![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 14 months ago
Closed 14 months ago
#15765 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-14.6-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Current thread 0x00000001f7078f40 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.coulombic._esp, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.mlp._mlp (total: 63)
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{
"uptime" : 330000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 866,
"osVersion" : {
"train" : "macOS 14.6",
"build" : "23G80",
"releaseType" : "User"
},
"captureTime" : "2024-08-14 14:18:20.2654 +0200",
"codeSigningMonitor" : 1,
"incident" : "63D4FC4C-5118-46FC-9FCA-59E8A47224AE",
"pid" : 15776,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-07-24 18:51:34.8613 +0200",
"procStartAbsTime" : 354491693963,
"procExitAbsTime" : 8041636950225,
"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":"35697BFF-4979-58E5-A5D3-75A9E7532035","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "120CE13A-3043-E34B-7D89-C14EC9E0C479",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 517,
"sleepWakeUUID" : "7AD15582-DF48-42F2-A350-A3FD7E7CCB8F",
"sip" : "enabled",
"vmRegionInfo" : "0x333061332d32 is not in any region. Bytes after previous region: 55801845853491 Bytes before following region: 49270234075854\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":"0x0000000000000101, 0x312d333061332d32","rawCodes":[257,3543544764692639026],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"UNKNOWN_0x101 at 0x312d333061332d32 -> 0x0000333061332d32 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":15776},
"vmregioninfo" : "0x333061332d32 is not in any region. Bytes after previous region: 55801845853491 Bytes before following region: 49270234075854\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 ",
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/GOLPH3-LYSET-GNPT-TMDonly.cxs" format session
opened ChimeraX session
> select clear
> select #3.2/B:44
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
285 atoms, 293 bonds, 35 residues, 2 models selected
> select up
10113 atoms, 10347 bonds, 1256 residues, 2 models selected
> show sel cartoons
> select #3.2/B:53
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3.2/B:53-883
6555 atoms, 6697 bonds, 831 residues, 1 model selected
> select ~sel
46053 atoms, 47093 bonds, 5707 residues, 15 models selected
> select ~sel
6555 atoms, 6697 bonds, 831 residues, 1 model selected
> select #3.2/B:152-153
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #3.2/B:152-157
46 atoms, 46 bonds, 6 residues, 1 model selected
> select #3.2/B:54
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.2/B:54-1194
9124 atoms, 9329 bonds, 1141 residues, 1 model selected
> color (#!3.2 & sel) #bfbfbfff
> color (#!3.2 & sel) #bebebeff
> color (#!3.2 & sel) #2a2a2aff
> color (#!3.2 & sel) #000000ff
> color (#!3.2 & sel) #66800bff
> color (#!3.2 & sel) #66800b05
> color (#!3.2 & sel) #66800b40
> select clear
> select #3.3/C:287
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
85 atoms, 87 bonds, 11 residues, 2 models selected
> select up
2371 atoms, 2402 bonds, 298 residues, 2 models selected
Alignment identifier is 3.3/C
> select #3.3/C:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.3/C:1-61
457 atoms, 456 bonds, 61 residues, 1 model selected
> color (#!3.3 & sel) #af302940
> select clear
> save "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/GOLPH3-LYSET-GNPT-TMDonly-Opacity.cxs"
> hide #!3.3 models
> show #!3.3 models
> interfaces #!3.1-3 & ~solvent
3 buried areas: #3.2/B #3.1/A 1705, #3.3/C #3.1/A 1033, #3.2/B #3.3/C 301
> select clear
> select add #3.2
10696 atoms, 10347 bonds, 1320 residues, 6 models selected
> select subtract #3.2
583 atoms, 64 residues, 5 models selected
> hide #!3.2 models
> coulombic sel
Coulombic values for LYSET_A SES surface #3.1.1: minimum, -12.85, mean 0.42,
maximum 12.41
Coulombic values for GOLPH3_C SES surface #3.3.1: minimum, -18.44, mean -1.37,
maximum 9.50
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for LYSET_A SES surface #3.1.1: minimum, -12.85, mean 0.42,
maximum 12.41
Coulombic values for GOLPH3_C SES surface #3.3.1: minimum, -18.44, mean -1.37,
maximum 9.50
To also show corresponding color key, enter the above coulombic command and
add key true
> show #!3.2 models
> coulombic sel
Coulombic values for GNPTAB_B SES surface #3.2.1: minimum, -22.67, mean -1.63,
maximum 19.85
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!3.2 models
> hide #!3.3 models
> select #3.1/A:21
4 atoms, 3 bonds, 1 residue, 1 model selected
Alignment identifier is 3.1/A
> select #3.1/A:21
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3.1/A:1-21
151 atoms, 154 bonds, 21 residues, 1 model selected
> color (#!3.1 & sel) #205ea640
> select clear
> save "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/LYSET-INTERACTION-Electrostatic.cxs"
> show #!3.2 models
> hide #!3.1 models
> save "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/GNPTAB-INTERACTION-Electrostatic.cxs"
> show #!3.3 models
> hide #!3.2 models
> coulombic sel & #!3.3
Coulombic values for GOLPH3_C SES surface #3.3.1: minimum, -18.44, mean -1.37,
maximum 9.50
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> select #3.3/C:270
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
129 atoms, 129 bonds, 15 residues, 2 models selected
> select up
2371 atoms, 2402 bonds, 298 residues, 2 models selected
> select clear
> select #3.3/C:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.3/C:115
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.3/C:115-118
34 atoms, 33 bonds, 4 residues, 1 model selected
> select #3.3/C:61-62
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #3.3/C:1-62
465 atoms, 464 bonds, 62 residues, 1 model selected
> select #3.3/C:65-117
415 atoms, 418 bonds, 53 residues, 1 model selected
> select #3.3/C:65-117
415 atoms, 418 bonds, 53 residues, 1 model selected
> select #3.3/C:62
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.3/C:62-298
1914 atoms, 1945 bonds, 237 residues, 1 model selected
> color (#!3.3 & sel) #af302940
> color (#!3.3 & sel) #af30290d
> color (#!3.3 & sel) #af302980
> coulombic sel & #!3.3
Coulombic values for GOLPH3_C SES surface #3.3.1: minimum, -18.44, mean -1.37,
maximum 9.50
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> save "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/GOLPH3-INTERACTION-Electrostatic.cxs"
> open "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/GNPTAB-INTERACTION-Electrostatic.cxs"
opened ChimeraX session
> open "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/LYSET-INTERACTION-Electrostatic.cxs"
opened ChimeraX session
> open "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/GOLPH3-INTERACTION-Electrostatic.cxs"
opened ChimeraX session
> interfaces #!3.3 & ~solvent
0 buried areas:
Cell requested for row 2 is out of bounds for table with 7 rows! Resizing
table model.
