChimeraX session
> rename #3 2_apo_y103a_aka_v2_model_0.cif
> show #!1 models
> hide #3 models
> hide #2 models
> mmaker #2 ro #1
> matchmaker #2 ro #1
Expected a keyword
> mmaker #2 to #1
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 9utc.pdb, chain A (#1) with 2_apo_wt_v1_model_0.cif, chain A (#2),
sequence alignment score = 2525.3
RMSD between 447 pruned atom pairs is 0.979 angstroms; (across all 500 pairs:
1.367)
> renumber #2/A seqStart 26
0 residues renumbered
> show #2 models
> rmsd #2:40,65,67,71,103,142,143,165,277,278,302,303,306 to
> #1:40,65,67,71,103,142,143,165,277,278,302,303,306
RMSD between 103 atom pairs is 1.356
> select :40,65,67,71,103,142,143,165,277,278,302,303,306
302 atoms, 277 bonds, 39 residues, 3 models selected
> show sel
> label sel
> view sel
> hide ~sel
> select ~sel
12274 atoms, 12570 bonds, 2 pseudobonds, 1519 residues, 7 models selected
> hide sel
> show sel & #!1-2 cartoons
> hide sel & #!1-2 cartoons
> select ligand
69 atoms, 72 bonds, 4 residues, 3 models selected
> show sel & #!1-2 atoms
> open
> /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/1_holo_templates/results_visualization.cxs
opened ChimeraX session
> mmaker #2 to #1
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 9utc.pdb, chain A (#1) with 1_holo_wt_aka_v2_model_0.cif, chain A
(#2), sequence alignment score = 2512.1
RMSD between 431 pruned atom pairs is 0.935 angstroms; (across all 500 pairs:
1.638)
> renumber #2/A seqStart 26
527 residues renumbered
> rmsd #2:40,65,67,71,103,142,143,165,277,278,302,303,306 to
> #3:40,65,67,71,103,142,143,165,277,278,302,303,306
Number of atoms from first atom spec (103) differs from number in second (96)
> rmsd #2:40,65,67,71,103,142,143,165,277,278,302,303,306 to
> #3:40,65,67,71,103,142,143,165,277,278,302,303,306
Number of atoms from first atom spec (103) differs from number in second (96)
> mmaker #2 to #1
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 9utc.pdb, chain A (#1) with 1_holo_wt_aka_v2_model_0.cif, chain A
(#2), sequence alignment score = 2512.1
RMSD between 431 pruned atom pairs is 0.935 angstroms; (across all 500 pairs:
1.638)
> renumber #2/A seqStart 26
0 residues renumbered
> rmsd #2:40,65,67,71,103,142,143,165,277,278,302,303,306 to
> #1:40,65,67,71,103,142,143,165,277,278,302,303,306
Number of atoms from first atom spec (103) differs from number in second (203)
> rmsd #2:40,65,67,71,103,142,143,165,277,278,302,303,306 to
> #1:40,65,67,71,103,142,143,165,277,278,302,303,306
Number of atoms from first atom spec (103) differs from number in second (203)
> rmsd #1:40,65,67,71,103,142,143,165,277,278,302,303,306 to
> #2:40,65,67,71,103,142,143,165,277,278,302,303,306
Number of atoms from first atom spec (203) differs from number in second (103)
> rmsd #1/A:40,65,67,71,103,142,143,165,277,278,302,303,306 to
> #2:40,65,67,71,103,142,143,165,277,278,302,303,306
RMSD between 103 atom pairs is 1.322
> select #1/B
4084 atoms, 4192 bonds, 1 pseudobond, 526 residues, 2 models selected
> delete sel
> select ligand
69 atoms, 72 bonds, 4 residues, 3 models selected
> view sel
> select all
12576 atoms, 12907 bonds, 2 pseudobonds, 1558 residues, 5 models selected
> hide sel & #!1,3 cartoons
> hide #!3 models
> show #2 models
> hide sel & #2#!1 cartoons
