![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 months ago
Closed 3 months ago
#18228 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.2-arm64-arm-64bit
ChimeraX Version: 1.10.dev202504300222 (2025-04-30 02:22:20 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x0000000205a6c240 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, psutil._psutil_osx, psutil._psutil_posix, 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, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PIL._imaging, PIL._imagingmath (total: 53)
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"procRole" : "Background",
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"deployVersion" : 210,
"modelCode" : "Mac14,10",
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"build" : "24C101",
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"captureTime" : "2025-07-18 13:14:57.7428 +0200",
"codeSigningMonitor" : 1,
"incident" : "14857758-D01F-466C-9896-FA97F159E6FE",
"pid" : 29352,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-07-16 14:08:08.0778 +0200",
"procStartAbsTime" : 12217760398951,
"procExitAbsTime" : 14195853331465,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"CD8A6858-8E05-5625-AFB5-FCD837AF934D","thirdParty":true},
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"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "D80C6BFF-C8D2-C560-1A0C-9D1E1BE4C54F",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "2A74EBA0-D62D-4D2E-84C2-D43BA9C00A15",
"wakeTime" : 5824,
"sleepWakeUUID" : "AC1B648B-5530-47F4-9070-EBCF1E4E7911",
"sip" : "enabled",
"vmRegionInfo" : "0x1844931ac470 is not in any region. Bytes after previous region: 26201768510577 Bytes before following region: 78870311418768\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00009844931ac470","rawCodes":[1,167420293203056],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00009844931ac470 -> 0x00001844931ac470 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":29352},
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===== Log before crash start =====
> alias analyse_af_screen_hit runscript
> /Users/carlotta/ChimeraX/scripts/analyse_af_screen_hit.cxc $1 $2
> alias analyse_af3 runscript
> /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction.cxc $1 $2
> alias analyse_auto-AF runscript
> /Users/carlotta/ChimeraX/scripts/analyse_auto-alphafold_prediction.cxc $1 $2
> alias analyse_af3_prediction_ac_bc_only runscript
> /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction_ac_bc_only.cxc $1 $2
> alias analyse_af3_prediction_modified runscript
> /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction_modified.cxc $1 $2
> alias analyse_af3_prediction_modified_PAE runscript
> /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction_modified_PAE.cxc $1
> $2
> alias analyse_af3_prediction_modified_5 runscript
> /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction_modified_5.cxc $1 $2
> alias analyse_af3_prediction_CT runscript
> /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction_CT.cxc $1 $2
UCSF ChimeraX version: 1.10.dev202504300222 (2025-04-30)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> cd /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255
Current working directory is:
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255
> analyse_af3_prediction_CT
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255
> fold_atg11_1_654_atg9_1_255_NEW
> echo "Usage: runscript analyse_af3_prediction.cxc
> "
"Usage: runscript analyse_af3_prediction.cxc
"
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_4*.cif
Chain information for model_4.cif #1
---
Chain | Description
A B | .
C | .
Computing secondary structure
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_4*.json
> structure last-opened
Opened AlphaFold PAE with values for 1563 residues and atoms
> hide
> show cartoons
> alphafold contacts last-opened &/C name
> model_4_af_contacts_fold_atg11_1_654_atg9_1_255_NEW distance 4.5 radius 1
Found 93 residue or atom pairs within distance 4.5
> select last-opened&pbonds
93 pseudobonds, 1 model selected
> label sel pseudobonds text "{0.atoms[0].residue.name}
> {0.atoms[0].residue.number} to {0.atoms[1].residue.name}
> {0.atoms[1].residue.number}"
> save
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt
> format pseudobonds selectedOnly true
Saved 93 pseudobonds to file
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt
> echo "AlphaFold contacts (derived from JSON file) saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt"
"AlphaFold contacts (derived from JSON file) saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt"
> interfaces select last-opened&/C contacting last-opened&~/C bothSides true
> areaCutoff 500
69 contacting residues
> name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 sel
> show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4
> style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 ball
Changed 576 atom styles
> info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4
> saveFile
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt
> rainbow last-opened chains palette bupu
> color byhetero
> echo "Interface residues saved in named selection
> interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 and info saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt"
"Interface residues saved in named selection
interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 and info saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt"
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_3*.cif
Chain information for model_3.cif #2
---
Chain | Description
A B | .
C | .
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_3*.json
> structure last-opened
Opened AlphaFold PAE with values for 1563 residues and atoms
> hide
> show cartoons
> alphafold contacts last-opened &/C distance 4.5 radius 1
Found 58 residue or atom pairs within distance 4.5
> select last-opened&pbonds
58 pseudobonds, 1 model selected
> label sel pseudobonds text "{0.atoms[0].residue.name}
> {0.atoms[0].residue.number} to {0.atoms[1].residue.name}
> {0.atoms[1].residue.number}"
> save
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt
> format pseudobonds selectedOnly true
Computing secondary structure
Saved 58 pseudobonds to file
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt
> echo "AlphaFold contacts (derived from JSON file) saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt"
"AlphaFold contacts (derived from JSON file) saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt"
> interfaces select last-opened&/C contacting last-opened&~/C bothSides true
> areaCutoff 500
44 contacting residues
> name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 sel
> show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3
> style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 ball
Changed 378 atom styles
> info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3
> saveFile
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt
> rainbow last-opened chains palette bupu
> color byhetero
> echo "Interface residues saved in named selection
> interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 and info saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt"
"Interface residues saved in named selection
interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 and info saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt"
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_2*.cif
Chain information for model_2.cif #3
---
Chain | Description
A B | .
C | .
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_2*.json
> structure last-opened
Opened AlphaFold PAE with values for 1563 residues and atoms
> hide
> show cartoons
> alphafold contacts last-opened &/C distance 4.5 radius 1
Found 90 residue or atom pairs within distance 4.5
> select last-opened&pbonds
90 pseudobonds, 1 model selected
> label sel pseudobonds text "{0.atoms[0].residue.name}
> {0.atoms[0].residue.number} to {0.atoms[1].residue.name}
> {0.atoms[1].residue.number}"
> save
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt
> format pseudobonds selectedOnly true
Computing secondary structure
Saved 90 pseudobonds to file
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt
> echo "AlphaFold contacts (derived from JSON file) saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt"
"AlphaFold contacts (derived from JSON file) saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt"
> interfaces select last-opened&/C contacting last-opened&~/C bothSides true
> areaCutoff 500
66 contacting residues
> name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 sel
> show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2
> style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 ball
Changed 553 atom styles
> info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2
> saveFile
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt
> rainbow last-opened chains palette bupu
> color byhetero
> echo "Interface residues saved in named selection
> interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 and info saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt"
"Interface residues saved in named selection
interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 and info saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt"
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_1*.cif
Chain information for model_1.cif #4
---
Chain | Description
A B | .