> select add #3
13807 atoms, 14113 bonds, 1717 residues, 4 models selected
> interfaces select & #!3.3 & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> show #!3.1 models
> show #!3.2 models
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select clear
> select #3.1/A:41
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
223 atoms, 230 bonds, 27 residues, 2 models selected
> select up
1323 atoms, 1364 bonds, 163 residues, 2 models selected
> select up
1323 atoms, 1364 bonds, 163 residues, 2 models selected
> select up
13807 atoms, 14113 bonds, 1717 residues, 4 models selected
Alignment identifier is 3.1/A
Alignment identifier is 3.2/B
Alignment identifier is 3.3/C
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> open "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/GOLPH3-LYSET-GNPT-TMDonly-Opacity.cxs"
opened ChimeraX session
> select add #3.1
1323 atoms, 1364 bonds, 163 residues, 1 model selected
Alignment identifier is 3.1/A
> select #3.1/A:115
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3.1/A:110-115
55 atoms, 57 bonds, 6 residues, 1 model selected
> select #3.1/A:21
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #3.1/A:1-21
151 atoms, 154 bonds, 21 residues, 1 model selected
> color (#!3.1 & sel) #205ea680
> color (#!3.1 & sel) #205ea605
> color (#!3.1 & sel) #205ea640
> select clear
> save "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/GOLPH3-LYSET-GNPT-TMDonly-Opacity-v2.cxs"
> open "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/GOLPH3-LYSET-GNPTAB_alphafold.cxs"
opened ChimeraX session
> save "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/GOLPH3-LYSET-GNPTAB_alphafold.cxs"
Cell requested for row 1 is out of bounds for table with 5 rows! Resizing
table model.
> select add #3
13807 atoms, 14113 bonds, 1717 residues, 4 models selected
Alignment identifier is 3.1/A
Alignment identifier is 3.2/B
Alignment identifier is 3.3/C
> select #3.3/C:62-63
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #3.3/C:62-67
49 atoms, 48 bonds, 6 residues, 1 model selected
> select #3.3/C:67-113
370 atoms, 373 bonds, 47 residues, 1 model selected
> select #3.3/C:67-113
370 atoms, 373 bonds, 47 residues, 1 model selected
> select #3.3/C:61-62
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #3.3/C:1-62
465 atoms, 464 bonds, 62 residues, 1 model selected
> select
> #3.3/C:18-23,62-70,84-99,131-142,149-157,163-168,173-183,207-221,229-231,234-245,249-251,258-272,276-281,287-297
1078 atoms, 1079 bonds, 134 residues, 1 model selected
> select #3.3/C:61
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.3/C:1-61
457 atoms, 456 bonds, 61 residues, 1 model selected
> select clear
> ui tool show "Color Key"
> ui mousemode right "color key"
> ui mousemode right translate
Fetching compressed palette hide from
https://www.colourlovers.com/api/palettes?keywords=hide&format=json&numResults=100
Could not find palette hide at COLOURlovers.com using keyword search
> key red:low orange: yellow: cornflowerblue: blue:high
> key alphafold
> color #3.1-3 bypolymer
> undo
> ui mousemode right pivot
> ui mousemode right select
> ui mousemode right rotate
> view list
No named views.
> view standard
Expected an objects specifier or a view name or a keyword
> view name standard
> ui tool show "Color Key"
> ui mousemode right "color key"
> key delete
> ui mousemode right rotate
> view name standard
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lightning depthCue t
Unknown command: lightning depthCue t
> lighting depthCue true
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> set bgColor gray
> set bgColor #80808000
> set bgColor black
> set bgColor transparent
> set bgColor white
> set bgColor #ffffff00
> lighting flat
> lighting full
> graphics silhouettes false
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> shadows true
Unknown command: shadows true
> shadows false
Unknown command: shadows false
> lighting shadows false
> lighting shadows true
> lighting qualityOfShadows fine
> lighting qualityOfShadows finer
> lighting ambientIntensity 0.9
> lighting ambientIntensity 0.2
> lighting ambientIntensity 0.3
> lighting ambientIntensity 0.4
> lighting ambientIntensity 0.8
> lighting ambientIntensity 0.6
> lighting ambientIntensity 0.7
> lighting intensity 0.5
> lighting intensity 0.9
> lighting intensity 0.5
> lighting intensity 0.6
> select clear
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> hide #!3.1-3 cartoons
> show #!3.1-3 cartoons
> hide #!3.1-3 surfaces
> show #!3.1-3 surfaces
> hide #!3.1-3 surfaces
> view standard
Cell requested for row 0 is out of bounds for table with 5 rows! Resizing
table model.
> transparency #3.2 75
> transparency #3.2 75 target r
> transparency #3.2 785target r
Missing or invalid "percent" argument: Expected a number
> transparency #3.2 85 target r
> transparency #3.2 100 target r
> transparency #3.2 15 target r
> transparency #3.2 25 target r
> transparency #3.2 50 target r
> transparency #3.3 50 target r
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-plddt-transparent.png format png 8000 8000
> supersample 4 transparentBackground true
Expected a keyword
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-plddt-transparent.png format png width 8000
> height 8000 supersample 4 transparentBackground true
> transparency #3.3 0 target r
> view standrd
Expected an objects specifier or a view name or a keyword
> view standrd
Expected an objects specifier or a view name or a keyword
> view standrd
Expected an objects specifier or a view name or a keyword
> view standrdard
Expected an objects specifier or a view name or a keyword
> view standard
> tranparency #3.2 50 target r
Unknown command: tranparency #3.2 50 target r
> transparency #3.2 50 target r
> transparency #3.3 50 target r
> save "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-26-plddt-transparent.cxs"
> transparency #3.3 0 target r
> transparency #3.2 0 target r
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-plddt.png format png width 8000 height 8000
> supersample 4 transparentBackground true
> save "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-26-plddt.cxs"
> select #3.2/B:36
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
285 atoms, 293 bonds, 35 residues, 2 models selected
> select up
10113 atoms, 10347 bonds, 1256 residues, 2 models selected
> color (#!3.2 & sel) light sea green
> color name flex-green-dark #66800b
Color 'flex-green-dark' is opaque: rgb(40%, 50.2%, 4.31%) hex: #66800b
> color #3.1 target r flex-green-dark
Expected a keyword
> color #3.1 flex-green-dark target r
> color #3.2 flex-green-dark target r
> color name flex-blue-dark #205ea6
Color 'flex-blue-dark' is opaque: rgb(12.5%, 36.9%, 65.1%) hex: #205ea6
> color #3.1 flex-blue-dark target r
> color name flex-red-dark #af3029