> select subtract #3
8321 atoms, 8542 bonds, 2 pseudobonds, 1030 residues, 3 models selected
> select all
12576 atoms, 12907 bonds, 2 pseudobonds, 1558 residues, 5 models selected
> hide sel & #2#!1 cartoons
> hide sel & #2#!1 atoms
> select ligand
69 atoms, 72 bonds, 4 residues, 3 models selected
> show sel & #2#!1 atoms
> select add #3
4301 atoms, 4413 bonds, 531 residues, 4 models selected
> select subtract #3
46 atoms, 48 bonds, 3 residues, 2 models selected
> select all
12576 atoms, 12907 bonds, 2 pseudobonds, 1558 residues, 5 models selected
> show sel & #2#!1 cartoons
> select :103
29 atoms, 28 bonds, 3 residues, 3 models selected
> show sel & #2#!1 atoms
> view
> hide #2 models
> select zone ligand 4 protein residues true
Selected 447 atoms
> show sel & #!1 atoms
> show #2 models
> hide #!1 models
> select ligand
69 atoms, 72 bonds, 4 residues, 3 models selected
> view
> view sel
> show hydrogen
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show ligand
> show #!1 models
> select protein
12507 atoms, 12835 bonds, 2 pseudobonds, 1554 residues, 4 models selected
> hide sel & #2#!1 cartoons
> select ligand,:103
Expected an objects specifier or a keyword
> select :103,LIG1,rryrrj
75 atoms, 76 bonds, 5 residues, 3 models selected
> select :103,LIG1,rry,rrj
98 atoms, 100 bonds, 7 residues, 3 models selected
> select ~sel
12478 atoms, 12801 bonds, 2 pseudobonds, 1551 residues, 5 models selected
> hide sel & #2#!1 atoms
> hide #2 models
> select zone 4 ligand protein res t
Missing or invalid "near" argument: invalid objects specifier
> select zone ligand 4 protein residues true
Selected 447 atoms
> select #1 & (zone ligand 4 protein res t)
Expected a keyword
> select (zone #1 & ligand 4 #1 & protein res t)
Expected an objects specifier or a keyword
> select (zone #1 & ligand 4 (#1 & protein) res t)
Expected an objects specifier or a keyword
> select zone #1 & ligand 4 (#1 & protein) residues true
Selected 103 atoms
> show sel atoms
> view sel
> label sel
> view sel
> select sel & @CA
13 atoms, 13 residues, 1 model selected
> select ~sel & !:rry,rrj
Expected a keyword
> select ~sel &! :rry,rrj
Expected a keyword
> select ~sel
12563 atoms, 12868 bonds, 2 pseudobonds, 1558 residues, 6 models selected
> hide sel & #!1 atoms
> undo
> select clear
> select :rrj,rry
23 atoms, 24 bonds, 2 residues, 1 model selected
> style sel sphere
Changed 23 atom styles
> style sel ball
Changed 23 atom styles
> hide sel atoms
> show sel atoms
> select up
4059 atoms, 4169 bonds, 502 residues, 1 model selected
> select up
12576 atoms, 12907 bonds, 1558 residues, 3 models selected
> select up
12576 atoms, 12907 bonds, 1558 residues, 3 models selected
> select down
4059 atoms, 4169 bonds, 502 residues, 1 model selected
> select down
23 atoms, 24 bonds, 2 residues, 1 model selected
> select down
23 atoms, 24 bonds, 2 residues, 1 model selected
> select down
23 atoms, 24 bonds, 2 residues, 1 model selected
Drag select of 126 atoms, 119 bonds
> info selection
atom id #1/A:40@N idatm_type Npl
atom id #1/A:40@CA idatm_type C3
atom id #1/A:40@C idatm_type C2
atom id #1/A:40@O idatm_type O2
atom id #1/A:40@CB idatm_type C3
atom id #1/A:40@OG idatm_type O3
atom id #1/A:65@N idatm_type Npl
atom id #1/A:65@CA idatm_type C3
