id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
19904	Crash on Mac waking from sleep	hijikata@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Bus error

Current thread 0x0000000209079f00 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in 
  File """", line 88 in _run_code
  File """", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.pdb_lib._load_libs, 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.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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.mlp._mlp (total: 56)


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===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/atsushi/Documents/works/Collabo/CyberneticAvatar/works/Dodo_251209/af3_models/AtGID1_S116G_AtGAI-
> NHCONHPh/AtGID1_S116G_AtGAI-NHCONHPh_model.cif format mmcif

Summary of feedback from opening
/Users/atsushi/Documents/works/Collabo/CyberneticAvatar/works/Dodo_251209/af3_models/AtGID1_S116G_AtGAI-
NHCONHPh/AtGID1_S116G_AtGAI-NHCONHPh_model.cif  
---  
warning | Unable to fetch template for 'LIG_L': will connect using distance criteria  
  
Chain information for AtGID1_S116G_AtGAI-NHCONHPh_model.cif #1  
---  
Chain | Description  
A | .  
B | .  
  

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

Computing secondary structure  

> graphics silhouettes true

> lighting soft

> select ligand

32 atoms, 37 bonds, 1 residue, 1 model selected  

> color sel byelement

> select clear

> style sphere

Changed 3354 atom styles  

> style ball

Changed 3354 atom styles  

> color bychain

> select ligand

32 atoms, 37 bonds, 1 residue, 1 model selected  

> color sel byelement

> cofr sel

> select clear

> open 2zsi fromDatabase pdb format mmcif

2zsi title:  
Structural basis of gibberellin(GA4)-induced DELLA recognition by the
gibberellin receptor [more info...]  
  
Chain information for 2zsi #2  
---  
Chain | Description | UniProt  
A | Probable gibberellin receptor GID1L1 | GI1L1_ARATH 1-344  
B | DELLA protein GAI | GAI_ARATH 11-113  
  
Non-standard residues in 2zsi #2  
---  
GA4 — gibberellin A4  
  

> open
> /Users/atsushi/Documents/works/Collabo/CyberneticAvatar/works/Dodo_251209/af3_models/AtGID1_AtGAI-
> GA3/AtGID1_AtGAI-GA3_model.cif

Summary of feedback from opening
/Users/atsushi/Documents/works/Collabo/CyberneticAvatar/works/Dodo_251209/af3_models/AtGID1_AtGAI-
GA3/AtGID1_AtGAI-GA3_model.cif  
---  
warning | Unable to fetch template for 'LIG_L': will connect using distance criteria  
  
Chain information for AtGID1_AtGAI-GA3_model.cif #3  
---  
Chain | Description  
A | .  
B | .  
  

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

Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #3 to #1 showAlignment true

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AtGID1_S116G_AtGAI-NHCONHPh_model.cif, chain A (#1) with
AtGID1_AtGAI-GA3_model.cif, chain A (#3), sequence alignment score = 1757  
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: AtGID1_S116G_AtGAI-
NHCONHPh_model.cif #1/A, AtGID1_AtGAI-GA3_model.cif #3/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1  
RMSD between 337 pruned atom pairs is 0.255 angstroms; (across all 345 pairs:
1.151)  
  

> close #2

> select ligand

57 atoms, 66 bonds, 2 residues, 2 models selected  

> color sel byelement

> open
> /Users/atsushi/Documents/works/Collabo/CyberneticAvatar/works/Dodo_251209/af3_models/AtGID1_S116GS192AM220GD243VR244T_AtGAI-
> NHCONHPh/AtGID1_S116GS192AM220GD243VR244T_AtGAI-NHCONHPh_model.cif

Summary of feedback from opening
/Users/atsushi/Documents/works/Collabo/CyberneticAvatar/works/Dodo_251209/af3_models/AtGID1_S116GS192AM220GD243VR244T_AtGAI-
NHCONHPh/AtGID1_S116GS192AM220GD243VR244T_AtGAI-NHCONHPh_model.cif  
---  
warning | Unable to fetch template for 'LIG_L': will connect using distance criteria  
  
Chain information for AtGID1_S116GS192AM220GD243VR244T_AtGAI-
NHCONHPh_model.cif #2  
---  
Chain | Description  
A | .  
B | .  
  