Color 'flex-red-dark' is opaque: rgb(68.6%, 18.8%, 16.1%) hex: #af3029
> color #3.3 flex-red-dark target r
> select clear
> view standard
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-simple-colors.png format png width 8000 height
> 8000 supersample 4 transparentBackground true
> color name flex-yellow-dark #ad8301
Color 'flex-yellow-dark' is opaque: rgb(67.8%, 51.4%, 0.392%) hex: #ad8301
> color #3.1:40-60,98-118,128-143 flex-yellow-dark
> color #3.2:22-42,1215-1235 flex-yellow-dark
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-tmds.png format png width 8000 height 8000
> supersample 4 transparentBackground true
> save "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-26-tmds.cxs"
> transparency #3.2 50 target r
> transparency #3.3 50 target r
> select clear
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-tmds-transparent.png format png width 8000
> height 8000 supersample 4 transparentBackground true
> save "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-26-tmds-transparent.cxs"
> transparency #3.3 0 target r
> transparency #3.2 0 target r
> interfaces #!3.1-3 & ~solvent
3 buried areas: #3.2/B #3.1/A 1705, #3.3/C #3.1/A 1033, #3.2/B #3.3/C 301
> transparency #3.2:42-1215 50 target r
> transparency #3.2 0 target r
> transparency #3.2:50-1200 50 target r
> transparency #3.2:50-1200 75 target r
> transparency #3.3:1-59 75 target r
> select clear
> view standard
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-transparent.png format png width 8000 height
> 8000 supersample 4 transparentBackground true
> save "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-26-transparent.cxs"
> view name zoom lyset-gnpt
Expected fewer arguments
> view name zoom-lyset-gnpt
> transparency #3.3:59-298 50 target r
> transparency #3.3:59-298 75 target r
> view zoom-lyset-gnpt
> view name zoom-lyset-gnpt
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-zoom-lyset-gnpt.png format png width 8000 height
> 8000 supersample 4 transparentBackground true
> save "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-26-zoom-lyset-gnpt.cxs"
> undo
> open "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-26-zoom-lyset-gnpt.cxs"
opened ChimeraX session
> interfaces #!3.1-3 & ~solvent
3 buried areas: #3.2/B #3.1/A 1705, #3.3/C #3.1/A 1033, #3.2/B #3.3/C 301
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for LYSET_A SES surface #3.1.1: minimum, -12.85, mean 0.42,
maximum 12.41
Coulombic values for GNPTAB_B SES surface #3.2.1: minimum, -22.67, mean -1.63,
maximum 19.85
Coulombic values for GOLPH3_C SES surface #3.3.1: minimum, -18.44, mean -1.37,
maximum 9.50
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> view zoom-lyset-gnpt
> view standard
> view zoom-lyset-gnpt
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/daniel/Desktop/movie2.mp4
Movie saved to /Users/daniel/Desktop/movie2.mp4
> view zoom-lyset-gnpt
> ui tool show "Selection Inspector"
> coulombic sel
Coulombic values for LYSET_A SES surface #3.1.1: minimum, -12.85, mean 0.42,
maximum 12.41
Coulombic values for GNPTAB_B SES surface #3.2.1: minimum, -22.67, mean -1.63,
maximum 19.85
Coulombic values for GOLPH3_C SES surface #3.3.1: minimum, -18.44, mean -1.37,
maximum 9.50
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!3.1 models
> hide #!3.2 models
> select clear
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-golph3-interaction.png format png width 8000
> height 8000 supersample 4 transparentBackground true
> show #!3.1 models
> show #!3.2 models
> hide #!3.3 models
> hide #!3.2 models
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-lyset-interaction.png format png width 8000
> height 8000 supersample 4 transparentBackground true
> hide #!3.1 models
> show #!3.2 models
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-gnpt-interaction.png format png width 8000
> height 8000 supersample 4 transparentBackground true
> show #!3.1 models
> show #!3.3 models
> view standard
> view zoom-lyset-gnpt
> coulombic sel
Coulombic values for LYSET_A SES surface #3.1.1: minimum, -12.85, mean 0.42,
maximum 12.41
Coulombic values for GNPTAB_B SES surface #3.2.1: minimum, -22.67, mean -1.63,
maximum 19.85
Coulombic values for GOLPH3_C SES surface #3.3.1: minimum, -18.44, mean -1.37,
maximum 9.50
To also show corresponding color key, enter the above coulombic command and
add key true
> transparency #3.3 50 target s
> transparency #3.2 50 target s
> transparency #3.1 50 target s
> select clear
> transparency #3.1 50 target r
> transparency #3.2 50 target r
> transparency #3.2 0 target r
> transparency #3.1 0 target r
> transparency #3.1 25 target r
> transparency #3.2 25 target r
> view zoom-lyset-gnpt-golph3
Expected an objects specifier or a view name or a keyword
> view name zoom-lyset-gnpt-golph3
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-interaction-all.png format png width 8000 height
> 8000 supersample 4 transparentBackground true
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/daniel/Desktop/movie2.mp4
Movie saved to /Users/daniel/Desktop/movie2.mp4
> select add #3
13807 atoms, 14113 bonds, 1717 residues, 4 models selected
> hide sel surfaces
> show sel atoms
> style sel stick
Changed 425 atom styles
> style sel ball
Changed 425 atom styles
> style sel stick
Changed 425 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 425 atom styles
> select add #3.2
10486 atoms, 10347 bonds, 1297 residues, 6 models selected
> select add #3
13807 atoms, 14113 bonds, 1717 residues, 7 models selected
> select subtract #3
3 models selected
> select add #3.2
10113 atoms, 10347 bonds, 1256 residues, 1 model selected
> hide sel atoms
> select add #3.3
12484 atoms, 12749 bonds, 1554 residues, 3 models selected
> select subtract #3.2
2371 atoms, 2402 bonds, 298 residues, 3 models selected
> hide sel atoms
> select clear
> select #3.1/A:133
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.1/A:129
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #3.1/A:133
15 atoms, 13 bonds, 2 residues, 2 models selected
> select add #3.1/A:43
23 atoms, 20 bonds, 3 residues, 2 models selected
> hide sel atoms
> select #3.1/A:36
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/A:124
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/A:127
9 atoms, 8 bonds, 1 residue, 1 model selected
Alignment identifier is 3.1/A
> select clear
> select #3.1/A:126
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/A:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/A:38
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/A:35
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/A:37
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.1/A:31
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.1/A:24
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #3.1/A:22
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3.2/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