atom id #1/A:65@C idatm_type C2
atom id #1/A:65@O idatm_type O2
atom id #1/A:65@CB idatm_type C3
atom id #1/A:65@CG idatm_type C3
atom id #1/A:65@CD idatm_type C3
atom id #1/A:65@CE idatm_type C3
atom id #1/A:65@NZ idatm_type N3+
atom id #1/A:67@N idatm_type Npl
atom id #1/A:67@CA idatm_type C3
atom id #1/A:67@C idatm_type C2
atom id #1/A:67@O idatm_type O2
atom id #1/A:67@CB idatm_type C3
atom id #1/A:67@CG1 idatm_type C3
atom id #1/A:67@CG2 idatm_type C3
atom id #1/A:67@CD1 idatm_type C3
atom id #1/A:71@N idatm_type Npl
atom id #1/A:71@CA idatm_type C3
atom id #1/A:71@C idatm_type C2
atom id #1/A:71@O idatm_type O2
atom id #1/A:71@CB idatm_type C3
atom id #1/A:71@CG idatm_type C3
atom id #1/A:71@CD1 idatm_type C3
atom id #1/A:71@CD2 idatm_type C3
atom id #1/A:103@N idatm_type Npl
atom id #1/A:103@CA idatm_type C3
atom id #1/A:103@C idatm_type C2
atom id #1/A:103@O idatm_type O2
atom id #1/A:103@CB idatm_type C3
atom id #1/A:103@CG idatm_type Car
atom id #1/A:103@CD1 idatm_type Car
atom id #1/A:103@CD2 idatm_type Car
atom id #1/A:103@CE1 idatm_type Car
atom id #1/A:103@CE2 idatm_type Car
atom id #1/A:103@CZ idatm_type Car
atom id #1/A:103@OH idatm_type O3
atom id #1/A:142@N idatm_type Npl
atom id #1/A:142@CA idatm_type C3
atom id #1/A:142@C idatm_type C2
atom id #1/A:142@O idatm_type O2
atom id #1/A:142@CB idatm_type C3
atom id #1/A:142@CG idatm_type Cac
atom id #1/A:142@OD1 idatm_type O2-
atom id #1/A:142@OD2 idatm_type O2-
atom id #1/A:143@N idatm_type Npl
atom id #1/A:143@CA idatm_type C3
atom id #1/A:143@C idatm_type C2
atom id #1/A:143@O idatm_type O2
atom id #1/A:143@CB idatm_type C3
atom id #1/A:143@CG idatm_type C2
atom id #1/A:143@OD1 idatm_type O2
atom id #1/A:143@ND2 idatm_type Npl
atom id #1/A:165@N idatm_type Npl
atom id #1/A:165@CA idatm_type C3
atom id #1/A:165@C idatm_type C2
atom id #1/A:165@O idatm_type O2
atom id #1/A:165@CB idatm_type C3
atom id #1/A:165@OG idatm_type O3
atom id #1/A:277@N idatm_type Npl
atom id #1/A:277@CA idatm_type C3
atom id #1/A:277@C idatm_type C2
atom id #1/A:277@O idatm_type O2
atom id #1/A:277@CB idatm_type C3
atom id #1/A:277@CG idatm_type C3
atom id #1/A:277@CD idatm_type C3
atom id #1/A:278@N idatm_type Npl
atom id #1/A:278@CA idatm_type C3
atom id #1/A:278@C idatm_type C2
atom id #1/A:278@O idatm_type O2
atom id #1/A:278@CB idatm_type C3
atom id #1/A:278@CG idatm_type Cac
atom id #1/A:278@OD1 idatm_type O2-
atom id #1/A:278@OD2 idatm_type O2-
atom id #1/A:302@N idatm_type Npl
atom id #1/A:302@CA idatm_type C3
atom id #1/A:302@C idatm_type C2
atom id #1/A:302@O idatm_type O2
atom id #1/A:302@CB idatm_type C3
atom id #1/A:302@CG idatm_type C3
atom id #1/A:302@CD idatm_type Cac
atom id #1/A:302@OE1 idatm_type O2-
atom id #1/A:302@OE2 idatm_type O2-
atom id #1/A:303@N idatm_type Npl
atom id #1/A:303@CA idatm_type C3
atom id #1/A:303@C idatm_type C2
atom id #1/A:303@O idatm_type O2
atom id #1/A:303@CB idatm_type C3
atom id #1/A:303@OG idatm_type O3
atom id #1/A:306@N idatm_type Npl
atom id #1/A:306@CA idatm_type C3
atom id #1/A:306@C idatm_type C2
atom id #1/A:306@O idatm_type O2
atom id #1/A:306@CB idatm_type C3
atom id #1/A:306@CG1 idatm_type C3
atom id #1/A:306@CG2 idatm_type C3
atom id #1/A:306@CD1 idatm_type C3
atom id #1/C:1@O3 idatm_type O3
atom id #1/C:1@C3 idatm_type C3