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

Associated AtGID1_S116GS192AM220GD243VR244T_AtGAI-NHCONHPh_model.cif chain A
to AtGID1_S116G_AtGAI-NHCONHPh_model.cif, chain A with 4 mismatches  
Chains used in RMSD evaluation for alignment 1: AtGID1_S116G_AtGAI-
NHCONHPh_model.cif #1/A, AtGID1_S116GS192AM220GD243VR244T_AtGAI-
NHCONHPh_model.cif #2/A, AtGID1_AtGAI-GA3_model.cif #3/A  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #3 to #1 showAlignment true

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AtGID1_S116G_AtGAI-NHCONHPh_model.cif, chain A (#1) with
AtGID1_AtGAI-GA3_model.cif, chain A (#3), sequence alignment score = 1757  
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: AtGID1_S116G_AtGAI-
NHCONHPh_model.cif #1/A, AtGID1_AtGAI-GA3_model.cif #3/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2  
RMSD between 337 pruned atom pairs is 0.255 angstroms; (across all 345 pairs:
1.151)  
  

> ui tool show Matchmaker

> matchmaker #2 to #1 showAlignment true

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AtGID1_S116G_AtGAI-NHCONHPh_model.cif, chain A (#1) with
AtGID1_S116GS192AM220GD243VR244T_AtGAI-NHCONHPh_model.cif, chain A (#2),
sequence alignment score = 1741.8  
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: AtGID1_S116G_AtGAI-
NHCONHPh_model.cif #1/A, AtGID1_S116GS192AM220GD243VR244T_AtGAI-
NHCONHPh_model.cif #2/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 3  
RMSD between 338 pruned atom pairs is 0.226 angstroms; (across all 345 pairs:
0.582)  
  

> select ligand

89 atoms, 103 bonds, 3 residues, 3 models selected  

> color sel byelement

> hide #2 models

> show #2 models

> hide #3 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #3 models

> hide #2 models

> show sel & #3 atoms

> select clear

> show #3 atoms

> color #3 bychain

> select ligand

89 atoms, 103 bonds, 3 residues, 3 models selected  

> color (#3 & sel) byelement

> select clear

> open
> /Users/atsushi/Documents/works/Collabo/CyberneticAvatar/works/Dodo_251209/migrate_vs_cxe/residue_importance_2ZSI_A.cxc

> setattr /A:1 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:2 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:3 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:4 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:5 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:6 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:7 residue score 0.01013 create true

Assigning score attribute to 3 items  

> setattr /A:8 residue score 0.01544 create true

Assigning score attribute to 3 items  

> setattr /A:9 residue score 0.01512 create true

Assigning score attribute to 3 items  

> setattr /A:10 residue score 0.00518 create true

Assigning score attribute to 3 items  

> setattr /A:11 residue score 0.01969 create true

Assigning score attribute to 3 items  

> setattr /A:12 residue score 0.00985 create true

Assigning score attribute to 3 items  

> setattr /A:13 residue score 0.02674 create true

Assigning score attribute to 3 items  

> setattr /A:14 residue score 0.00138 create true

Assigning score attribute to 3 items  

> setattr /A:15 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:16 residue score 0.01239 create true

Assigning score attribute to 3 items  

> setattr /A:17 residue score 0.00021 create true

Assigning score attribute to 3 items  

> setattr /A:18 residue score 0.00662 create true

Assigning score attribute to 3 items  

> setattr /A:19 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:20 residue score 0.00412 create true

Assigning score attribute to 3 items  

> setattr /A:21 residue score 0.00969 create true

Assigning score attribute to 3 items  

> setattr /A:22 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:23 residue score 0.00596 create true

Assigning score attribute to 3 items  

> setattr /A:24 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:25 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:26 residue score 0.00505 create true

Assigning score attribute to 3 items  

> setattr /A:27 residue score 0.00148 create true

Assigning score attribute to 3 items  

> setattr /A:28 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:29 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:30 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:31 residue score 0.01932 create true

Assigning score attribute to 3 items  

> setattr /A:32 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:33 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:34 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:35 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:36 residue score 0.00507 create true

Assigning score attribute to 3 items  

> setattr /A:37 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:38 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:39 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:40 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:41 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:42 residue score 0.01325 create true