Alignment identifier is 3.2/B
> select #3.2/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3.2/B:1-1235
9925 atoms, 10155 bonds, 1235 residues, 1 model selected
> select #3.2/B:1215
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.2/B:725-1215
4021 atoms, 4110 bonds, 491 residues, 1 model selected
> select #3.2/B:1215
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3.2/B:1-1215
9764 atoms, 9990 bonds, 1215 residues, 1 model selected
> transparency #3.2:1-1200 50 target r
> select clear
> transparency #3.2:1-1200 75 target r
> select clear
> ui tool show "Side View"
> select #3.1/A:22
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
183 atoms, 187 bonds, 25 residues, 2 models selected
> select up
1323 atoms, 1364 bonds, 163 residues, 2 models selected
> color (#!3.1 & sel) byhetero
> color (#!3.1 & sel) byelement
> select clear
> select #3.2/B:1232
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
89 atoms, 88 bonds, 11 residues, 2 models selected
> select up
10113 atoms, 10347 bonds, 1256 residues, 2 models selected
> select down
89 atoms, 88 bonds, 11 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 52 atom styles
> color (#!3.2 & sel) byelement
> select clear
> select #3.2/B:1246
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.2/B:1230
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3.1/A:33
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3.2/B:1230
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-interaction-top.png format png width 8000 height
> 8000 supersample 4 transparentBackground true
> transparency #3.3 0 target r
> transparency #3.3 25 target r
> transparency #3.3 0 target r
> ui tool show "Side View"
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
> select #2.1/A:3 #3.1/A:3
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #2.1/A:3 #3.1/A:3
18 atoms, 16 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [3] RMSD: 42.077
> select #2.1/A:22 #3.1/A:22
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #2.1/A:22 #3.1/A:22
22 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [22] RMSD: 85.817
> select #2.1/A:123 #3.1/A:123
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #2.1/A:123 #3.1/A:123
22 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [123] RMSD: 102.638
> select #2.1/A:127 #3.1/A:127
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #2.1/A:127 #3.1/A:127
18 atoms, 16 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [127] RMSD: 109.949
> select #2.1/A:163 #3.1/A:163
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2.1/A:162-163 #3.1/A:162-163
32 atoms, 30 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [162-163] RMSD: 98.920
> select clear
> select #2.2/B:1236 #3.2/B:1236
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #2.2/B:1236 #3.2/B:1236
18 atoms, 16 bonds, 2 residues, 2 models selected
2 [ID: 2] region 2 chains [1236] RMSD: 2.584
> select #2.2/B:1237 #3.2/B:1237
22 atoms, 20 bonds, 2 residues, 2 models selected
> select #2.2/B:1237 #3.2/B:1237
22 atoms, 20 bonds, 2 residues, 2 models selected
2 [ID: 2] region 2 chains [1237] RMSD: 2.931
> label #3.1:22,29,32,37,39,123,127 residues attribute chain_id height 4
> label #3.1:22,29,32,37,39,123,127 residues attribute height 4
Expected a keyword
> label #3.1:22,29,32,37,39,123,127 residues height 4
> label #3.1:22,29,32,37,39,123,127 text {0.name}{0.number} height 1.5
> label listfonts
249 fonts available:
.Apple Color Emoji UI
.Apple Symbols Fallback
.AppleHongKongChineseFont
.AppleJapaneseFont
.AppleKoreanFont
.AppleSimplifiedChineseFont
.AppleSystemFallback
.AppleSystemUIFont
.AppleTraditionalChineseFont
.Lucida Grande UI
.Noto Nastaliq Urdu UI
.SF Arabic
.SF Armenian
.SF Georgian
.SF Hebrew
.ThonburiUI
Academy Engraved LET
Al Bayan
Al Nile
Al Tarikh
American Typewriter
Andale Mono
Apple Braille
Apple Chancery
Apple Color Emoji
Apple SD Gothic Neo
Apple Symbols
AppleGothic
AppleMyungjo
Aquire
Arial
Arial Black
Arial Hebrew
Arial Hebrew Scholar
Arial Narrow
Arial Nova
Arial Rounded MT Bold
Arial Unicode MS
Avenir
Avenir Next
Avenir Next Condensed
Ayuthaya
Baghdad
Bangla MN
Bangla Sangam MN
Baskerville
Beirut
Big Caslon
Bodoni 72
Bodoni 72 Oldstyle
Bodoni 72 Smallcaps
Bodoni Ornaments
Bradley Hand
Brush Script MT
Chalkboard
Chalkboard SE
Chalkduster
Charter
Cochin
Comic Sans MS
Copperplate
Corsiva Hebrew
Courier New
DIN Alternate
DIN Condensed
Damascus
Darlington Demo
Darwin Serif Regular ALPHA
DecoType Naskh
Devanagari MT
Devanagari Sangam MN
Didot
Diwan Kufi
Diwan Thuluth
Euphemia UCAS
Farah
Farisi
Fira Sans
Fira Sans Black
Fira Sans ExtraBold
Fira Sans ExtraLight
Fira Sans Light
Fira Sans Medium
Fira Sans SemiBold
Fira Sans Thin
Font Awesome 5 Brands
Font Awesome 5 Free
Font Awesome 6 Brands
Font Awesome 6 Free
Font Awesome v4 Compatibility
FontAwesome
Futura
GB18030 Bitmap
Galvji
Geeza Pro
Geneva
Georgia
Georgia Pro
Gill Sans
Grantha Sangam MN
Gujarati MT
Gujarati Sangam MN
Gurmukhi MN
Gurmukhi MT
Gurmukhi Sangam MN
Heiti SC
Heiti TC
Helvetica
Helvetica Neue
Herculanum
Hiragino Maru Gothic ProN
Hiragino Mincho ProN
Hiragino Sans
Hiragino Sans GB
Hoefler Text
ITF Devanagari
ITF Devanagari Marathi
Impact
InaiMathi
JetBrains Mono
JetBrains Mono NL
Kailasa
Kannada MN
Kannada Sangam MN
Kefa
Khmer MN
Khmer Sangam MN
Kohinoor Bangla
Kohinoor Devanagari
Kohinoor Gujarati
Kohinoor Telugu
Kokonor
Krungthep
KufiStandardGK
Lao MN
Lao Sangam MN
Lato
Lucida Grande
Luminari
Malayalam MN
Malayalam Sangam MN
Marker Felt
Material Icons
Menlo
Microsoft Sans Serif
Mishafi
Mishafi Gold
Monaco
Montserrat
Montserrat Alternates
Mshtakan
Mukta Mahee
Muna
Myanmar MN
Myanmar Sangam MN
Nadeem
New Peninim MT
Nimbus Sans
Noteworthy
Noto Nastaliq Urdu
Noto Sans Armenian
Noto Sans Batak
Noto Sans Kannada
Noto Sans Myanmar
Noto Sans NKo
Noto Sans Oriya
Noto Sans Tagalog
Noto Sans Zawgyi
Noto Serif Myanmar
Nunito Sans
Nunito Sans 10pt
Nunito Sans 10pt Condensed
Nunito Sans 10pt Expanded
Nunito Sans 10pt SemiCondensed
Nunito Sans 10pt SemiExpanded
Nunito Sans 7pt
Nunito Sans 7pt Condensed
Nunito Sans 7pt Expanded
Nunito Sans 7pt SemiCondensed
Nunito Sans 7pt SemiExpanded
Open Sans
Open Sans Condensed
Open Sans SemiCondensed
Optima
Oriya MN
Oriya Sangam MN
PT Mono
PT Sans
PT Sans Caption
PT Sans Narrow
PT Serif
PT Serif Caption
Palatino
Papyrus
Party LET
Phosphate
PingFang HK
PingFang SC
PingFang TC
Plantagenet Cherokee
Poppins
Raanana
Raleway
Rockwell
SF Pro
SF Pro Display
SF Pro Rounded
SF Pro Text
STIX Two Math
STIX Two Text
STSong
Sana
Sathu
Savoye LET
Shree Devanagari 714
SignPainter
Silom
Sinhala MN
Sinhala Sangam MN
Skia
Snell Roundhand
Songti SC
Songti TC
Source Sans 3
Sukhumvit Set
Symbol
Tahoma
Tamil MN
Tamil Sangam MN
Telugu MN
Telugu Sangam MN
Thonburi
Times
Times New Roman
Trattatello
Trebuchet MS
Verdana