atom id #1/C:1@C4 idatm_type C3
atom id #1/C:1@O4 idatm_type O3
atom id #1/C:1@C5 idatm_type C3
atom id #1/C:1@C6 idatm_type C3
atom id #1/C:1@CL6 idatm_type Cl
atom id #1/C:1@O5 idatm_type O3
atom id #1/C:1@C2 idatm_type C3
atom id #1/C:1@C1 idatm_type C3
atom id #1/C:1@CL1 idatm_type Cl
atom id #1/C:1@O2 idatm_type O3
atom id #1/C:2@C1 idatm_type C3
atom id #1/C:2@O5 idatm_type O3
atom id #1/C:2@C5 idatm_type C3
atom id #1/C:2@C6 idatm_type C3
atom id #1/C:2@O6 idatm_type O3
atom id #1/C:2@C4 idatm_type C3
atom id #1/C:2@CL4 idatm_type Cl
atom id #1/C:2@C3 idatm_type C3
atom id #1/C:2@O3 idatm_type O3
atom id #1/C:2@C2 idatm_type C3
atom id #1/C:2@O2 idatm_type O3
> info residues sel
residue id #1/A:40 name SER index 43
residue id #1/A:65 name LYS index 68
residue id #1/A:67 name ILE index 70
residue id #1/A:71 name LEU index 74
residue id #1/A:103 name TYR index 106
residue id #1/A:142 name ASP index 145
residue id #1/A:143 name ASN index 146
residue id #1/A:165 name SER index 168
residue id #1/A:277 name PRO index 280
residue id #1/A:278 name ASP index 281
residue id #1/A:302 name GLU index 305
residue id #1/A:303 name SER index 306
residue id #1/A:306 name ILE index 309
residue id #1/C:1 name RRY
residue id #1/C:2 name RRJ
Drag select of 126 atoms, 119 bonds
> ui tool show "Side View"
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/suhasgotla/Desktop/movie1.mp4
Movie saved to /Users/suhasgotla/Desktop/movie1.mp4
> view
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #2 models
> select add #1
4059 atoms, 4169 bonds, 2 pseudobonds, 502 residues, 3 models selected
> select add #2
8321 atoms, 8542 bonds, 2 pseudobonds, 1030 residues, 4 models selected
> select subtract #1
4262 atoms, 4373 bonds, 528 residues, 1 model selected
Drag select of 23 atoms, 24 bonds
> label sel
> info selection
atom id #2/B:1@O23 idatm_type O3
atom id #2/B:1@C32 idatm_type C3
atom id #2/B:1@C41 idatm_type C3
atom id #2/B:1@O29 idatm_type O3
atom id #2/B:1@C34 idatm_type C3
atom id #2/B:1@O24 idatm_type O3
atom id #2/B:1@C35 idatm_type C3
atom id #2/B:1@C31 idatm_type C3
atom id #2/B:1@CL20 idatm_type Cl
atom id #2/B:1@O30 idatm_type O3
atom id #2/B:1@C42 idatm_type C3
atom id #2/B:1@C33 idatm_type C3
atom id #2/B:1@CL21 idatm_type Cl
atom id #2/B:1@C39 idatm_type C3
atom id #2/B:1@O27 idatm_type O3
atom id #2/B:1@C40 idatm_type C3
atom id #2/B:1@O28 idatm_type O3
atom id #2/B:1@C37 idatm_type C3
atom id #2/B:1@O25 idatm_type O3
atom id #2/B:1@C38 idatm_type C3
atom id #2/B:1@O26 idatm_type O3
atom id #2/B:1@C36 idatm_type C3
atom id #2/B:1@CL22 idatm_type Cl
> select #2/B:1@CL22
1 atom, 1 residue, 1 model selected
> label sel
> selete label
Unknown command: selete label
> delete label
Missing or invalid "atoms" argument: invalid atoms specifier
> label delete
Drag select of 11 atoms, 12 bonds
Drag select of 12 atoms, 12 bonds
> hide sel atoms
Drag select of 23 atoms, 24 bonds
> label sel atoms
> save /Users/suhasgotla/Desktop/image1.png supersample 3
> save /Users/suhasgotla/Desktop/image2.png supersample 3
> hide #!2 models
> select add #2
4262 atoms, 4373 bonds, 528 residues, 2 models selected
> show #!1 models
> select subtract #2
Nothing selected
> ui tool show Distances
Exactly two atoms must be selected!