Assigning score attribute to 3 items  

> setattr /A:43 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:44 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:45 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:46 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:47 residue score 0.00144 create true

Assigning score attribute to 3 items  

> setattr /A:48 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:49 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:50 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:51 residue score 0.00966 create true

Assigning score attribute to 3 items  

> setattr /A:52 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:53 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:54 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:55 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:56 residue score 0.00469 create true

Assigning score attribute to 3 items  

> setattr /A:57 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:58 residue score 0.00412 create true

Assigning score attribute to 3 items  

> setattr /A:59 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:60 residue score 0.00829 create true

Assigning score attribute to 3 items  

> setattr /A:61 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:62 residue score 0.00639 create true

Assigning score attribute to 3 items  

> setattr /A:63 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:64 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:65 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:66 residue score 0.01931 create true

Assigning score attribute to 3 items  

> setattr /A:67 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:68 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:69 residue score 0.00329 create true

Assigning score attribute to 3 items  

> setattr /A:70 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:71 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:72 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:73 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:74 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:75 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:76 residue score 0.01494 create true

Assigning score attribute to 3 items  

> setattr /A:77 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:78 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:79 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:80 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:81 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:82 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:83 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:84 residue score 0.00058 create true

Assigning score attribute to 3 items  

> setattr /A:85 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:86 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:87 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:88 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:89 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:90 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:91 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:92 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:93 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:94 residue score 0.00457 create true

Assigning score attribute to 3 items  

> setattr /A:95 residue score 0.00470 create true

Assigning score attribute to 3 items  

> setattr /A:96 residue score 0.00505 create true

Assigning score attribute to 3 items  

> setattr /A:97 residue score 0.01410 create true

Assigning score attribute to 3 items  

> setattr /A:98 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:99 residue score 0.01009 create true

Assigning score attribute to 3 items  

> setattr /A:100 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:101 residue score 0.00546 create true

Assigning score attribute to 3 items  

> setattr /A:102 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:103 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:104 residue score 0.00035 create true

Assigning score attribute to 3 items  

> setattr /A:105 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:106 residue score 0.00721 create true

Assigning score attribute to 3 items  

> setattr /A:107 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:108 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:109 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:110 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:111 residue score 0.00101 create true

Assigning score attribute to 3 items  

> setattr /A:112 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:113 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:114 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:115 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:116 residue score 0.03942 create true

Assigning score attribute to 3 items  

> setattr /A:117 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:118 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:119 residue score 0.01516 create true

Assigning score attribute to 3 items  

> setattr /A:120 residue score 0.00497 create true

Assigning score attribute to 3 items  

> setattr /A:121 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:122 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:123 residue score 0.01087 create true

Assigning score attribute to 3 items  

> setattr /A:124 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:125 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:126 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:127 residue score 0.00831 create true

Assigning score attribute to 3 items  

> setattr /A:128 residue score 0.00441 create true

Assigning score attribute to 3 items  

> setattr /A:129 residue score 0.00960 create true

Assigning score attribute to 3 items  

> setattr /A:130 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:131 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:132 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:133 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:134 residue score 0.00123 create true

Assigning score attribute to 3 items  

> setattr /A:135 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:136 residue score 0.00065 create true

Assigning score attribute to 3 items  

> setattr /A:137 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:138 residue score 0.00477 create true

Assigning score attribute to 3 items  

> setattr /A:139 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:140 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:141 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:142 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:143 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:144 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:145 residue score 0.00115 create true

Assigning score attribute to 3 items  

> setattr /A:146 residue score 0.00280 create true

Assigning score attribute to 3 items  

> setattr /A:147 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:148 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:149 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:150 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:151 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:152 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:153 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:154 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:155 residue score 0.02383 create true

Assigning score attribute to 3 items  

> setattr /A:156 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:157 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:158 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:159 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:160 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:161 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:162 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:163 residue score 0.01873 create true

Assigning score attribute to 3 items  

> setattr /A:164 residue score 0.00061 create true

Assigning score attribute to 3 items  

> setattr /A:165 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:166 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:167 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:168 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:169 residue score 0.00793 create true

Assigning score attribute to 3 items  

> setattr /A:170 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:171 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:172 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:173 residue score 0.00276 create true