Verdana Pro
Waseem
Weather Icons
Webdings
Wingdings
Wingdings 2
Wingdings 3
Zapf Dingbats
Zapfino
all-the-icons
file-icons
github-octicons
> label #3.1:22,29,32,37,39,123,127 text {0.name}{0.number} height 1.5 font
> "Source Sans 3"
> label #3.1:22,29,32,37,39,123,127 text {0.name}{0.number} height 2.5 font
> "Source Sans 3"
> label #3.1:22,29,32,37,39,123,127 text {0.name}{0.number} height 2 font
> "Source Sans 3"
> select clear
> label #3.1:22,29,32,37,39,123,127 text {0.name}{0.number} height 2 font
> "Source Sans 3" offset 2,2,2
> label #3.1:22,29,32,37,39,123,127 text {0.name}{0.number} height 2 font
> "Source Sans 3" offset 2,1,2
> label #3.1:22,29,32,37,39,123,127 text {0.name}{0.number} height 2 font
> "Source Sans 3" offset 2,1,0
> label #3.1:22,29,32,37,39,123,127 text {0.name}{0.number} height 2 font
> "Source Sans 3" offset 1,1,0
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> "Source Sans 3" offset -1,1,0
> label #3.1:22,29,32,37,39,123,127 text {0.name}{0.number} height 2 font
> "Source Sans 3" offset -1,-1,0
> label #3.1:22,29,32,37,39,123,127 text {0.name}{0.number} height 2 font
> "Source Sans 3" offset -2,-1,0
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> label #3.1:29 text {0.name}{0.number} height 2 font "Source Sans 3" offset
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> label #3.1:29 text {0.name}{0.number} height 2 font "Source Sans 3" offset
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> label #3.1:32 text {0.name}{0.number} height 2 font "Source Sans 3" offset
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> label #3.1:32 text {0.name}{0.number} height 2 font "Source Sans 3" offset
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> label #3.1:32 text {0.name}{0.number} height 2 font "Source Sans 3" offset
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> label #3.1:32 text {0.name}{0.number} height 2 font "Source Sans 3" offset
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> label #3.1:39 text {0.name}{0.number} height 2 font "Source Sans 3" offset
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> label #3.1:39 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
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> label #3.1:39 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
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> label #3.1:37 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
> -2.4,0,0
> label #3.1:37 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
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> offset -1.4,1,0
> label #3.1:123 text {0.name}{0.number} height 1.8 font "Source Sans 3"
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> label #3.1:123 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset -4.5,1,0
> label #3.1:123 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset -4.3,1,0
> label #3.1:123 text {0.name}{0.number} height 1.5 font "Source Sans 3"
> offset -4.3,1,0
> label #3.1:123 text {0.name}{0.number} height 1.6 font "Source Sans 3"
> offset -4.3,1,0
> label #3.1:123 text {0.name}{0.number} height 1.6 font "Source Sans 3"
> offset -4.1,1,0
> label #3.1:123 text {0.name}{0.number} height 1.6 font "Source Sans 3"
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> label #3.1:123 text {0.name}{0.number} height 1.7 font "Source Sans 3"
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> label #3.1:123 text {0.name}{0.number} height 1.7 font "Source Sans 3"
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> offset 1,1,0
> label #3.1:127 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 1,1,0
> label #3.1:127 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 1,2,0
> save "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-26-label-interface.cxs"
> label #3.2:1237 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 1,2,0
> label #3.2:1237 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 1,-2,0
> label #3.2:1237 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 1,-4,0
> label #3.2:1237 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 2,-4,0
> label #3.2:1237 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 3,-4,0
> label #3.2:1242 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 3,-4,0
> label #3.2:1242 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 3,-6,0
> label #3.2:1242 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 3,-5,0
> label #3.2:1242 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 2,-5,0
> label #3.2:1242 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 2.5,-5,0
> label #3.2:1244 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 2.5,-5,0
> label #3.2:1244 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 2.5,-4,0
> label #3.2:1244 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 2,-4,0
> label #3.2:1244 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 2,-4.2,0
> label #3.2:1244 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 2,-4.5,0
> label #3.2:1244 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 2,-3.5,0
> label #3.2:1244 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 2,-2.5,0
> label #3.2:1244 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 3,-2.5,0
> label #3.2:1244 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 2.5,-2.5,0
> label #3.2:1244 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 2.5,-2.5,0 bgColor rgb(206, 205, 195)
> label #3.2:1242 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 2.5,-2.5,0 bgColor rgb(206, 205, 195)
> label #3.2:1242 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 2.5,-5,0 bgColor rgb(206, 205, 195)
> label #3.2:1242 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 2.5,-5,0 bgColor #FFFCF0
> label #3.2:1237 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 3,-4,0 bgColor #FFFCF0
> label #3.2:1244 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 2.5,-2.5,0 bgColor #FFFCF0
> label #3.2:1244 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 2.5,-2.5,0 bgColor #FFFFFF
> label #3.2:1237 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 3,-4,0 bgColor #FFFFFF
> label #3.2:1242 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 2.5,-5,0 bgColor #FFFFFF
> save "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-26-label-interface-top.cxs"
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-interaction-top-label.png format png width 8000
> height 8000 supersample 4 transparentBackground true
> save "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-26-label-interface-top.cxs"
> save "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-26-label-interface-top-aa.cxs"
> open "/Users/daniel/Downloads/Fold G3 Lysetiso2
> GNPTab/fold_g3_lysetiso2_gnptab_model_4.cif"
Chain information for fold_g3_lysetiso2_gnptab_model_4.cif #1
---
Chain | Description
A | .