> select #1/A:142@CG
1 atom, 1 residue, 1 model selected
> select add #1/C:2@O5
2 atoms, 2 residues, 1 model selected
> distance #1/A:142@CG #1/C:2@O5
Distance between 9utc.pdb #1/A ASP 142 CG and /C RRJ 2 O5: 3.060Å
> view sel
> ui tool show "Side View"
> label sel atoms
> label sel residues
Drag select of 13 atoms, 12 bonds
> hide sel atoms
Drag select of 6 atoms, 5 bonds
> hide sel atoms
Drag select of 3 atoms, 2 bonds
Drag select of 11 atoms, 10 bonds
> hide sel atoms
Drag select of 7 atoms, 2 bonds
> hide sel atoms
Drag select of 6 atoms, 3 bonds
> hide sel atoms
Drag select of 6 atoms, 5 bonds
> hide sel atoms
Drag select of 8 atoms, 7 bonds
> hide sel atoms
Drag select of 6 atoms, 5 bonds
> hide sel atoms
Drag select of 9 atoms, 8 bonds
> hide sel atoms
Drag select of 7 atoms, 6 bonds
> hide sel atoms
Drag select of 8 atoms, 8 bonds
> hide sel atoms
> view
> save /Users/suhasgotla/Desktop/image1.png supersample 3
> show #!2 models
> hide #!1 models
> show #2/142
> show #2:142
> select #2/A:142@CG
1 atom, 1 residue, 1 model selected
> select #2/B:1@O29
1 atom, 1 residue, 1 model selected
> select add #2/A:142@CG
2 atoms, 2 residues, 1 model selected
> distance #2/B:1@O29 #2/A:142@CG
Distance between 1_holo_wt_aka_v2_model_0.cif #2/B LIG1 1 O29 and /A ASP 142
CG: 7.365Å
> hide #!2 models
> show #!1 models
> select add #1
4061 atoms, 4169 bonds, 3 pseudobonds, 504 residues, 5 models selected
> show #!2 models
> hide #!1 models
> label delete ~sel
> select #2/A:142@CG
1 atom, 1 residue, 1 model selected
> label atoms sel
Expected a keyword
> label sel atoms
> label sel residues
> select add #2/B:1@O29
1 atom, 1 pseudobond, 1 residue, 2 models selected
> select add #2/A:142@CG
2 atoms, 1 pseudobond, 2 residues, 2 models selected
> view sel
> save /Users/suhasgotla/Desktop/image1.png supersample 3
> hide #!2 models
> select add #2
4262 atoms, 4373 bonds, 1 pseudobond, 528 residues, 3 models selected
> show #3 models
> select subtract #2
Nothing selected
> select add #3
4255 atoms, 4365 bonds, 528 residues, 1 model selected
> select #3,ligand
Expected an objects specifier or a keyword
> select #3&ligand
23 atoms, 24 bonds, 1 residue, 1 model selected
> select #3/A:302@CA
1 atom, 1 residue, 1 model selected
> select add #3/A:302@CB
2 atoms, 1 residue, 1 model selected
> select #3&ligand
23 atoms, 24 bonds, 1 residue, 1 model selected
> select add #3:142
31 atoms, 31 bonds, 2 residues, 1 model selected
> hide ~sel
> select #3/A:142@CG
1 atom, 1 residue, 1 model selected
> select add #3/B:1@O29
2 atoms, 2 residues, 1 model selected
> label sel atoms
> label :142
> select #3/A:142@CG
1 atom, 1 residue, 1 model selected
> select add #3/B:1@O29
2 atoms, 2 residues, 1 model selected
> distance #3/A:142@CG #3/B:1@O29
Distance between 1_holo_y103a_aka_v3_model_0.cif #3/A ASP 142 CG and /B LIG1 1
O29: 6.600Å
> save /Users/suhasgotla/Desktop/image1.png supersample 3
> open
> /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/1_holo_templates/v4/boltz_results_v4/predictions/v4/v4_model_0.cif
Summary of feedback from opening
/Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/1_holo_templates/v4/boltz_results_v4/predictions/v4/v4_model_0.cif
---
warning | Unable to fetch template for 'LIG1': will connect using distance criteria
v4_model_0.cif title:
. [more info...]