Assigning score attribute to 3 items  

> setattr /A:174 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:175 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:176 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:177 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:178 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:179 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:180 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:181 residue score 0.00877 create true

Assigning score attribute to 3 items  

> setattr /A:182 residue score 0.00407 create true

Assigning score attribute to 3 items  

> setattr /A:183 residue score 0.00714 create true

Assigning score attribute to 3 items  

> setattr /A:184 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:185 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:186 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:187 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:188 residue score 0.00822 create true

Assigning score attribute to 3 items  

> setattr /A:189 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:190 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:191 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:192 residue score 0.02563 create true

Assigning score attribute to 3 items  

> setattr /A:193 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:194 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:195 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:196 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:197 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:198 residue score 0.04133 create true

Assigning score attribute to 3 items  

> setattr /A:199 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:200 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:201 residue score 0.00403 create true

Assigning score attribute to 3 items  

> setattr /A:202 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:203 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:204 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:205 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:206 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:207 residue score 0.00204 create true

Assigning score attribute to 3 items  

> setattr /A:208 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:209 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:210 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:211 residue score 0.00797 create true

Assigning score attribute to 3 items  

> setattr /A:212 residue score 0.00056 create true

Assigning score attribute to 3 items  

> setattr /A:213 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:214 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:215 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:216 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:217 residue score 0.00476 create true

Assigning score attribute to 3 items  

> setattr /A:218 residue score 0.00302 create true

Assigning score attribute to 3 items  

> setattr /A:219 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:220 residue score 0.00381 create true

Assigning score attribute to 3 items  

> setattr /A:221 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:222 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:223 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:224 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:225 residue score 0.00076 create true

Assigning score attribute to 3 items  

> setattr /A:226 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:227 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:228 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:229 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:230 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:231 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:232 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:233 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:234 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:235 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:236 residue score 0.01777 create true

Assigning score attribute to 3 items  

> setattr /A:237 residue score 0.00465 create true

Assigning score attribute to 3 items  

> setattr /A:238 residue score 0.00955 create true

Assigning score attribute to 3 items  

> setattr /A:239 residue score 0.02459 create true

Assigning score attribute to 3 items  

> setattr /A:240 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:241 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:242 residue score 0.00132 create true

Assigning score attribute to 3 items  

> setattr /A:243 residue score 0.01979 create true

Assigning score attribute to 3 items  

> setattr /A:244 residue score 0.00484 create true

Assigning score attribute to 3 items  

> setattr /A:245 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:246 residue score 0.02930 create true

Assigning score attribute to 3 items  

> setattr /A:247 residue score 0.02542 create true

Assigning score attribute to 3 items  

> setattr /A:248 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:249 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:250 residue score 0.00613 create true

Assigning score attribute to 3 items  

> setattr /A:251 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:252 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:253 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:254 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:255 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:256 residue score 0.00250 create true

Assigning score attribute to 3 items  

> setattr /A:257 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:258 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:259 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:260 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:261 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:262 residue score 0.00584 create true

Assigning score attribute to 3 items  

> setattr /A:263 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:264 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:265 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:266 residue score 0.00862 create true

Assigning score attribute to 3 items  

> setattr /A:267 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:268 residue score 0.00703 create true

Assigning score attribute to 3 items  

> setattr /A:269 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:270 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:271 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:272 residue score 0.00296 create true

Assigning score attribute to 3 items  

> setattr /A:273 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:274 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:275 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:276 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:277 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:278 residue score 0.00849 create true

Assigning score attribute to 3 items  

> setattr /A:279 residue score 0.00558 create true

Assigning score attribute to 3 items  

> setattr /A:280 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:281 residue score 0.00533 create true

Assigning score attribute to 3 items  

> setattr /A:282 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:283 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:284 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:285 residue score 0.00457 create true

Assigning score attribute to 3 items  

> setattr /A:286 residue score 0.02065 create true

Assigning score attribute to 3 items  

> setattr /A:287 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:288 residue score 0.00347 create true

Assigning score attribute to 3 items  

> setattr /A:289 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:290 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:291 residue score 0.00125 create true

Assigning score attribute to 3 items  

> setattr /A:292 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:293 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:294 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:295 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:296 residue score 0.00853 create true