B | .
C | .
> hide #!3 models
Cell requested for row 0 is out of bounds for table with 6 rows! Resizing
table model.
> open "/Users/daniel/Downloads/Fold G3 Lysetiso2 GNPTab
> 2/fold_g3_lysetiso2_gnptab_model_4.cif"
Chain information for fold_g3_lysetiso2_gnptab_model_4.cif #4
---
Chain | Description
A | .
B | .
C | .
> hide #1 models
> split
Did not split LYSET, has only one piece
Did not split GNPTAB, has only one piece
Did not split GOLPH3, has only one piece
Did not split LYSET, has only one piece
Did not split GNPTAB, has only one piece
Did not split GOLPH3, has only one piece
Split fold_g3_lysetiso2_gnptab_model_4.cif (#1) into 3 models
Split fold_g3_lysetiso2_gnptab_model_4.cif (#4) into 3 models
Chain information for fold_g3_lysetiso2_gnptab_model_4.cif A #1.1
---
Chain | Description
A | No description available
Chain information for fold_g3_lysetiso2_gnptab_model_4.cif B #1.2
---
Chain | Description
B | No description available
Chain information for fold_g3_lysetiso2_gnptab_model_4.cif C #1.3
---
Chain | Description
C | No description available
Chain information for fold_g3_lysetiso2_gnptab_model_4.cif A #4.1
---
Chain | Description
A | No description available
Chain information for fold_g3_lysetiso2_gnptab_model_4.cif B #4.2
---
Chain | Description
B | No description available
Chain information for fold_g3_lysetiso2_gnptab_model_4.cif C #4.3
---
Chain | Description
C | No description available
Cell requested for row 0 is out of bounds for table with 10 rows! Resizing
table model.
> hide #!1 models
> hide #!4 models
> show #!4 models
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> hide #4.2 models
> select add #4.1
1074 atoms, 1106 bonds, 131 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_g3_lysetiso2_gnptab_model_4.cif A_A SES surface
#4.1.1: minimum, -11.42, mean 0.02, maximum 10.70
To also show corresponding color key, enter the above coulombic command and
add key true
> select add #4.3
3445 atoms, 3508 bonds, 429 residues, 3 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_g3_lysetiso2_gnptab_model_4.cif A_A SES surface
#4.1.1: minimum, -11.42, mean 0.02, maximum 10.70
Coulombic values for fold_g3_lysetiso2_gnptab_model_4.cif C_C SES surface
#4.3.1: minimum, -19.15, mean -1.44, maximum 9.10
To also show corresponding color key, enter the above coulombic command and
add key true
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> show #4.2 models
> select add #4.2
13558 atoms, 13855 bonds, 1685 residues, 5 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_g3_lysetiso2_gnptab_model_4.cif A_A SES surface
#4.1.1: minimum, -11.42, mean 0.02, maximum 10.70
Coulombic values for fold_g3_lysetiso2_gnptab_model_4.cif B_B SES surface
#4.2.1: minimum, -20.73, mean -1.66, maximum 15.46
Coulombic values for fold_g3_lysetiso2_gnptab_model_4.cif C_C SES surface
#4.3.1: minimum, -19.15, mean -1.44, maximum 9.10
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> hide #!4.3 models
> show #!4.3 models
> hide #!4.2 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.3 models
> select add #4.1
1074 atoms, 1106 bonds, 131 residues, 1 model selected
> hide sel surfaces
> coulombic sel
Coulombic values for fold_g3_lysetiso2_gnptab_model_4.cif A_A SES surface
#4.1.1: minimum, -11.42, mean 0.02, maximum 10.70
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> show #!4.2 models
> show #!4.3 models
> hide #!4.2 models
> show #!4.2 models
> select add #4.2
10113 atoms, 10347 bonds, 1256 residues, 2 models selected
> hide sel atoms
> hide sel surfaces
> select add #4.3
12484 atoms, 12749 bonds, 1554 residues, 5 models selected
> hide sel surfaces
> select add #4.1
13558 atoms, 13855 bonds, 1685 residues, 7 models selected
> hide sel surfaces
> select clear
Cell requested for row 3 is out of bounds for table with 7 rows! Resizing
table model.
> hide #!4.1 models
> show #!4.1 models
> color #4.1 flex--blue-dark
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color list
4 custom colors: flex-blue-dark
, flex-green-dark
, flex-red-dark
, and flex-yellow-dark
.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color #4.1 flex-blue-dark
> hide #!4.2 models
> show #!4.2 models
> color #4.2 flex-green-dark
> color #4.3 flex-red-dark
> save "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-28-iso2.cxs"
> open "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-26-plddt-transparent.cxs"
opened ChimeraX session
> transparency #3.2 50 taarget r
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency #3.2 50 target r
> transparency #3.2 25 target r
> transparency #3.3 25 target r
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-plddt-2.png format png width 8000 height 8000
> supersample 4 transparentBackground true
> open "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-26-tmds-transparent.cxs"
opened ChimeraX session
> transparency #3.3 25 target r
> transparency #3.2 25 target r
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-tmd-transparent-2.png format png width 8000
> height 8000 supersample 4 transparentBackground true
> open "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-26-label-interface-top-aa.cxs"
opened ChimeraX session
> open "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-26-label-interface-top.cxs"
opened ChimeraX session
> open "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-26-label-interface.cxs"
opened ChimeraX session
> label delete
> select clear
> interfaces #!3.1-3 & ~solvent
3 buried areas: #3.2/B #3.1/A 1705, #3.3/C #3.1/A 1033, #3.2/B #3.3/C 301
> coulombic sel
Coulombic values for LYSET_A SES surface #3.1.1: minimum, -12.85, mean 0.42,
maximum 12.41
Coulombic values for GNPTAB_B SES surface #3.2.1: minimum, -22.67, mean -1.63,
maximum 19.85
Coulombic values for GOLPH3_C SES surface #3.3.1: minimum, -18.44, mean -1.37,
maximum 9.50
To also show corresponding color key, enter the above coulombic command and
add key true
> ui tool show "Side View"
> select ~sel
27189 atoms, 27757 bonds, 3388 residues, 8 models selected
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> hide #!3.1 models
> show #!3.1 models
> transparency #3.1 50 target. s
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency #3.1 50 target s
> transparency #3.2 50 target s
> select add #3.1
27341 atoms, 27922 bonds, 3405 residues, 14 models selected
> select subtract #3.1
26018 atoms, 26558 bonds, 3242 residues, 13 models selected
> select add #3
27614 atoms, 28226 bonds, 3434 residues, 13 models selected
> select subtract #3