Chain information for v4_model_0.cif #5
---
Chain | Description
A | .
Non-standard residues in v4_model_0.cif #5
---
LIG1 — (LIG1)
No chain in structure corresponds to chain ID given in local score info (chain
'B')
> rename #5 1_holo_wt_pocket_aka_v4_model_0.cif
> hide #5 models
> show #5 models
> hide #4.1 models
> hide #!4 models
> hide #!3 models
> view
> show #!1 models
> view
> clear
Unknown command: clear
> clear
Unknown command: clear
> mmaker #4 to #1
No molecules/chains to match specified
> mmaker #5 to #1
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 9utc.pdb, chain A (#1) with 1_holo_wt_pocket_aka_v4_model_0.cif,
chain A (#5), sequence alignment score = 2531.9
RMSD between 431 pruned atom pairs is 0.958 angstroms; (across all 500 pairs:
1.520)
> select add #1
4061 atoms, 4169 bonds, 3 pseudobonds, 504 residues, 5 models selected
> show sel & #!1 cartoons
> select subtract #1
2 atoms, 2 residues, 1 model selected
> view
> show #1&ligand
> view sel
No displayed objects specified.
> select ligand
92 atoms, 96 bonds, 5 residues, 4 models selected
> view sel
> hide #!1 models
> select #5&ligand
23 atoms, 24 bonds, 1 residue, 1 model selected
> renumber #5/A seqStart 26
527 residues renumbered
> select add #5:142
31 atoms, 31 bonds, 2 residues, 1 model selected
> hide ~sel
> select ~sel
16807 atoms, 17247 bonds, 5 pseudobonds, 2084 residues, 10 models selected
> hide sel & #5 cartoons
> select #5/B:1@O29
1 atom, 1 residue, 1 model selected
> select add #5/A:142@CG
2 atoms, 2 residues, 1 model selected
> select #5/A:142@CG
1 atom, 1 residue, 1 model selected
> select clear
> select #5/A:142@CG
1 atom, 1 residue, 1 model selected
> select add #5/B:1@O29
2 atoms, 2 residues, 1 model selected
> distance #5/A:142@CG #5/B:1@O29
Distance between 1_holo_wt_pocket_aka_v4_model_0.cif #5/A ASP 142 CG and /B
LIG1 1 O29: 6.647Å
> show #!4 models
> show #4.1 models
> label (sel #5@O29 or :142@CG) atoms
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> select #5@O29 or :142@CG
Expected a keyword
> label (sel #5@O29 | :142@CG) atoms
Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword
> label atoms (sel #5@O29 | :142@CG)
Expected a keyword
> select #5@O29 | #4:142@CG
1 atom, 1 residue, 1 model selected
> label sel atoms
> select #5/A:142@CG
1 atom, 1 residue, 1 model selected
> label sel atoms
> select :142
32 atoms, 28 bonds, 4 residues, 4 models selected
> label sel
> save /Users/suhasgotla/Desktop/image1.png supersample 3
> open
> /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/1_holo_templates/v5/boltz_results_v5/predictions/v5/v5_model_0.cif
Summary of feedback from opening
/Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/1_holo_templates/v5/boltz_results_v5/predictions/v5/v5_model_0.cif
---
warning | Unable to fetch template for 'LIG1': will connect using distance criteria
v5_model_0.cif title:
. [more info...]