C | .
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_1*.json
> structure last-opened
Opened AlphaFold PAE with values for 1563 residues and atoms
> hide
> show cartoons
> alphafold contacts last-opened &/C distance 4.5 radius 1
Found 89 residue or atom pairs within distance 4.5
> select last-opened&pbonds
89 pseudobonds, 1 model selected
> label sel pseudobonds text "{0.atoms[0].residue.name}
> {0.atoms[0].residue.number} to {0.atoms[1].residue.name}
> {0.atoms[1].residue.number}"
> save
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt
> format pseudobonds selectedOnly true
Computing secondary structure
Saved 89 pseudobonds to file
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt
> echo "AlphaFold contacts (derived from JSON file) saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt"
"AlphaFold contacts (derived from JSON file) saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt"
> interfaces select last-opened&/C contacting last-opened&~/C bothSides true
> areaCutoff 500
84 contacting residues
> name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 sel
> show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1
> style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 ball
Changed 713 atom styles
> info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1
> saveFile
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt
> rainbow last-opened chains palette bupu
> color byhetero
> echo "Interface residues saved in named selection
> interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 and info saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt"
"Interface residues saved in named selection
interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 and info saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt"
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_0*.cif
Chain information for model_0.cif #5
---
Chain | Description
A B | .
C | .
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_0*.json
> structure last-opened
Opened AlphaFold PAE with values for 1563 residues and atoms
> hide
> show cartoons
> alphafold contacts last-opened &/C distance 4.5 radius 1
Found 70 residue or atom pairs within distance 4.5
> select last-opened&pbonds
70 pseudobonds, 1 model selected
> label sel pseudobonds text "{0.atoms[0].residue.name}
> {0.atoms[0].residue.number} to {0.atoms[1].residue.name}
> {0.atoms[1].residue.number}"
> save
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt
> format pseudobonds selectedOnly true
Computing secondary structure
Saved 70 pseudobonds to file
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt
> echo "AlphaFold contacts (derived from JSON file) saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt"
"AlphaFold contacts (derived from JSON file) saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt"
> interfaces select last-opened&/C contacting last-opened&~/C bothSides true
> areaCutoff 500
55 contacting residues
> name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 sel
> show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0
> style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 ball
Changed 466 atom styles
> info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0
> saveFile
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt
> echo "Interface residues saved in named selection
> interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 and info saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt"
"Interface residues saved in named selection
interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 and info saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt"
> mmaker #*&~last-opened&/B to last-opened&/B
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 model_0.cif, chain B (#5) with model_4.cif, chain B (#1), sequence
alignment score = 3359.5
RMSD between 420 pruned atom pairs is 0.942 angstroms; (across all 654 pairs:
4.670)
Matchmaker model_0.cif, chain B (#5) with model_3.cif, chain B (#2), sequence
alignment score = 3307.9
RMSD between 424 pruned atom pairs is 1.109 angstroms; (across all 654 pairs:
4.430)
Matchmaker model_0.cif, chain B (#5) with model_2.cif, chain B (#3), sequence
alignment score = 3366.1
RMSD between 501 pruned atom pairs is 1.013 angstroms; (across all 654 pairs:
5.032)
Matchmaker model_0.cif, chain B (#5) with model_1.cif, chain B (#4), sequence
alignment score = 3335.5
RMSD between 308 pruned atom pairs is 0.700 angstroms; (across all 654 pairs:
7.060)
> mseries slider #1-5 title fold_atg11_1_654_atg9_1_255_NEW name
> fold_atg11_1_654_atg9_1_255_NEW_slider
> mseries #1-5
> echo "Use the slider to go through the models!"
"Use the slider to go through the models!"
> echo "Pairwise contacts (based on the JSON fle) and all residues involved in
> an interface (based on a buried surface are of 500 Angstrom or more) have
> been saved in the input folder for each prediction"
"Pairwise contacts (based on the JSON fle) and all residues involved in an
interface (based on a buried surface are of 500 Angstrom or more) have been
saved in the input folder for each prediction"
> echo "You might want to increase stringency by calcualting the overlap
> between all predictions"
"You might want to increase stringency by calcualting the overlap between all
predictions"
> key red:20 orange: yellow:10 cornflowerblue: blue:0 size .15,.03 pos .025,.1
> ticks true
> 2dlabels text PAE xpos .075 ypos .15
> matchmaker #2-5/A to #1/A
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 model_4.cif, chain A (#1) with model_3.cif, chain A (#2), sequence
alignment score = 3363.1
RMSD between 558 pruned atom pairs is 0.670 angstroms; (across all 654 pairs:
4.877)
Matchmaker model_4.cif, chain A (#1) with model_2.cif, chain A (#3), sequence
alignment score = 3357.7
RMSD between 474 pruned atom pairs is 0.870 angstroms; (across all 654 pairs:
5.548)
Matchmaker model_4.cif, chain A (#1) with model_1.cif, chain A (#4), sequence
alignment score = 3397.3
RMSD between 457 pruned atom pairs is 0.935 angstroms; (across all 654 pairs:
4.037)
Matchmaker model_4.cif, chain A (#1) with model_0.cif, chain A (#5), sequence
alignment score = 3363.1
RMSD between 432 pruned atom pairs is 0.896 angstroms; (across all 654 pairs:
4.891)
> color sequential /a palette cornflower:teal
> color sequential /c palette #f768a1:#7a0177
> color sequential /b palette lightgreen:seagreen
> cartoon style protein thickness 2 width 3
> transparency 40 target s
> lighting soft
> graphics silhouettes true
> select clear
> hide #5.1.1 models
> hide target a
> analyse_af3_prediction_CT
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255
> fold_atg11_1_654_atg9_1_255_NEW
> echo "Usage: runscript analyse_af3_prediction.cxc
> "
"Usage: runscript analyse_af3_prediction.cxc
"
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_4*.cif
Chain information for model_4.cif #8
---
Chain | Description
A B | .
C | .