13807 atoms, 14113 bonds, 1717 residues, 10 models selected
> select add #3.1
15130 atoms, 15477 bonds, 1880 residues, 8 models selected
> show sel & #!3.1 cartoons
> select clear
> select add #3.1
1323 atoms, 1364 bonds, 163 residues, 1 model selected
> show sel cartoons
> rainbow sel
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> undo
> select clear
> select add #3.1
1323 atoms, 1364 bonds, 163 residues, 1 model selected
> hide #!3 models
> show #!3 models
> hide #!3.2 models
> hide #!3.3 models
Drag select of LYSET_A SES surface, 3291 of 234658 triangles, 4 atoms, 3
residues, 3 bonds
> select clear
> transparency #3.2 0 target r
> transparency #3.1 0 target r
> select clear
> transparency #3.1 0 target s
> transparency #3.1 50 target s
> show #!3.2 models
> show #!3.3 models
> transparency #3.1 755 target s
> transparency #3.1 75 target s
> transparency #3.3 75 target s
> select clear
> coulombic sel
Coulombic values for LYSET_A SES surface #3.1.1: minimum, -12.85, mean 0.42,
maximum 12.41
Coulombic values for GNPTAB_B SES surface #3.2.1: minimum, -22.67, mean -1.63,
maximum 19.85
Coulombic values for GOLPH3_C SES surface #3.3.1: minimum, -18.44, mean -1.37,
maximum 9.50
To also show corresponding color key, enter the above coulombic command and
add key true
> select up
1786 atoms, 1820 bonds, 220 residues, 6 models selected
> select up
13807 atoms, 14113 bonds, 1717 residues, 6 models selected
> color ~sel white target s transparency 80
> show sel surfaces
> hide sel surfaces
> undo
Alignment identifier is 3.1/A
Alignment identifier is 3.2/B
Alignment identifier is 3.3/C
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select clear
> interfaces #!3.1-3 & ~solvent
3 buried areas: #3.2/B #3.1/A 1705, #3.3/C #3.1/A 1033, #3.2/B #3.3/C 301
> undo
> select add #3.1
1596 atoms, 1364 bonds, 192 residues, 6 models selected
> select add #3.2
11657 atoms, 11711 bonds, 1443 residues, 6 models selected
> show sel cartoons
> hide sel atoms
> coulombic sel
Coulombic values for LYSET_A SES surface #3.1.1: minimum, -12.85, mean 0.42,
maximum 12.41
Coulombic values for GNPTAB_B SES surface #3.2.1: minimum, -22.67, mean -1.63,
maximum 19.85
Coulombic values for GOLPH3_C SES surface #3.3.1: minimum, -18.44, mean -1.37,
maximum 9.50
To also show corresponding color key, enter the above coulombic command and
add key true
> transparency targ s 25
Missing or invalid "percent" argument: Expected a number
> transparency #3.1targ s 25
Missing or invalid "percent" argument: Expected a number
> transparency #3.1 targ s 25
Missing or invalid "percent" argument: Expected a number
> transparency #3.1 25 target s
> transparency #3.2 25 target s
> transparency #3.3 25 target s
> select clear
> transparency #3.3 25 target r
> transparency #3.2 25 target r
> transparency #3.1 25 target r
> view list
Named views: standard, zoom-lyset-gnpt, zoom-lyset-gnpt-golph3
> view zoom-lyset-gnpt-gplph3
Expected an objects specifier or a view name or a keyword
> view zoom-lyset-gnpt-golph3
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-interaction-2.png format png width 8000 height
> 8000 supersample 4 transparentBackground true
> transparency #3.1 0 target r
> transparency #3.2 0 target r
> transparency #3.3 0 target r
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-interaction-2.png format png width 8000 height
> 8000 supersample 4 transparentBackground true
> view zoom-lyset-gnpt
> view list
Named views: standard, zoom-lyset-gnpt, zoom-lyset-gnpt-golph3
> view zoom-lyset-gnpt-golph3
> transparency #3.3 50 target s
> transparency #3.3 25 target s
> transparency #3.3 25 target r
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-interaction-3.png format png width 8000 height
> 8000 supersample 4 transparentBackground true
> transparency #3.3 0 target r
> transparency #3.3 0 target s
> transparency #3.3 25 target s
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-interaction-3.png format png width 8000 height
> 8000 supersample 4 transparentBackground true
> open "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-26-label-interface-top-aa.cxs"
opened ChimeraX session
> select add #3.3
2371 atoms, 2402 bonds, 298 residues, 1 model selected
> coulombic sel
Coulombic values for GOLPH3_C SES surface #3.3.1: minimum, -18.44, mean -1.37,
maximum 9.50
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-label-interaction-top-2.png format png width
> 8000 height 8000 supersample 4 transparentBackground true
> label #3.1:127 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 1,2,0 bgColor #FFFFFF
> label #3.1:127 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 1,3,0 bgColor #FFFFFF
> label #3.1:127 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset 1,2.5,0 bgColor #FFFFFF
> label #3.1:39 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
> 1,2.5,0 bgColor #FFFFFF
> select clear
> label #3.1:39 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
> 1,0,0 bgColor #FFFFFF
> label #3.1:39 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
> 1,4,0 bgColor #FFFFFF
> label #3.1:39 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
> 3,4,0 bgColor #FFFFFF
> label #3.1:39 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
> -5,4,0 bgColor #FFFFFF
> label #3.1:39 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
> -5,2,0 bgColor #FFFFFF
> label #3.1:39 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
> -5,-2,0 bgColor #FFFFFF
> label #3.1:39 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
> -5,-3,0 bgColor #FFFFFF
> label #3.1:37 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
> -5,-3,0 bgColor #FFFFFF
> label #3.1:123 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset -5,-3,0 bgColor #FFFFFF
> label #3.1:123 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset -5,0,0 bgColor #FFFFFF
> label #3.1:123 text {0.name}{0.number} height 1.8 font "Source Sans 3"
> offset -5,1,0 bgColor #FFFFFF
> label #3.1:29 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
> -5,1,0 bgColor #FFFFFF
> label #3.1:29 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
> -3,1,0 bgColor #FFFFFF
> label #3.1:29 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
> -3,3,0 bgColor #FFFFFF
> label #3.1:29 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
> -3,4,0 bgColor #FFFFFF
> label #3.1:29 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
> -1,4,0 bgColor #FFFFFF
> label #3.1:29 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
> -1,3,0 bgColor #FFFFFF