Chain information for v5_model_0.cif #6
---
Chain | Description
A | .
Non-standard residues in v5_model_0.cif #6
---
LIG1 — (LIG1)
No chain in structure corresponds to chain ID given in local score info (chain
'B')
> rename #6 1_holo_wt_contact_aka_v5_model_0.cif
> mmaker #6 to #1
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 9utc.pdb, chain A (#1) with 1_holo_wt_contact_aka_v5_model_0.cif,
chain A (#6), sequence alignment score = 2545.1
RMSD between 469 pruned atom pairs is 0.904 angstroms; (across all 500 pairs:
1.132)
> hide #!5 models
> show #!1 models
> show ligand
> show zone ligand 4 protein res t
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show zone 4 ligand protein res t
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show zone 4 ligand #1&protein res t
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select zone 4 ligand #1&protein res t
Missing or invalid "near" argument: invalid objects specifier
> select zone ligand 4 #1&protein residues true
Selected 147 atoms
> select zone #1&ligand 4 #1&protein residues true
Selected 103 atoms
> show sel atoms
> hide #6 models
> show #6 models
> hide sel cartoons
> show sel cartoons
> select add #1
4059 atoms, 4169 bonds, 3 pseudobonds, 502 residues, 4 models selected
> select #6,1 & (ligand | :142)
62 atoms, 62 bonds, 1 pseudobond, 5 residues, 3 models selected
> hide ~sel
> select ~sel
21038 atoms, 21587 bonds, 5 pseudobonds, 2609 residues, 12 models selected
> hide sel & #6#!1 cartoons
> hide #!1 models
Alignment identifier is 1/A
Alignment identifier is 1
Alignment identifier is 3/A
> select #6:142
8 atoms, 7 bonds, 1 residue, 1 model selected
Alignment identifier is 6/A
> renumber #6 seqStart 26
528 residues renumbered
> select #6:142
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel cartoons
Drag select of 5 atoms, 1 residues, 4 bonds
> hide sel atoms
> hide sel cartoons
Drag select of 5 atoms, 1 residues, 4 bonds
> label sel
> select #6/A:142@CG
1 atom, 1 residue, 1 model selected
> select add #6/B:26@O29
2 atoms, 2 residues, 1 model selected
> label sel atoms
> distance #6/A:142@CG #6/B:26@O29
Distance between 1_holo_wt_contact_aka_v5_model_0.cif #6/A ASP 142 CG and /B
LIG1 26 O29: 6.248Å
> view sel
> save /Users/suhasgotla/Desktop/image1.png supersample 3
> show #!1 models
> select add #1
4061 atoms, 4169 bonds, 3 pseudobonds, 504 residues, 5 models selected
> hide #!6 models
> select add #6
8321 atoms, 8542 bonds, 4 pseudobonds, 1030 residues, 6 models selected
> select subtract #6
4059 atoms, 4169 bonds, 3 pseudobonds, 502 residues, 4 models selected
> hide #4.1 models
> show #4.1 models
> view
> select #1&ligand
23 atoms, 24 bonds, 2 residues, 1 model selected
> style sel sphere
Changed 23 atom styles
> style sel sphere
Changed 23 atom styles
> style sel ball
Changed 23 atom styles
> style sel stick
Changed 23 atom styles
> save /Users/suhasgotla/Desktop/image1.png supersample 3
> show #!6 models
> show #!5 models
> show #4&ligand
> select #4&ligand
Nothing selected
> show #5&ligand
> hide #!1 models
> show #5:142
> show #!1 models
> hide #!5 models
> hide #!6 models
> select #1/C:2@C4
1 atom, 1 residue, 1 model selected
> select add #1/C:2@C1
2 atoms, 1 residue, 1 model selected
> select add #1/C:1@C2
3 atoms, 2 residues, 1 model selected
> select add #1/C:1@C4
4 atoms, 2 residues, 1 model selected
> show #!6 models
> hide #!1 models
> select #6/B:26@C36
1 atom, 1 residue, 1 model selected
> select add #6/B:26@C34
2 atoms, 1 residue, 1 model selected
> select add #6/B:26@C35
3 atoms, 1 residue, 1 model selected
> select subtract #6/B:26@C35
2 atoms, 1 residue, 1 model selected
> select add #6/B:26@C35
3 atoms, 1 residue, 1 model selected