Assigning score attribute to 3 items  

> setattr /A:297 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:298 residue score 0.03468 create true

Assigning score attribute to 3 items  

> setattr /A:299 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:300 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:301 residue score 0.01623 create true

Assigning score attribute to 3 items  

> setattr /A:302 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:303 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:304 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:305 residue score 0.00029 create true

Assigning score attribute to 3 items  

> setattr /A:306 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:307 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:308 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:309 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:310 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:311 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:312 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:313 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:314 residue score 0.00305 create true

Assigning score attribute to 3 items  

> setattr /A:315 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:316 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:317 residue score 0.00423 create true

Assigning score attribute to 3 items  

> setattr /A:318 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:319 residue score 0.01642 create true

Assigning score attribute to 3 items  

> setattr /A:320 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:321 residue score 0.00499 create true

Assigning score attribute to 3 items  

> setattr /A:322 residue score 0.00024 create true

Assigning score attribute to 3 items  

> setattr /A:323 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:324 residue score 0.00228 create true

Assigning score attribute to 3 items  

> setattr /A:325 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:326 residue score 0.05443 create true

Assigning score attribute to 3 items  

> setattr /A:327 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:328 residue score 0.00178 create true

Assigning score attribute to 3 items  

> setattr /A:329 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:330 residue score 0.00741 create true

Assigning score attribute to 3 items  

> setattr /A:331 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:332 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:333 residue score 0.00262 create true

Assigning score attribute to 3 items  

> setattr /A:334 residue score 0.00177 create true

Assigning score attribute to 3 items  

> setattr /A:335 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:336 residue score 0.00089 create true

Assigning score attribute to 3 items  

> setattr /A:337 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:338 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:339 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:340 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:341 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:342 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:343 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:344 residue score 0.00000 create true

Assigning score attribute to 3 items  

> setattr /A:345 residue score 0.00000 create true

Assigning score attribute to 3 items  

> color byattribute score protein palette white:yellow:red range 0.0, 0.05

9958 atoms, 1263 residues, atom score range 0 to 0.0544  
executed residue_importance_2ZSI_A.cxc  

> open
> /Users/atsushi/Documents/works/Collabo/CyberneticAvatar/works/Dodo_251209/af3_models/OsGID1_OsGAI-
> GA3/OsGID1_OsGAI-GA3_model.cif

Summary of feedback from opening
/Users/atsushi/Documents/works/Collabo/CyberneticAvatar/works/Dodo_251209/af3_models/OsGID1_OsGAI-
GA3/OsGID1_OsGAI-GA3_model.cif  
---  
warning | Unable to fetch template for 'LIG_L': will connect using distance criteria  
  
Chain information for OsGID1_OsGAI-GA3_model.cif #4  
---  
Chain | Description  
A | .  
B | .  
  

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

Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #4 to #1 showAlignment true

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AtGID1_S116G_AtGAI-NHCONHPh_model.cif, chain A (#1) with
OsGID1_OsGAI-GA3_model.cif, chain A (#4), sequence alignment score = 1263.8  
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: AtGID1_S116G_AtGAI-
NHCONHPh_model.cif #1/A, OsGID1_OsGAI-GA3_model.cif #4/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2  
RMSD between 315 pruned atom pairs is 0.557 angstroms; (across all 344 pairs:
1.895)  
  

> hide #3 models

> color #4 bychain

> select ligand

114 atoms, 132 bonds, 4 residues, 4 models selected  

> color (#4 & sel) byelement

> select clear

> show #4 atoms

> color #4 byhetero

> show #3 models

> color #3-4 byhetero

> sequence refreshAttrs 2

> select ::seq_identity hide #3 models

> color (#4 & sel) magenta

> color sel & #4 bychain

> open 2zsi fromDatabase pdb format mmcif

2zsi title:  
Structural basis of gibberellin(GA4)-induced DELLA recognition by the
gibberellin receptor [more info...]  
  