> label #3.1:29 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
> -1,3.5,0 bgColor #FFFFFF
> label #3.1:22 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
> -1,3.5,0 bgColor #FFFFFF
> label #3.1:22 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
> -1,0,0 bgColor #FFFFFF
> label #3.1:22 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
> -1,-5,0 bgColor #FFFFFF
> label #3.1:22 text {0.name}{0.number} height 1.8 font "Source Sans 3" offset
> 0,-5,0 bgColor #FFFFFF
> save /Users/daniel/Documents/10-projects/glyco-
> module/AlphaFold/2024-07-26-label-interaction-top-4.png format png width
> 8000 height 8000 supersample 4 transparentBackground true
> open "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-28-iso2.cxs"
opened ChimeraX session
> save /Users/daniel/Documents/10-projects/glyco-module/AlphaFold/iso2.png
> format png width 8000 height 8000 supersample 4 transparentBackground true
> open "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-26-zoom-lyset-gnpt.cxs"
opened ChimeraX session
> transparency #3.2 25 target r
> transparency #3.3 25 target r
> save /Users/daniel/Documents/10-projects/glyco-module/AlphaFold/tmd-
> interaction.png format png width 8000 height 8000 supersample 4
> transparentBackground true
> interfaces #!3.1-3 & ~solvent
3 buried areas: #3.2/B #3.1/A 1705, #3.3/C #3.1/A 1033, #3.2/B #3.3/C 301
> mlp sel
Map values for surface "LYSET_A SES surface": minimum -26.08, mean -0.7895,
maximum 23.67
Map values for surface "GNPTAB_B SES surface": minimum -29.02, mean -4.487,
maximum 26.76
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for LYSET_A SES surface #3.1.1: minimum, -12.85, mean 0.42,
maximum 12.41
Coulombic values for GNPTAB_B SES surface #3.2.1: minimum, -22.67, mean -1.63,
maximum 19.85
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> hide sel surfaces
> show sel atoms
> select clear
> mlp sel
Map values for surface "LYSET_A SES surface": minimum -26.08, mean -0.7895,
maximum 23.67
Map values for surface "GNPTAB_B SES surface": minimum -29.02, mean -4.487,
maximum 26.76
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Coulombic values for LYSET_A SES surface #3.1.1: minimum, -12.85, mean 0.42,
maximum 12.41
Coulombic values for GNPTAB_B SES surface #3.2.1: minimum, -22.67, mean -1.63,
maximum 19.85
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel atoms
> select clear
> coulombic sel
Coulombic values for LYSET_A SES surface #3.1.1: minimum, -12.85, mean 0.42,
maximum 12.41
Coulombic values for GNPTAB_B SES surface #3.2.1: minimum, -22.67, mean -1.63,
maximum 19.85
To also show corresponding color key, enter the above coulombic command and
add key true
Drag select of LYSET_A SES surface, 2208 of 234658 triangles, 13 residues
> select clear
> hide sel surfaces
> select clear
> save /Users/daniel/Documents/10-projects/glyco-module/AlphaFold/tmd-
> interaction-2.png format png width 8000 height 8000 supersample 4
> transparentBackground true
> open "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-26-label-interface-top-aa.cxs"
opened ChimeraX session
> interfaces #!3.1-3 & ~solvent
3 buried areas: #3.2/B #3.1/A 1705, #3.3/C #3.1/A 1033, #3.2/B #3.3/C 301
> ui tool show "Side View"
> select clear
> select #3.1/A:37
11 atoms, 10 bonds, 1 residue, 1 model selected
> coulombic sel
Coulombic values for LYSET_A SES surface #3.1.1: minimum, -12.85, mean 0.42,
maximum 12.41
To also show corresponding color key, enter the above coulombic command and
add key true
> select #3.1/A:39
11 atoms, 10 bonds, 1 residue, 1 model selected
> coulombic sel
Coulombic values for LYSET_A SES surface #3.1.1: minimum, -12.85, mean 0.42,
maximum 12.41
To also show corresponding color key, enter the above coulombic command and
add key true
> select #3.1/A:37
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #3.1/A:39
22 atoms, 20 bonds, 2 residues, 2 models selected
> coulombic sel
Coulombic values for LYSET_A SES surface #3.1.1: minimum, -12.85, mean 0.42,
maximum 12.41
To also show corresponding color key, enter the above coulombic command and
add key true
> select #3.3/C:163
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
54 atoms, 56 bonds, 6 residues, 2 models selected
> select up
2371 atoms, 2402 bonds, 298 residues, 2 models selected
> coulombic sel
Coulombic values for GOLPH3_C SES surface #3.3.1: minimum, -18.44, mean -1.37,
maximum 9.50
To also show corresponding color key, enter the above coulombic command and
add key true
> select #3.3/C:159@O
1 atom, 1 residue, 1 model selected
> select #3.3/C:196@O
1 atom, 1 residue, 1 model selected
> select clear
> open "/Users/daniel/Documents/10-projects/glyco-module/AlphaFold Chimera
> Sessions/2024-07-28-iso2.cxs"
opened ChimeraX session
> select #4.1/A:7
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #4.1/A:5
22 atoms, 20 bonds, 2 residues, 2 models selected
> coulombic sel
Coulombic values for fold_g3_lysetiso2_gnptab_model_4.cif A_A SES surface
#4.1.1: minimum, -11.42, mean 0.02, maximum 10.70
To also show corresponding color key, enter the above coulombic command and
add key true
> select #4.3/C:81
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
115 atoms, 118 bonds, 13 residues, 2 models selected
> select up
2371 atoms, 2402 bonds, 298 residues, 2 models selected
> coulombic sel
Coulombic values for fold_g3_lysetiso2_gnptab_model_4.cif C_C SES surface
#4.3.1: minimum, -19.15, mean -1.44, maximum 9.10
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> hide #!4.2 models
Cell requested for row 3 is out of bounds for table with 7 rows! Resizing
table model.
> hide #!4 models
> show #!4 models
> show #!1 models
> hide #!4 models
> show #1.1 models
> show #1.2 models
> show #1.3 models
> close #1
> show #!3 models
> show #!4 models
> hide #!3 models
> interfaces #!4.1,3 & ~solvent
1 buried areas: #4.3/C #4.1/A 468
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: Z11D00025D/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6 (23G80)
Kernel Version: Darwin 23.6.0
Time since boot: 21 days, 4 hours, 36 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
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 , 14 months 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 , 14 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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The usual crash in _NSViewHierarchyDidChangeBackingProperties either waking from sleep or connecting/disconnecting external display. Still have never seen this reported in Qt 6.7 in daily builds.