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_4*.json
> structure last-opened
Opened AlphaFold PAE with values for 1563 residues and atoms
> hide
> show cartoons
> alphafold contacts last-opened &/C name
> model_4_af_contacts_fold_atg11_1_654_atg9_1_255_NEW distance 4.5 radius 1
> dashes 4
Found 93 residue or atom pairs within distance 4.5
> select last-opened&pbonds
93 pseudobonds, 1 model selected
> label sel pseudobonds text "{0.atoms[0].residue.name}
> {0.atoms[0].residue.number} to {0.atoms[1].residue.name}
> {0.atoms[1].residue.number}"
> save
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt
> format pseudobonds selectedOnly true
Computing secondary structure
Saved 93 pseudobonds to file
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt
> echo "AlphaFold contacts (derived from JSON file) saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt"
"AlphaFold contacts (derived from JSON file) saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt"
> interfaces select last-opened&/C contacting last-opened&~/C bothSides true
> areaCutoff 500
69 contacting residues
> name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 sel
> show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4
> style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 ball
Changed 576 atom styles
> info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4
> saveFile
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt
> rainbow last-opened chains palette bupu
> color byhetero
> echo "Interface residues saved in named selection
> interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 and info saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt"
"Interface residues saved in named selection
interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 and info saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt"
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_3*.cif
Chain information for model_3.cif #9
---
Chain | Description
A B | .
C | .
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_3*.json
> structure last-opened
Opened AlphaFold PAE with values for 1563 residues and atoms
> hide
> show cartoons
> alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 4
Found 58 residue or atom pairs within distance 4.5
> select last-opened&pbonds
58 pseudobonds, 1 model selected
> label sel pseudobonds text "{0.atoms[0].residue.name}
> {0.atoms[0].residue.number} to {0.atoms[1].residue.name}
> {0.atoms[1].residue.number}"
> save
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt
> format pseudobonds selectedOnly true
Computing secondary structure
Saved 58 pseudobonds to file
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt
> echo "AlphaFold contacts (derived from JSON file) saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt"
"AlphaFold contacts (derived from JSON file) saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt"
> interfaces select last-opened&/C contacting last-opened&~/C bothSides true
> areaCutoff 500
44 contacting residues
> name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 sel
> show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3
> style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 ball
Changed 378 atom styles
> info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3
> saveFile
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt
> rainbow last-opened chains palette bupu
> color byhetero
> echo "Interface residues saved in named selection
> interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 and info saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt"
"Interface residues saved in named selection
interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 and info saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt"
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_2*.cif
Chain information for model_2.cif #10
---
Chain | Description
A B | .
C | .
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_2*.json
> structure last-opened
Opened AlphaFold PAE with values for 1563 residues and atoms
> hide
> show cartoons
> alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 4
Found 90 residue or atom pairs within distance 4.5
> select last-opened&pbonds
90 pseudobonds, 1 model selected
> label sel pseudobonds text "{0.atoms[0].residue.name}
> {0.atoms[0].residue.number} to {0.atoms[1].residue.name}
> {0.atoms[1].residue.number}"
> save
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt
> format pseudobonds selectedOnly true
Computing secondary structure
Saved 90 pseudobonds to file
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt
> echo "AlphaFold contacts (derived from JSON file) saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt"
"AlphaFold contacts (derived from JSON file) saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt"
> interfaces select last-opened&/C contacting last-opened&~/C bothSides true
> areaCutoff 500
66 contacting residues
> name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 sel
> show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2
> style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 ball
Changed 553 atom styles
> info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2
> saveFile
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt
> rainbow last-opened chains palette bupu
> color byhetero
> echo "Interface residues saved in named selection
> interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 and info saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt"
"Interface residues saved in named selection
interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 and info saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt"
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_1*.cif
Chain information for model_1.cif #11
---
Chain | Description
A B | .
C | .
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_1*.json
> structure last-opened
Opened AlphaFold PAE with values for 1563 residues and atoms
> hide
> show cartoons
> alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 4
Found 89 residue or atom pairs within distance 4.5
> select last-opened&pbonds
89 pseudobonds, 1 model selected
> label sel pseudobonds text "{0.atoms[0].residue.name}
> {0.atoms[0].residue.number} to {0.atoms[1].residue.name}
> {0.atoms[1].residue.number}"
> save
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt
> format pseudobonds selectedOnly true
Computing secondary structure
Saved 89 pseudobonds to file
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt
> echo "AlphaFold contacts (derived from JSON file) saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt"
"AlphaFold contacts (derived from JSON file) saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt"
> interfaces select last-opened&/C contacting last-opened&~/C bothSides true
> areaCutoff 500
84 contacting residues
> name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 sel
> show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1
> style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 ball
Changed 713 atom styles
> info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1
> saveFile
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt
> rainbow last-opened chains palette bupu
> color byhetero
> echo "Interface residues saved in named selection
> interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 and info saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt"
"Interface residues saved in named selection
interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 and info saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt"
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_0*.cif
Chain information for model_0.cif #12
---
Chain | Description
A B | .
C | .
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_0*.json
> structure last-opened
Opened AlphaFold PAE with values for 1563 residues and atoms
> hide
> show cartoons
> alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 4
Found 70 residue or atom pairs within distance 4.5
> select last-opened&pbonds
70 pseudobonds, 1 model selected
> label sel pseudobonds text "{0.atoms[0].residue.name}
> {0.atoms[0].residue.number} to {0.atoms[1].residue.name}
> {0.atoms[1].residue.number}"
> save
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt
> format pseudobonds selectedOnly true
Computing secondary structure
Saved 70 pseudobonds to file
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt
> echo "AlphaFold contacts (derived from JSON file) saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt"
"AlphaFold contacts (derived from JSON file) saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt"
> interfaces select last-opened&/C contacting last-opened&~/C bothSides true
> areaCutoff 500
55 contacting residues
> name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 sel
> show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0
> style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 ball
Changed 466 atom styles
> info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0
> saveFile
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt
> echo "Interface residues saved in named selection
> interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 and info saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt"
"Interface residues saved in named selection
interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 and info saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt"
> mmaker #*&~last-opened&/B to last-opened&/B
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 model_0.cif, chain B (#12) with model_4.cif, chain B (#1), sequence
alignment score = 3359.5
RMSD between 420 pruned atom pairs is 0.942 angstroms; (across all 654 pairs:
4.670)
Matchmaker model_0.cif, chain B (#12) with model_3.cif, chain B (#2), sequence
alignment score = 3307.9
RMSD between 424 pruned atom pairs is 1.109 angstroms; (across all 654 pairs:
4.430)
Matchmaker model_0.cif, chain B (#12) with model_2.cif, chain B (#3), sequence
alignment score = 3366.1
RMSD between 501 pruned atom pairs is 1.013 angstroms; (across all 654 pairs:
5.032)
Matchmaker model_0.cif, chain B (#12) with model_1.cif, chain B (#4), sequence
alignment score = 3335.5
RMSD between 308 pruned atom pairs is 0.700 angstroms; (across all 654 pairs:
7.060)
Matchmaker model_0.cif, chain B (#12) with model_0.cif, chain B (#5), sequence
alignment score = 3426.7
RMSD between 654 pruned atom pairs is 0.000 angstroms; (across all 654 pairs:
0.000)
Matchmaker model_0.cif, chain B (#12) with model_4.cif, chain B (#8), sequence
alignment score = 3359.5
RMSD between 420 pruned atom pairs is 0.942 angstroms; (across all 654 pairs:
4.670)
Matchmaker model_0.cif, chain B (#12) with model_3.cif, chain B (#9), sequence
alignment score = 3307.9
RMSD between 424 pruned atom pairs is 1.109 angstroms; (across all 654 pairs:
4.430)
Matchmaker model_0.cif, chain B (#12) with model_2.cif, chain B (#10),
sequence alignment score = 3366.1
RMSD between 501 pruned atom pairs is 1.013 angstroms; (across all 654 pairs:
5.032)
Matchmaker model_0.cif, chain B (#12) with model_1.cif, chain B (#11),
sequence alignment score = 3335.5
RMSD between 308 pruned atom pairs is 0.700 angstroms; (across all 654 pairs:
7.060)
> mseries slider #1-5 title fold_atg11_1_654_atg9_1_255_NEW name
> fold_atg11_1_654_atg9_1_255_NEW_slider
> mseries #1-5
> echo "Use the slider to go through the models!"
"Use the slider to go through the models!"
> echo "Pairwise contacts (based on the JSON fle) and all residues involved in
> an interface (based on a buried surface are of 500 Angstrom or more) have
> been saved in the input folder for each prediction"
"Pairwise contacts (based on the JSON fle) and all residues involved in an
interface (based on a buried surface are of 500 Angstrom or more) have been
saved in the input folder for each prediction"
> echo "You might want to increase stringency by calcualting the overlap
> between all predictions"
"You might want to increase stringency by calcualting the overlap between all
predictions"
> key red:20 orange: yellow:10 cornflowerblue: blue:0 size .15,.03 pos .025,.1
> ticks true
> 2dlabels text PAE xpos .075 ypos .15
> matchmaker #2-5/A to #1/A
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 model_4.cif, chain A (#1) with model_3.cif, chain A (#2), sequence
alignment score = 3363.1
RMSD between 558 pruned atom pairs is 0.670 angstroms; (across all 654 pairs:
4.877)
Matchmaker model_4.cif, chain A (#1) with model_2.cif, chain A (#3), sequence
alignment score = 3357.7
RMSD between 474 pruned atom pairs is 0.870 angstroms; (across all 654 pairs:
5.548)
Matchmaker model_4.cif, chain A (#1) with model_1.cif, chain A (#4), sequence
alignment score = 3397.3
RMSD between 457 pruned atom pairs is 0.935 angstroms; (across all 654 pairs:
4.037)
Matchmaker model_4.cif, chain A (#1) with model_0.cif, chain A (#5), sequence
alignment score = 3363.1
RMSD between 432 pruned atom pairs is 0.896 angstroms; (across all 654 pairs:
4.891)
> color sequential /a palette cornflower:teal
> color sequential /c palette #f768a1:#7a0177
> color sequential /b palette lightgreen:seagreen
> cartoon style protein thickness 2 width 3
> transparency 40 target s
> lighting soft
> graphics silhouettes true
> hide #!5 models
> hide #!5.1 models
> hide #6 models
> show #6 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> select clear
> hide target a
> hide #12.1.1 models
> lighting soft
> lighting simple
> lighting full
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting simple
> cartoon style protein thickness 1 width 2
> lighting soft
> graphics silhouettes true
> lighting flat
> lighting shadows true intensity 0.5
> lighting soft
> set bgColor gray
> set bgColor black
> lighting simple
> lighting soft
> graphics silhouettes false
> hide #!12 models
> hide #!12.1 models
> show #!5 models
> show #!5.1 models
> hide #!5 models
> hide #!5.1 models
> analyse_af3_prediction_CT
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255
> fold_atg11_1_654_atg9_1_255_NEW
> echo "Usage: runscript analyse_af3_prediction.cxc
> "
"Usage: runscript analyse_af3_prediction.cxc
"
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_4*.cif
Chain information for model_4.cif #13
---
Chain | Description
A B | .
C | .
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_4*.json
> structure last-opened
Opened AlphaFold PAE with values for 1563 residues and atoms
> hide
> show cartoons
> alphafold contacts last-opened &/C name
> model_4_af_contacts_fold_atg11_1_654_atg9_1_255_NEW distance 4.5 radius 1
> dashes 4
Found 93 residue or atom pairs within distance 4.5
> select last-opened&pbonds
93 pseudobonds, 1 model selected
> label sel pseudobonds text "{0.atoms[0].residue.name}
> {0.atoms[0].residue.number} to {0.atoms[1].residue.name}
> {0.atoms[1].residue.number}"
> save
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt
> format pseudobonds selectedOnly true
Computing secondary structure
Saved 93 pseudobonds to file
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt
> echo "AlphaFold contacts (derived from JSON file) saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt"
"AlphaFold contacts (derived from JSON file) saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt"
> interfaces select last-opened&/C contacting last-opened&~/C bothSides true
> areaCutoff 500
69 contacting residues
> name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 sel
> show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4
> style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 ball
Changed 576 atom styles
> info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4
> saveFile
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt
> rainbow last-opened chains palette bupu
> color byhetero
> echo "Interface residues saved in named selection
> interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 and info saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt"
"Interface residues saved in named selection
interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 and info saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt"
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_3*.cif
Chain information for model_3.cif #14
---
Chain | Description
A B | .
C | .
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_3*.json
> structure last-opened
Opened AlphaFold PAE with values for 1563 residues and atoms
> hide
> show cartoons
> alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 4
Found 58 residue or atom pairs within distance 4.5
> select last-opened&pbonds
58 pseudobonds, 1 model selected
> label sel pseudobonds text "{0.atoms[0].residue.name}
> {0.atoms[0].residue.number} to {0.atoms[1].residue.name}
> {0.atoms[1].residue.number}"
> save
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt
> format pseudobonds selectedOnly true
Computing secondary structure
Saved 58 pseudobonds to file
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt
> echo "AlphaFold contacts (derived from JSON file) saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt"
"AlphaFold contacts (derived from JSON file) saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt"
> interfaces select last-opened&/C contacting last-opened&~/C bothSides true
> areaCutoff 500
44 contacting residues
> name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 sel
> show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3
> style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 ball
Changed 378 atom styles
> info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3
> saveFile
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt
> rainbow last-opened chains palette bupu
> color byhetero
> echo "Interface residues saved in named selection
> interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 and info saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt"
"Interface residues saved in named selection
interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 and info saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt"
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_2*.cif
Chain information for model_2.cif #15
---
Chain | Description
A B | .
C | .
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_2*.json
> structure last-opened
Opened AlphaFold PAE with values for 1563 residues and atoms
> hide
> show cartoons
> alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 4
Found 90 residue or atom pairs within distance 4.5
> select last-opened&pbonds
90 pseudobonds, 1 model selected
> label sel pseudobonds text "{0.atoms[0].residue.name}
> {0.atoms[0].residue.number} to {0.atoms[1].residue.name}
> {0.atoms[1].residue.number}"
> save
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt
> format pseudobonds selectedOnly true
Computing secondary structure
Saved 90 pseudobonds to file
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt
> echo "AlphaFold contacts (derived from JSON file) saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt"
"AlphaFold contacts (derived from JSON file) saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt"
> interfaces select last-opened&/C contacting last-opened&~/C bothSides true
> areaCutoff 500
66 contacting residues
> name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 sel
> show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2
> style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 ball
Changed 553 atom styles
> info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2
> saveFile
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt
> rainbow last-opened chains palette bupu
> color byhetero
> echo "Interface residues saved in named selection
> interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 and info saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt"
"Interface residues saved in named selection
interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 and info saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt"
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_1*.cif
Chain information for model_1.cif #16
---
Chain | Description
A B | .
C | .
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_1*.json
> structure last-opened
Opened AlphaFold PAE with values for 1563 residues and atoms
> hide
> show cartoons
> alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 4
Found 89 residue or atom pairs within distance 4.5
> select last-opened&pbonds
89 pseudobonds, 1 model selected
> label sel pseudobonds text "{0.atoms[0].residue.name}
> {0.atoms[0].residue.number} to {0.atoms[1].residue.name}
> {0.atoms[1].residue.number}"
> save
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt
> format pseudobonds selectedOnly true
Computing secondary structure
Saved 89 pseudobonds to file
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt
> echo "AlphaFold contacts (derived from JSON file) saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt"
"AlphaFold contacts (derived from JSON file) saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt"
> interfaces select last-opened&/C contacting last-opened&~/C bothSides true
> areaCutoff 500
84 contacting residues
> name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 sel
> show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1
> style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 ball
Changed 713 atom styles
> info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1
> saveFile
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt
> rainbow last-opened chains palette bupu
> color byhetero
> echo "Interface residues saved in named selection
> interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 and info saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt"
"Interface residues saved in named selection
interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 and info saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt"
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_0*.cif
Chain information for model_0.cif #17
---
Chain | Description
A B | .
C | .
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_0*.json
> structure last-opened
Opened AlphaFold PAE with values for 1563 residues and atoms
> hide
> show cartoons
> alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 4
Found 70 residue or atom pairs within distance 4.5
> select last-opened&pbonds
70 pseudobonds, 1 model selected
> label sel pseudobonds text "{0.atoms[0].residue.name}
> {0.atoms[0].residue.number} to {0.atoms[1].residue.name}
> {0.atoms[1].residue.number}"
> save
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt
> format pseudobonds selectedOnly true
Computing secondary structure
Saved 70 pseudobonds to file
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt
> echo "AlphaFold contacts (derived from JSON file) saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt"
"AlphaFold contacts (derived from JSON file) saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt"
> interfaces select last-opened&/C contacting last-opened&~/C bothSides true
> areaCutoff 500
55 contacting residues
> name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 sel
> show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0
> style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 ball
Changed 466 atom styles
> info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0
> saveFile
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt
> echo "Interface residues saved in named selection
> interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 and info saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt"
"Interface residues saved in named selection
interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 and info saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt"
> mmaker #*&~last-opened&/B to last-opened&/B
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 model_0.cif, chain B (#17) with model_4.cif, chain B (#1), sequence
alignment score = 3359.5
RMSD between 420 pruned atom pairs is 0.942 angstroms; (across all 654 pairs:
4.670)
Matchmaker model_0.cif, chain B (#17) with model_3.cif, chain B (#2), sequence
alignment score = 3307.9
RMSD between 424 pruned atom pairs is 1.109 angstroms; (across all 654 pairs:
4.430)
Matchmaker model_0.cif, chain B (#17) with model_2.cif, chain B (#3), sequence
alignment score = 3366.1
RMSD between 501 pruned atom pairs is 1.013 angstroms; (across all 654 pairs:
5.032)
Matchmaker model_0.cif, chain B (#17) with model_1.cif, chain B (#4), sequence
alignment score = 3335.5
RMSD between 308 pruned atom pairs is 0.700 angstroms; (across all 654 pairs:
7.060)
Matchmaker model_0.cif, chain B (#17) with model_0.cif, chain B (#5), sequence
alignment score = 3426.7
RMSD between 654 pruned atom pairs is 0.000 angstroms; (across all 654 pairs:
0.000)
Matchmaker model_0.cif, chain B (#17) with model_4.cif, chain B (#8), sequence
alignment score = 3359.5
RMSD between 420 pruned atom pairs is 0.942 angstroms; (across all 654 pairs:
4.670)
Matchmaker model_0.cif, chain B (#17) with model_3.cif, chain B (#9), sequence
alignment score = 3307.9
RMSD between 424 pruned atom pairs is 1.109 angstroms; (across all 654 pairs:
4.430)
Matchmaker model_0.cif, chain B (#17) with model_2.cif, chain B (#10),
sequence alignment score = 3366.1
RMSD between 501 pruned atom pairs is 1.013 angstroms; (across all 654 pairs:
5.032)
Matchmaker model_0.cif, chain B (#17) with model_1.cif, chain B (#11),
sequence alignment score = 3335.5
RMSD between 308 pruned atom pairs is 0.700 angstroms; (across all 654 pairs:
7.060)
Matchmaker model_0.cif, chain B (#17) with model_0.cif, chain B (#12),
sequence alignment score = 3426.7
RMSD between 654 pruned atom pairs is 0.000 angstroms; (across all 654 pairs:
0.000)
Matchmaker model_0.cif, chain B (#17) with model_4.cif, chain B (#13),
sequence alignment score = 3359.5
RMSD between 420 pruned atom pairs is 0.942 angstroms; (across all 654 pairs:
4.670)
Matchmaker model_0.cif, chain B (#17) with model_3.cif, chain B (#14),
sequence alignment score = 3307.9
RMSD between 424 pruned atom pairs is 1.109 angstroms; (across all 654 pairs:
4.430)
Matchmaker model_0.cif, chain B (#17) with model_2.cif, chain B (#15),
sequence alignment score = 3366.1
RMSD between 501 pruned atom pairs is 1.013 angstroms; (across all 654 pairs:
5.032)
Matchmaker model_0.cif, chain B (#17) with model_1.cif, chain B (#16),
sequence alignment score = 3335.5
RMSD between 308 pruned atom pairs is 0.700 angstroms; (across all 654 pairs:
7.060)
> mseries slider #1-5 title fold_atg11_1_654_atg9_1_255_NEW name
> fold_atg11_1_654_atg9_1_255_NEW_slider
> mseries #1-5
> echo "Use the slider to go through the models!"
"Use the slider to go through the models!"
> echo "Pairwise contacts (based on the JSON fle) and all residues involved in
> an interface (based on a buried surface are of 500 Angstrom or more) have
> been saved in the input folder for each prediction"
"Pairwise contacts (based on the JSON fle) and all residues involved in an
interface (based on a buried surface are of 500 Angstrom or more) have been
saved in the input folder for each prediction"
> echo "You might want to increase stringency by calcualting the overlap
> between all predictions"
"You might want to increase stringency by calcualting the overlap between all
predictions"
> key red:20 orange: yellow:10 cornflowerblue: blue:0 size .15,.03 pos .025,.1
> ticks true
> 2dlabels text PAE xpos .075 ypos .15
> matchmaker #2-5/A to #1/A
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 model_4.cif, chain A (#1) with model_3.cif, chain A (#2), sequence
alignment score = 3363.1
RMSD between 558 pruned atom pairs is 0.670 angstroms; (across all 654 pairs:
4.877)
Matchmaker model_4.cif, chain A (#1) with model_2.cif, chain A (#3), sequence
alignment score = 3357.7
RMSD between 474 pruned atom pairs is 0.870 angstroms; (across all 654 pairs:
5.548)
Matchmaker model_4.cif, chain A (#1) with model_1.cif, chain A (#4), sequence
alignment score = 3397.3
RMSD between 457 pruned atom pairs is 0.935 angstroms; (across all 654 pairs:
4.037)
Matchmaker model_4.cif, chain A (#1) with model_0.cif, chain A (#5), sequence
alignment score = 3363.1
RMSD between 432 pruned atom pairs is 0.896 angstroms; (across all 654 pairs:
4.891)
> color sequential /a palette cornflower:teal
> color sequential /c palette #f768a1:#7a0177
> color sequential /b palette lightgreen:seagreen
> cartoon style protein thickness 2 width 3
> transparency 40 target s
> lighting soft
> graphics silhouettes true
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> close all
> analyse_af3_prediction_CT
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255
> fold_atg11_1_654_atg9_1_255_NEW
> echo "Usage: runscript analyse_af3_prediction.cxc
> "
"Usage: runscript analyse_af3_prediction.cxc
"
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_4*.cif
Chain information for model_4.cif #1
---
Chain | Description
A B | .
C | .
Computing secondary structure
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_4*.json
> structure last-opened
Opened AlphaFold PAE with values for 1563 residues and atoms
> hide
> show cartoons
> alphafold contacts last-opened &/C name
> model_4_af_contacts_fold_atg11_1_654_atg9_1_255_NEW distance 4.5 radius 1
> dashes 10
Found 93 residue or atom pairs within distance 4.5
> select last-opened&pbonds
93 pseudobonds, 1 model selected
> label sel pseudobonds text "{0.atoms[0].residue.name}
> {0.atoms[0].residue.number} to {0.atoms[1].residue.name}
> {0.atoms[1].residue.number}"
> save
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt
> format pseudobonds selectedOnly true
Saved 93 pseudobonds to file
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt
> echo "AlphaFold contacts (derived from JSON file) saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt"
"AlphaFold contacts (derived from JSON file) saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_4_fold_atg11_1_654_atg9_1_255_NEW.txt"
> interfaces select last-opened&/C contacting last-opened&~/C bothSides true
> areaCutoff 500
69 contacting residues
> name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 sel
> show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4
> style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 ball
Changed 576 atom styles
> info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4
> saveFile
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt
> rainbow last-opened chains palette bupu
> color byhetero
> echo "Interface residues saved in named selection
> interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 and info saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt"
"Interface residues saved in named selection
interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4 and info saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_4_buriedArea_500.txt"
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_3*.cif
Chain information for model_3.cif #2
---
Chain | Description
A B | .
C | .
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_3*.json
> structure last-opened
Opened AlphaFold PAE with values for 1563 residues and atoms
> hide
> show cartoons
> alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 10
Found 58 residue or atom pairs within distance 4.5
> select last-opened&pbonds
58 pseudobonds, 1 model selected
> label sel pseudobonds text "{0.atoms[0].residue.name}
> {0.atoms[0].residue.number} to {0.atoms[1].residue.name}
> {0.atoms[1].residue.number}"
> save
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt
> format pseudobonds selectedOnly true
Computing secondary structure
Saved 58 pseudobonds to file
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt
> echo "AlphaFold contacts (derived from JSON file) saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt"
"AlphaFold contacts (derived from JSON file) saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_3_fold_atg11_1_654_atg9_1_255_NEW.txt"
> interfaces select last-opened&/C contacting last-opened&~/C bothSides true
> areaCutoff 500
44 contacting residues
> name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 sel
> show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3
> style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 ball
Changed 378 atom styles
> info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3
> saveFile
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt
> rainbow last-opened chains palette bupu
> color byhetero
> echo "Interface residues saved in named selection
> interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 and info saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt"
"Interface residues saved in named selection
interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3 and info saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_3_buriedArea_500.txt"
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_2*.cif
Chain information for model_2.cif #3
---
Chain | Description
A B | .
C | .