> select add #6/B:26@C39
4 atoms, 1 residue, 1 model selected
> show #!1 models
> hide #!4 models
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!6 models
> hide #!5 models
> select zone #1:rry 3.1 #1/A residues true
Selected 22 atoms
> info residues sel
residue id #1/A:142 name ASP index 145
residue id #1/A:278 name ASP index 281
residue id #1/A:303 name SER index 306
> show sel
> show sel cartoons
> select zone #1:rrj 3.1 #1/A residues true
Selected 23 atoms
> show sel
> show sel cartoons
Drag select of 45 atoms, 5 residues, 41 bonds
> info residues sel
residue id #1/A:142 name ASP index 145
residue id #1/A:165 name SER index 168
residue id #1/A:278 name ASP index 281
residue id #1/A:302 name GLU index 305
residue id #1/A:303 name SER index 306
residue id #1/C:1 name RRY
residue id #1/C:2 name RRJ
> rmsd #6:40,65,67,71,103,142,143,165,277,278,302,303,306 to
> #1:40,65,67,71,103,142,143,165,277,278,302,303,306
RMSD between 103 atom pairs is 1.246
> rmsd #5:40,65,67,71,103,142,143,165,277,278,302,303,306 to
> #1:40,65,67,71,103,142,143,165,277,278,302,303,306
RMSD between 103 atom pairs is 1.184
> rmsd #3:40,65,67,71,103,142,143,165,277,278,302,303,306 to
> #1:40,65,67,71,103,142,143,165,277,278,302,303,306
Number of atoms from first atom spec (96) differs from number in second (103)
> rmsd #3:40,65,67,71,142,143,165,277,278,302,303,306 to
> #1:40,65,67,71,142,143,165,277,278,302,303,306
RMSD between 91 atom pairs is 1.297
> rmsd #2:40,65,67,71,103,142,143,165,277,278,302,303,306 to
> #1:40,65,67,71,103,142,143,165,277,278,302,303,306
RMSD between 103 atom pairs is 1.322
> mmaker #6 to #1
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 9utc.pdb, chain A (#1) with 1_holo_wt_contact_aka_v5_model_0.cif,
chain A (#6), sequence alignment score = 2545.1
RMSD between 469 pruned atom pairs is 0.904 angstroms; (across all 500 pairs:
1.132)
> mmaker #5 to #1
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 9utc.pdb, chain A (#1) with 1_holo_wt_pocket_aka_v4_model_0.cif,
chain A (#5), sequence alignment score = 2531.9
RMSD between 431 pruned atom pairs is 0.958 angstroms; (across all 500 pairs:
1.520)
> mmaker #3 to #1
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 9utc.pdb, chain A (#1) with 1_holo_y103a_aka_v3_model_0.cif, chain
A (#3), sequence alignment score = 2525.6
RMSD between 453 pruned atom pairs is 0.855 angstroms; (across all 500 pairs:
1.163)
> mmaker #2 to #1
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 9utc.pdb, chain A (#1) with 1_holo_wt_aka_v2_model_0.cif, chain A
(#2), sequence alignment score = 2521.1
RMSD between 431 pruned atom pairs is 0.935 angstroms; (across all 500 pairs:
1.638)
===== Log before crash end =====
Log:
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 - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.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 Air
Model Identifier: Mac15,12
Model Number: MXCU3LL/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 36 days, 10 hours, 15 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
VX2703 SERIES:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
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 , 5 weeks ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 5 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
This ChimeraX crash is caused by a bug in the Qt window toolkit that ChimeraX uses that happens on Macs usually with multiple displays, when plugging in or unplugging displays (or closing/opening laptop after sleep). We have not seen this crash in the current ChimeraX daily build which uses a newer Qt version so you might want to try that.
Note:
See TracTickets
for help on using tickets.
Reported by Suhas