Chain information for 2zsi #5  
---  
Chain | Description | UniProt  
A | Probable gibberellin receptor GID1L1 | GI1L1_ARATH 1-344  
B | DELLA protein GAI | GAI_ARATH 11-113  
  
Non-standard residues in 2zsi #5  
---  
GA4 — gibberellin A4  
  

> ui tool show Matchmaker

> matchmaker #!5 to #4 showAlignment true

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker OsGID1_OsGAI-GA3_model.cif, chain A (#4) with 2zsi, chain A (#5),
sequence alignment score = 1242.1  
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: OsGID1_OsGAI-GA3_model.cif
#4/A, 2zsi #5/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1  
RMSD between 314 pruned atom pairs is 0.599 angstroms; (across all 338 pairs:
1.487)  
  

> select add #1

4395 atoms, 4420 bonds, 557 residues, 2 models selected  

> select subtract #1

1041 atoms, 984 bonds, 135 residues, 1 model selected  

> select add #4

3428 atoms, 3514 bonds, 439 residues, 1 model selected  

> select subtract #4

Nothing selected  

> select ::seq_identity select add #5

4482 atoms, 4236 bonds, 1 pseudobond, 801 residues, 4 models selected  

> select subtract #5

1035 atoms, 979 bonds, 134 residues, 1 model selected  

> color sel magenta

> style sel sphere

Changed 1035 atom styles  

> select clear

> select ligand

138 atoms, 160 bonds, 5 residues, 5 models selected  

> style sel & #4#!5 sphere

Changed 49 atom styles  

> hide #!5 models

> select clear

> select #4/A:185

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #4/A:185-186 #5/A:178-179

22 atoms, 20 bonds, 4 residues, 2 models selected  
MatchMaker Alignment [ID: 1] region OsGID1_OsGAI-GA3_model.cif, chain A..2zsi,
chain A [193-194] RMSD: 2.395  
  

> open 2o7r fromDatabase pdb format mmcif

2o7r title:  
Plant carboxylesterase AeCXE1 from Actinidia eriantha with acyl adduct [more
info...]  
  
Chain information for 2o7r #6  
---  
Chain | Description | UniProt  
A | CXE carboxylesterase | Q0ZPV7_9ERIC 1-335  
  
Non-standard residues in 2o7r #6  
---  
4PA — propyl acetate  
  

> ui tool show Matchmaker

> matchmaker #!6 to #5 showAlignment true

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 2zsi, chain A (#5) with 2o7r, chain A (#6), sequence alignment
score = 497.6  
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: 2zsi #5/A, 2o7r #6/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2  
RMSD between 220 pruned atom pairs is 0.895 angstroms; (across all 292 pairs:
4.364)  
  

> hide #4 models

> show #4 models

> hide #4 models

> show #!5 models

> hide #!6 models

> show #!6 models

> show #3 models

> hide #!5 models

> ui tool show ""Show Sequence Viewer""

> sequence chain #1/A

Alignment identifier is 1/A  

> select #1/A:291

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

> select #1/A:291

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

> open I3PLR2 fromDatabase alphafold format mmcif

Summary of feedback from opening I3PLR2 fetched from alphafold  
---  
notes | Fetching compressed AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Fetching compressed AlphaFold I3PLR2 from
https://alphafold.ebi.ac.uk/files/AF-I3PLR2-F1-model_v6.cif  
  
Chain information for AlphaFold I3PLR2 #7  
---  
Chain | Description | UniProt  
A | 3-O-acetylpapaveroxine carboxylesterase CXE1 | CXE1_PAPSO 1-320  
  
Color AlphaFold I3PLR2 by residue attribute pLDDT_score  

> ui tool show Matchmaker

> matchmaker #7 to #6 showAlignment true

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 2o7r, chain A (#6) with AlphaFold I3PLR2, chain A (#7), sequence
alignment score = 840.4  
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: 2o7r #6/A, AlphaFold I3PLR2
#7/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1  
RMSD between 252 pruned atom pairs is 0.784 angstroms; (across all 292 pairs:
2.487)  
  

> sequence refreshAttrs 1

> select ::seq_identity hide #3 models

> select #6/A:203

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #6/A:203 #7/A:190

15 atoms, 14 bonds, 2 residues, 2 models selected  
MatchMaker Alignment [ID: 1] region 2o7r, chain A..AlphaFold I3PLR2, chain A
[214] RMSD: 0.228  
  