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_2*.json
> structure last-opened
Opened AlphaFold PAE with values for 1563 residues and atoms
> hide
> show cartoons
> alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 10
Found 90 residue or atom pairs within distance 4.5
> select last-opened&pbonds
90 pseudobonds, 1 model selected
> label sel pseudobonds text "{0.atoms[0].residue.name}
> {0.atoms[0].residue.number} to {0.atoms[1].residue.name}
> {0.atoms[1].residue.number}"
> save
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt
> format pseudobonds selectedOnly true
Computing secondary structure
Saved 90 pseudobonds to file
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt
> echo "AlphaFold contacts (derived from JSON file) saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt"
"AlphaFold contacts (derived from JSON file) saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_2_fold_atg11_1_654_atg9_1_255_NEW.txt"
> interfaces select last-opened&/C contacting last-opened&~/C bothSides true
> areaCutoff 500
66 contacting residues
> name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 sel
> show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2
> style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 ball
Changed 553 atom styles
> info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2
> saveFile
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt
> rainbow last-opened chains palette bupu
> color byhetero
> echo "Interface residues saved in named selection
> interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 and info saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt"
"Interface residues saved in named selection
interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2 and info saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_2_buriedArea_500.txt"
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_1*.cif
Chain information for model_1.cif #4
---
Chain | Description
A B | .
C | .
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_1*.json
> structure last-opened
Opened AlphaFold PAE with values for 1563 residues and atoms
> hide
> show cartoons
> alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 10
Found 89 residue or atom pairs within distance 4.5
> select last-opened&pbonds
89 pseudobonds, 1 model selected
> label sel pseudobonds text "{0.atoms[0].residue.name}
> {0.atoms[0].residue.number} to {0.atoms[1].residue.name}
> {0.atoms[1].residue.number}"
> save
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt
> format pseudobonds selectedOnly true
Computing secondary structure
Saved 89 pseudobonds to file
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt
> echo "AlphaFold contacts (derived from JSON file) saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt"
"AlphaFold contacts (derived from JSON file) saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_1_fold_atg11_1_654_atg9_1_255_NEW.txt"
> interfaces select last-opened&/C contacting last-opened&~/C bothSides true
> areaCutoff 500
84 contacting residues
> name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 sel
> show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1
> style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 ball
Changed 713 atom styles
> info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1
> saveFile
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt
> rainbow last-opened chains palette bupu
> color byhetero
> echo "Interface residues saved in named selection
> interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 and info saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt"
"Interface residues saved in named selection
interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1 and info saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_1_buriedArea_500.txt"
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*model_0*.cif
Chain information for model_0.cif #5
---
Chain | Description
A B | .
C | .
> open
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/*data_0*.json
> structure last-opened
Opened AlphaFold PAE with values for 1563 residues and atoms
> hide
> show cartoons
> alphafold contacts last-opened &/C distance 4.5 radius 1 dashes 10
Found 70 residue or atom pairs within distance 4.5
> select last-opened&pbonds
70 pseudobonds, 1 model selected
> label sel pseudobonds text "{0.atoms[0].residue.name}
> {0.atoms[0].residue.number} to {0.atoms[1].residue.name}
> {0.atoms[1].residue.number}"
> save
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt
> format pseudobonds selectedOnly true
Computing secondary structure
Saved 70 pseudobonds to file
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt
> echo "AlphaFold contacts (derived from JSON file) saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt"
"AlphaFold contacts (derived from JSON file) saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/af_contacts_model_0_fold_atg11_1_654_atg9_1_255_NEW.txt"
> interfaces select last-opened&/C contacting last-opened&~/C bothSides true
> areaCutoff 500
55 contacting residues
> name frozen interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 sel
> show interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0
> style interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 ball
Changed 466 atom styles
> info residues interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0
> saveFile
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt
> echo "Interface residues saved in named selection
> interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 and info saved to
> /Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt"
"Interface residues saved in named selection
interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0 and info saved to
/Users/carlotta/Desktop/Chimera/fold_atg11_1_654_atg9_1_255/interface_residuesfold_atg11_1_654_atg9_1_255_NEW_model_0_buriedArea_500.txt"
> mmaker #*&~last-opened&/B to last-opened&/B
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 model_0.cif, chain B (#5) with model_4.cif, chain B (#1), sequence
alignment score = 3359.5
RMSD between 420 pruned atom pairs is 0.942 angstroms; (across all 654 pairs:
4.670)
Matchmaker model_0.cif, chain B (#5) with model_3.cif, chain B (#2), sequence
alignment score = 3307.9
RMSD between 424 pruned atom pairs is 1.109 angstroms; (across all 654 pairs:
4.430)
Matchmaker model_0.cif, chain B (#5) with model_2.cif, chain B (#3), sequence
alignment score = 3366.1
RMSD between 501 pruned atom pairs is 1.013 angstroms; (across all 654 pairs:
5.032)
Matchmaker model_0.cif, chain B (#5) with model_1.cif, chain B (#4), sequence
alignment score = 3335.5
RMSD between 308 pruned atom pairs is 0.700 angstroms; (across all 654 pairs:
7.060)
> mseries slider #1-5 title fold_atg11_1_654_atg9_1_255_NEW name
> fold_atg11_1_654_atg9_1_255_NEW_slider
> mseries #1-5
> echo "Use the slider to go through the models!"
"Use the slider to go through the models!"
> echo "Pairwise contacts (based on the JSON fle) and all residues involved in
> an interface (based on a buried surface are of 500 Angstrom or more) have
> been saved in the input folder for each prediction"
"Pairwise contacts (based on the JSON fle) and all residues involved in an
interface (based on a buried surface are of 500 Angstrom or more) have been
saved in the input folder for each prediction"
> echo "You might want to increase stringency by calcualting the overlap
> between all predictions"
"You might want to increase stringency by calcualting the overlap between all
predictions"
> key red:20 orange: yellow:10 cornflowerblue: blue:0 size .15,.03 pos .025,.1
> ticks true
> 2dlabels text PAE xpos .075 ypos .15
> matchmaker #2-5/A to #1/A
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 model_4.cif, chain A (#1) with model_3.cif, chain A (#2), sequence
alignment score = 3363.1
RMSD between 558 pruned atom pairs is 0.670 angstroms; (across all 654 pairs:
4.877)
Matchmaker model_4.cif, chain A (#1) with model_2.cif, chain A (#3), sequence
alignment score = 3357.7
RMSD between 474 pruned atom pairs is 0.870 angstroms; (across all 654 pairs:
5.548)
Matchmaker model_4.cif, chain A (#1) with model_1.cif, chain A (#4), sequence
alignment score = 3397.3
RMSD between 457 pruned atom pairs is 0.935 angstroms; (across all 654 pairs:
4.037)
Matchmaker model_4.cif, chain A (#1) with model_0.cif, chain A (#5), sequence
alignment score = 3363.1
RMSD between 432 pruned atom pairs is 0.896 angstroms; (across all 654 pairs:
4.891)
> color sequential /a palette cornflower:teal
> color sequential /c palette #f768a1:#7a0177
> color sequential /b palette lightgreen:seagreen
> cartoon style protein thickness 2 width 3
> transparency 40 target s
> lighting soft
> graphics silhouettes true
> hide #5.1.1 models
> select up
3662 atoms, 3717 bonds, 455 residues, 1 model selected
> select down
466 atoms, 55 residues, 1 model selected
> select clear
> hide target a
> set bgColor white
> lighting simple
> lighting soft
> lighting gentle
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> cartoon style protein thickness 1 width 2
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting soft
> cartoon style protein thickness 2 width 3
> ui mousemode right rotate
> view
> ui tool show "Side View"
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> show target s
> transparency 70 target s
> transparency 40 target s
> transparency 70 target s
> hide #!5.1 models
> lighting soft
> lighting gentle
> lighting soft
> lighting simple
> lighting soft
> lighting flat
> graphics silhouettes false
> ui mousemode right translate
> ui mousemode right zoom
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> lighting simple
> graphics silhouettes false
> lighting full
> lighting soft
> lighting gentle
> ui mousemode right rotate
> show #!4 models
> hide #!4.1 models
> show #!3 models
> hide #!3.1 models
> hide #3.2 models
> hide #3.3 models
> hide #3.4 models
> hide #4.2 models
> hide #4.3 models
> hide #4.4 models
> hide #5.2 models
> hide #5.3 models
> hide #5.4 models
> hide #!5 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> graphics silhouettes true
> show #!4 models
> show #!5 models
> lighting simple
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> hide #6 models
> hide #!7 models
> save superimposed.png supersample 4 transparentBackground true width 4000
> height 2000
> view name super
> view super
> hide #!3 models
> hide #!4 models
> show surfaces
> hide surfaces /c
Expected ',' or a keyword
> hide /c target s
> transparency 40 target s
> transparency 0 target s
> view super
> lighting soft
> lighting gentle
> lighting full
> lighting simple
> lighting soft
> graphics silhouettes false
> cartoon style protein thickness 2 width 3
> hide #4.2 models
> hide #4.3 models
> show #4.3 models
> show #4.2 models
> hide #5.4 models
> show #5.4 models
> hide #5.3 models
> show #5.3 models
> hide #5.3 models
> hide #3.2 models
> hide #3.3 models
> hide #3.4 models
> hide #!4 models
> hide #4.2 models
> hide #4.3 models
> hide #4.4 models
> hide #!5 models
> show #!5 models
> show #5.3 models
> show #3.3 models
> hide #3.3 models
> hide #!3 models
> hide #5.2 models
> hide #5.3 models
> show #!4 models
> show #!3 models
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> show #5.3 models
> show #5.2 models
> hide #!4 models
> hide #!3 models
> save model_0_NEW.png supersample 4 transparentBackground true width 4000
> height 2000
> hide #!5 models
> hide #5.2 models
> hide #5.3 models
> hide #5.4 models
> show #!4 models
> show #4.2 models
> show #4.3 models
> view super
> save model_1_NEW.png supersample 4 transparentBackground true width 4000
> height 2000
> hide #!4 models
> hide #4.2 models
> hide #4.3 models
> show #!3 models
> show #3.2 models
> show #3.3 models
> save model_2_NEW.png supersample 4 transparentBackground true width 4000
> height 2000
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> save model_2_NEW.png supersample 4 transparentBackground true width 4000
> height 4000
> hide #!3 models
> hide #3.2 models
> hide #3.3 models
> show #!4 models
> show #4.2 models
> show #4.3 models
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> save model_1_NEW.png supersample 4 transparentBackground true width 4000
> height 4000
> hide #!4 models
> hide #4.2 models
> hide #4.3 models
> show #!5 models
> show #5.2 models
> show #5.3 models
> ui mousemode right zoom
> ui mousemode right translate
> hide /a target c
> transparency 40 target s
> transparency 0 target s
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> save model_0_NEW.png supersample 4 transparentBackground true width 4000
> height 4000
> color
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color #5.2-3#!5 #f050acff
> color #5.2-3#!5 #ff40ffff
> undo
> color #5.2-3#!5 #f050aeff
> undo
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> color
> color show
Illegal color name: ""
> color #5.2-3#!5 #6fdf88ff
> undo
> color #5.2-3#!5 #0edf01ff
> undo
> color #5.2-3#!5 #3aa2d6ff
> undo
> color #5.2-3#!5 #6fdf88ff
> color #5.2-3#!5 #3aa2d6ff
> color #5.2-3#!5 #64c87aff
> color #5.2-3#!5 #3aa2d6ff
> color #5.2-3#!5 #0edf01ff
> color #5.2-3#!5 #39a1d4ff
===== Log before crash end =====
Log:
> alias analyse_af_screen_hit runscript
> /Users/carlotta/ChimeraX/scripts/analyse_af_screen_hit.cxc $1 $2
> alias analyse_af3 runscript
> /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction.cxc $1 $2
> alias analyse_auto-AF runscript
> /Users/carlotta/ChimeraX/scripts/analyse_auto-alphafold_prediction.cxc $1 $2
> alias analyse_af3_prediction_ac_bc_only runscript
> /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction_ac_bc_only.cxc $1 $2
> alias analyse_af3_prediction_modified runscript
> /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction_modified.cxc $1 $2
> alias analyse_af3_prediction_modified_PAE runscript
> /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction_modified_PAE.cxc $1
> $2
> alias analyse_af3_prediction_modified_5 runscript
> /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction_modified_5.cxc $1 $2
> alias analyse_af3_prediction_CT runscript
> /Users/carlotta/ChimeraX/scripts/analyse_af3_prediction_CT.cxc $1 $2
UCSF ChimeraX version: 1.10.dev202504300222 (2025-04-30)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,10
Model Number: Z178000G3D/A
Chip: Apple M2 Pro
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: 11881.61.3
OS Loader Version: 11881.61.3
Software:
System Software Overview:
System Version: macOS 15.2 (24C101)
Kernel Version: Darwin 24.2.0
Time since boot: 25 days, 16 hours, 8 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 19
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.3.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.3.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.1
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.3
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.5
ChimeraX-AtomicLibrary: 14.1.17
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.6
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.dev202504300222
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.1
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: 2.2.1
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.9
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.8.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.57.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.13.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.6
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.14
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.9.2
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: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.7
pluggy: 1.5.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.3.5
pytest-cov: 6.1.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 26.4.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.13.2
tzdata: 2025.2
urllib3: 2.4.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 3 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 , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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