> show sel atoms

> hide #!6 models

> show #!6 models

> hide #7 models

> show #3 models

> show #2 models

> hide #!6 models

> hide #3 models

> show #1 models

> hide #2 models

> show #1 atoms

> show #!6 models

> hide #1 models

> show #7 models

> show #1 models

> hide #!6 models

> hide #7 models

> open
> /Users/atsushi/Documents/works/Collabo/CyberneticAvatar/works/Dodo_251209/fold_260226_es789959/fold_260226_es789959_model_0.cif

Chain information for fold_260226_es789959_model_0.cif #8  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #8 to #6 showAlignment true

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 2o7r, chain A (#6) with fold_260226_es789959_model_0.cif, chain A
(#8), sequence alignment score = 602.4  
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: 2o7r #6/A,
fold_260226_es789959_model_0.cif #8/A  
Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2  
RMSD between 234 pruned atom pairs is 0.873 angstroms; (across all 299 pairs:
4.280)  
  

> hide #1 models

> show #8 atoms

> style #8 ball

Changed 2870 atom styles  

> show #!6 models

> show #!5 models

> hide #!5 models

> show #4 models

> hide #4 models

> show #1 models

> hide #!6 models

> hide #8 models

> show #8 models

> hide #1 models

> show #8 atoms

> style #8 sphere

Changed 2870 atom styles  

> mlp #8

Map values for surface ""fold_260226_es789959_model_0.cif_A SES surface"":
minimum -27.88, mean -4.924, maximum 21.89  
To also show corresponding color key, enter the above mlp command and add key
true  

> style #!8 stick

Changed 2870 atom styles  

> ui tool show ""Side View""

> hide #!8 surfaces

> style #!8 sphere

Changed 2870 atom styles  

> hide #!8 cartoons

> lighting flat

> lighting full

> lighting soft

> lighting simple

> style #!8 ball

Changed 2870 atom styles  

> show #!8 cartoons

> select #8/A:238

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

> select #6/A:203 #8/A:238

15 atoms, 14 bonds, 2 residues, 2 models selected  
MatchMaker Alignment [ID: 2] region 2o7r, chain
A..fold_260226_es789959_model_0.cif, chain A [241] RMSD: 0.232  
  

> color (#!8 & sel) light gray

> style sel & #!8 sphere

Changed 11 atom styles  

> select clear

> select #8/A:309

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

> select #6/A:278 #8/A:309

16 atoms, 14 bonds, 2 residues, 2 models selected  
MatchMaker Alignment [ID: 2] region 2o7r, chain
A..fold_260226_es789959_model_0.cif, chain A [317] RMSD: 0.522  
  

> color (#!8 & sel) light gray

> style sel & #!8 sphere

Changed 8 atom styles  

> show #!6 models

> select ::name=""LEU""

2568 atoms, 2271 bonds, 321 residues, 8 models selected  

> color (#!6,8 & sel) light gray

> select ::name=""LEU""

2568 atoms, 2271 bonds, 321 residues, 8 models selected  

> select ::name=""ILE""

1040 atoms, 915 bonds, 130 residues, 8 models selected  

> color (#!6,8 & sel) light gray

> select ::name=""MET""

512 atoms, 452 bonds, 64 residues, 8 models selected  

> color (#!6,8 & sel) light gray

> select ::name=""TYR""

1301 atoms, 1303 bonds, 108 residues, 8 models selected  

> color (#!6,8 & sel) light gray

> select ::name=""PHE""

1529 atoms, 1538 bonds, 139 residues, 8 models selected  

> color (#!6,8 & sel) light gray

> hide #!6 models

> show #1 models

> hide #!8 models

> select #1/A:218

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

> select #1/A:218-221

34 atoms, 35 bonds, 4 residues, 1 model selected  

> set bgColor white


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

Log:
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 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 M4 Max
OpenGL vendor: Apple

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

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac16,6
      Model Number: Z1FG000P9J/A
      Chip: Apple M4 Max
      Total Number of Cores: 16 (12 performance and 4 efficiency)
      Memory: 128 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 11881.121.1

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 16時間

Graphics/Displays:

    Apple M4 Max:

      Chipset Model: Apple M4 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 40
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-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-GoodsellPalette: 0.1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.10.8
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    narwhals: 2.16.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 2.4.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    plotly: 6.5.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pyKVFinder: 0.9.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomlkit: 0.14.0
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX