![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 75 minutes ago
#20468 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.4-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
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"procRole" : "Foreground",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "Mac15,7",
"coalitionID" : 23080,
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"build" : "25E246",
"releaseType" : "User"
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"captureTime" : "2026-06-08 11:42:57.7583 +0200",
"codeSigningMonitor" : 2,
"incident" : "6DE78893-C6D7-42C4-B82E-B429A63BCD8D",
"pid" : 59789,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-05-26 12:55:53.7128 +0200",
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"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "2653DFB6-AC8E-C699-A2C1-E9CFA5A92DCB",
"appleIntelligenceStatus" : {"state":"available"},
"developerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"sleepWakeUUID" : "891DE88B-0323-437E-8D34-48EB643BF669",
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"vmRegionInfo" : "0x8 is not in any region. Bytes before following region: 4376215544
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 104d7c000-104d80000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"},
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"vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4376215544
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
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Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Volumes/bzmh01$/_Members/casano0002/For Chris A3 paper /Chimera
> /Models_ATP13A3-AZ1_yeast_worm_fly.cxs"
Log from Mon Jun 8 08:35:03 2026UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/casano0002/Downloads/fold_catp6_oaz1_celegans_shortaz1/fold_catp6_oaz1_celegans_shortaz1_model_3.cif
Chain information for fold_catp6_oaz1_celegans_shortaz1_model_3.cif #1
---
Chain | Description
A | .
B | .
Computing secondary structure
> select /B:1-121
976 atoms, 1004 bonds, 121 residues, 1 model selected
> show sel cartoons
> log metadata #1
The model has no metadata
> log chains #1
Chain information for fold_catp6_oaz1_celegans_shortaz1_model_3.cif #1
---
Chain | Description
A | .
B | .
> set bgColor white
> ui tool show "Color Actions"
> color sel bychain
> color sel #ff8758ff
> color sel #ff944eff
> color sel #ff8d48ff
> color sel #ff8e48ff
> color sel #ff944eff
> color sel #ff9751ff
[Repeated 1 time(s)]
> color sel #ff9953ff
> color sel #ff9a54ff
> color sel #ff9b54ff
> color sel #ff9c54ff
> color sel #ff9c53ff
> color sel #ff9d53ff
> color sel #ff9e52ff
[Repeated 2 time(s)]
> color sel #ff9f52ff
> color sel #ffa150ff
> color sel #ffa04fff
> color sel #ffa14eff
> color sel #ffa14dff
> color sel #ffa14bff
> color sel #ffa24bff
> color sel #ffa24aff
[Repeated 1 time(s)]
> color sel #ffa148ff
> color sel #ffa146ff
> color sel #ffa044ff
> color sel #ff9f44ff
> color sel #ff9f43ff
> color sel #ff9f42ff
> color sel #f99c1c
> select /B:1-121
976 atoms, 1004 bonds, 121 residues, 1 model selected
> select /B:1-121
976 atoms, 1004 bonds, 121 residues, 1 model selected
> select /B:1-121
976 atoms, 1004 bonds, 121 residues, 1 model selected
> select/B
Unknown command: select/B
> select /B:1-121
976 atoms, 1004 bonds, 121 residues, 1 model selected
> select/A
Unknown command: select/A
> select/A:1-1267
Unknown command: select/A:1-1267
> select /A:1-1267
9985 atoms, 10198 bonds, 1267 residues, 1 model selected
> color #1 #3e8bf6ff
> color #1 #5cc9f8ff
> color #1 #3272f4ff
> color #1 #2250f1ff
> color #1 #316aedff
> color #1 #336decff
> color #1 #346beaff
> color #1 #2532e6ff
> color #1 #416ae3ff
> color #1 #4a7ce3ff
> select /B:1-121 color sel #f99c1c,
Expected a keyword
> select /B:1-121
976 atoms, 1004 bonds, 121 residues, 1 model selected
> color sel #f99c1c
> show sel cartoons
> select /B:1-121, select /A:1-1267
10961 atoms, 11202 bonds, 1388 residues, 1 model selected
> show sel cartoons
> select /A:1-1267
9985 atoms, 10198 bonds, 1267 residues, 1 model selected
> color #1 #5eb4e6ff
> color #1 #60b0e4ff
> color #1 #4884e5ff
> color #1 #5487e3ff
> select /B:1-121
976 atoms, 1004 bonds, 121 residues, 1 model selected
> color sel #f99c1c
> select /A:1-1267 select /B:1-121
Expected a keyword
> select /A:1-1267, select /B:1-121
10961 atoms, 11202 bonds, 1388 residues, 1 model selected
> cartoon style sel xsection oval modeHelix default
> cartoon style (sel & coil) xsection oval
> cartoon style sel xsection barbell modeHelix default
> cartoon style sel xsection oval modeHelix default
> cartoon
> cartoon style width 1.5 thickness 0.5
> graphics silhouettes true
> graphics silhouettes width 2
> graphics silhouettes color black
> lighting flatck
Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword
> lighting flat
> lighting simple
> cartoon
> graphics silhouettes true width 3 color black
> lighting flat
> set bgColor white
> graphics depthCue false
Expected a keyword
> graphics depthCue false
Expected a keyword
> select subtract #1
Nothing selected
> select add #1
10961 atoms, 11202 bonds, 1388 residues, 1 model selected
> select subtract #1
Nothing selected
> graphics silhouettes false
> graphics silhouettes color white
> graphics silhouettes color grey
> cartoon
> graphics silhouettes true width 3 color black
> lighting flat
> set bgColor white
> graphics depthCue false
Expected a keyword
> ~display
> cartoon
> cartoon style modeHelix tube
> cartoon style width 2.0 thickness 0.3
> graphics silhouettes false
> lighting soft
> set bgColor white
> cartoon style default
Expected an atoms specifier or a keyword
> cartoon style modeHelix ribbon
Invalid "modeHelix" argument: Should be one of 'default', 'tube', or 'wrap'
> cartoon
> graphics silhouettes true width 3 color black
> lighting flat
> set bgColor white
> graphics depthCue false
Expected a keyword
> ~display
> cartoon
> lighting soft
> set bgColor white
> graphics silhouettes false
> ~display
> cartoon
> lighting soft
> set bgColor white
> graphics silhouettes false
> ~display
> cartoon
> lighting soft
> set bgColor white
> graphics silhouettes false
> cartoon style width 1.5 thickness 0.5
> lighting soft
> lighting shadows true intensity 0.5
> graphics silhouettes true width 8
> set bgColor white
> cartoon style modeHelix ribbon
Invalid "modeHelix" argument: Should be one of 'default', 'tube', or 'wrap'
> cartoon style modeHelix default
> graphics silhouettes true width 5
> graphics silhouettes true width 4
> graphics silhouettes true width 3
> graphics silhouettes true width 2
> save /Users/casano0002/ATP13A3_canonicalOrganisms.cxs
> graphics silhouettes true width 8
> save mystructure.png supersample 3
> save /Users/casano0002/ATP13A3_canonicalOrganisms.png supersample 3
> save /Users/casano0002/ATP13A3_canonicalOrganisms.png width 6000 height 6000
> supersample 3
> open
> /Users/casano0002/Downloads/fold_catp5_oaz1_celegans_shortaz1/fold_catp5_oaz1_celegans_shortaz1_model_1.cif
Chain information for fold_catp5_oaz1_celegans_shortaz1_model_1.cif #2
---
Chain | Description
A | .
B | .
Computing secondary structure
> hide #1 models
> select add #2
10432 atoms, 10648 bonds, 1324 residues, 1 model selected
> select /A:1-1327
19441 atoms, 19842 bonds, 2470 residues, 2 models selected
> select add #1
20417 atoms, 20846 bonds, 2591 residues, 2 models selected
> select subtract #1
9456 atoms, 9644 bonds, 1203 residues, 1 model selected
> color #2 #6a91e0ff
> select #2/B:1-121
976 atoms, 1004 bonds, 121 residues, 1 model selected
> color #f99c1c
> select /A:1-1327, color #2 #6a91e0ff
Expected a keyword
> select /A:1-1327, color #6a91e0ff
Expected a keyword
> select /A:1-1327,
Expected an objects specifier or a keyword
> select /A:1-1327
19441 atoms, 19842 bonds, 2470 residues, 2 models selected
> color #2 #2c57e9ff
> color #2 #0f1deeff
> color #2 #5f81e0ff
> select #2/B:1-121
976 atoms, 1004 bonds, 121 residues, 1 model selected
> color sel #eeaa43ff
> hide #2 models
> show #1 models
> select add #1
11937 atoms, 12206 bonds, 1509 residues, 2 models selected
> select #2/A:1-1203
9456 atoms, 9644 bonds, 1203 residues, 1 model selected
> select #2/A:1-1203
9456 atoms, 9644 bonds, 1203 residues, 1 model selected
> select /A:1-1267
19441 atoms, 19842 bonds, 2470 residues, 2 models selected
> color #1 #718bdeff
> select #2/B:1-121
976 atoms, 1004 bonds, 121 residues, 1 model selected
> select #2/B:1-121
976 atoms, 1004 bonds, 121 residues, 1 model selected
> select #2/B:1-121
976 atoms, 1004 bonds, 121 residues, 1 model selected
> select #2/B:1-121
976 atoms, 1004 bonds, 121 residues, 1 model selected
> hide #1 models
> show #2 models
> hide #2 models
> show #1 models
> select #2/B:1-121
976 atoms, 1004 bonds, 121 residues, 1 model selected
> select #2/B:1-121
976 atoms, 1004 bonds, 121 residues, 1 model selected
> select #2/A:1-1203
9456 atoms, 9644 bonds, 1203 residues, 1 model selected
> hide #1 models
> show #2 models
> hide #2 models
> show #1 models
> select add #2
10432 atoms, 10648 bonds, 1324 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #1
10961 atoms, 11202 bonds, 1388 residues, 1 model selected
> select /B:1-121
1952 atoms, 2008 bonds, 242 residues, 2 models selected
> select #2/B:1-121, color #f99c1c
Expected a keyword
> select #2/B:1-121, color #2 #f99c1c
Expected a keyword
> color (#1 & sel) #deaa4cff
> color (#1 & sel) #deb03fff
> color (#1 & sel) #deab3cff
[Repeated 1 time(s)]
> color (#1 & sel) #deaa3cff
> color (#1 & sel) #dea93cff
> color (#1 & sel) #dea73eff
> color (#1 & sel) #dea53fff
> color (#1 & sel) #dea440ff
> color (#1 & sel) #dea341ff
> color (#1 & sel) #dea242ff
> color (#1 & sel) #de9f46ff
> color (#1 & sel) #de9e47ff
> color (#1 & sel) #de9d48ff
> color (#1 & sel) #de9e4bff
> color (#1 & sel) #dea051ff
> color (#1 & sel) #dea357ff
> color (#1 & sel) #dea459ff
> color (#1 & sel) #dea45aff
[Repeated 1 time(s)]
> color (#1 & sel) #dea55bff
> color (#1 & sel) #dea65dff
> color (#1 & sel) #dea75eff
> color (#1 & sel) #dea862ff
> color (#1 & sel) #dea963ff
> color (#1 & sel) #deaa64ff
> color (#1 & sel) #deaa66ff
> color (#1 & sel) #deaa67ff
> color (#1 & sel) #deac69ff
[Repeated 1 time(s)]
> color (#1 & sel) #dead6bff
> color (#1 & sel) #dead6cff
[Repeated 1 time(s)]
> color (#1 & sel) #deae6dff
> color (#1 & sel) #deae6eff
> color (#1 & sel) #deaf6fff
> color (#1 & sel) #deaf70ff
> color (#1 & sel) #deb071ff
> color (#1 & sel) #deb173ff
> color (#1 & sel) #deb276ff
> color (#1 & sel) #deb378ff
> color (#1 & sel) #deb47aff
> color (#1 & sel) #deb67cff
> color (#1 & sel) #deb77eff
> color (#1 & sel) #deb880ff
> color (#1 & sel) #deb981ff
> color (#1 & sel) #debc85ff
> color (#1 & sel) #debe88ff
> color (#1 & sel) #debe89ff
> color (#1 & sel) #debe8aff
> color (#1 & sel) #debf8aff
> color (#1 & sel) #dec08cff
> color (#1 & sel) #dec08dff
> color (#1 & sel) #dec18fff
> color (#1 & sel) #dec190ff
> color (#1 & sel) #dec291ff
> color (#1 & sel) #dec293ff
> color (#1 & sel) #dec394ff
> color (#1 & sel) #dec395ff
> color (#1 & sel) #dec396ff
> color (#1 & sel) #dec498ff
> color (#1 & sel) #debd82ff
> color (#1 & sel) #deba7fff
> color (#1 & sel) #deb77bff
> color (#1 & sel) #deb376ff
> color (#1 & sel) #deb374ff
> color (#1 & sel) #deb172ff
> color (#1 & sel) #deb070ff
> color (#1 & sel) #deaf6eff
> color (#1 & sel) #dead6bff
> color (#1 & sel) #deab68ff
> color (#1 & sel) #deab66ff
> color (#1 & sel) #deab62ff
> color (#1 & sel) #deaa61ff
> color (#1 & sel) #deaa60ff
> color #2 #f99c1c
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #1 models
> select #2/A:1-1203
9456 atoms, 9644 bonds, 1203 residues, 1 model selected
> color #2 #8195ddff
> select #2/B:1-121
976 atoms, 1004 bonds, 121 residues, 1 model selected
> color #2 #f99c1c
> select #2/A:1-1203
9456 atoms, 9644 bonds, 1203 residues, 1 model selected
> color #2 #8195ddff
> select #2/B:1-1211203
976 atoms, 1004 bonds, 121 residues, 1 model selected
> select #2/B:1-1211203 color #2 #f99c1c
Expected a keyword
> select #2/B:1-1211203, color #2 #f99c1c
Expected a keyword
> color #2 #f99c1c
> select #2/A:1-1203
9456 atoms, 9644 bonds, 1203 residues, 1 model selected
> select #2/A:1-1203, color #2 #8195ddff
Expected a keyword
> select #2/A:1-1203, color #2 #8195ddf
Expected a keyword
> select #2/A:1-1203, color #2 #8195dd
Expected a keyword
> select #2/A:1-1203, color #2 #8195d
Expected a keyword
> color #2 #8195ddff
> select #2/B:1-121, color #2 #f99c1c
Expected a keyword
> select #2/B:1-121
976 atoms, 1004 bonds, 121 residues, 1 model selected
> select #2/B:1-121
976 atoms, 1004 bonds, 121 residues, 1 model selected
> select #2/B:1-121
976 atoms, 1004 bonds, 121 residues, 1 model selected
> select #2/B:1-121
976 atoms, 1004 bonds, 121 residues, 1 model selected
> color #2 #f99c1c
> select #2/A:1-1203
9456 atoms, 9644 bonds, 1203 residues, 1 model selected
> select #2/A:1-1203, color #2A:1-1203 #8195d
Expected a keyword
> select #2/A:1-1203, color #2/A:1-1203 #8195d
Expected a keyword
> select #2/A:1-1203, color #2/A:1-1203 #8195d
Expected a keyword
> color #2 #8195ddff
> elect #2/B:1-121, color #2/B:1-121, #f99c1c
Unknown command: elect #2/B:1-121, color #2/B:1-121, #f99c1c
> elect #2/B:1-121, color #2/B:1-121 #f99c1c
Unknown command: elect #2/B:1-121, color #2/B:1-121 #f99c1c
> select #2/B:1-121, color #2/B:1-121 #f99c1c
Expected a keyword
> color #2/B:1-121 #f99c1c
> select add #2
10432 atoms, 10648 bonds, 1324 residues, 1 model selected
> select subtract #2
Nothing selected
> show #1 models
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #1/B#2/B
Alignment identifier is 1
> sequence chain #2/A
Alignment identifier is 2/A
> matchmaker #1 to #2 alwaysAlign true
Expected a keyword
> matchmaker #1 to #2
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 fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2) with
fold_catp6_oaz1_celegans_shortaz1_model_3.cif, chain A (#1), sequence
alignment score = 3396.8
RMSD between 948 pruned atom pairs is 0.860 angstroms; (across all 1124 pairs:
4.359)
> alwaysAlign true
Unknown command: alwaysAlign true
> always Align true
Unknown command: always Align true
> hide #1 models
> save /Users/casano0002/ATP13A3_canonicalOrganismsCATP6.png width 6000 height
> 6000 supersample 3
[Repeated 1 time(s)]
> hide #2 models
> show #1 models
> show #2 models
> hide #2 models
> hide #1 models
> show #1 models
> show #2 models
> save /Users/casano0002/catp5_catp6_alphafoldmodels.cxs
Unsupported scale factor (0.000000) detected on Display0
[Repeated 3 time(s)]Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
> open
> /Users/casano0002/Downloads/fold_oaz1_ypk9_yeast_shortyeast/fold_oaz1_ypk9_yeast_shortyeast_model_2.cif
Chain information for fold_oaz1_ypk9_yeast_shortyeast_model_2.cif #3
---
Chain | Description
A | .
B | .
Computing secondary structure
> matchmaker #1 to #2
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 fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2) with
fold_catp6_oaz1_celegans_shortaz1_model_3.cif, chain A (#1), sequence
alignment score = 3396.8
RMSD between 948 pruned atom pairs is 0.860 angstroms; (across all 1124 pairs:
4.359)
> matchmaker #1 to #2 #3
Specify a single 'to' model only
> matchmaker #1 to #3
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 fold_oaz1_ypk9_yeast_shortyeast_model_2.cif, chain B (#3) with
fold_catp6_oaz1_celegans_shortaz1_model_3.cif, chain A (#1), sequence
alignment score = 2515
RMSD between 398 pruned atom pairs is 1.011 angstroms; (across all 1115 pairs:
9.507)
> matchmaker #1 to #2
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 fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2) with
fold_catp6_oaz1_celegans_shortaz1_model_3.cif, chain A (#1), sequence
alignment score = 3396.8
RMSD between 948 pruned atom pairs is 0.860 angstroms; (across all 1124 pairs:
4.359)
> matchmaker #1 to #3
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 fold_oaz1_ypk9_yeast_shortyeast_model_2.cif, chain B (#3) with
fold_catp6_oaz1_celegans_shortaz1_model_3.cif, chain A (#1), sequence
alignment score = 2515
RMSD between 398 pruned atom pairs is 1.011 angstroms; (across all 1115 pairs:
9.507)
> matchmaker #2 to #3
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 fold_oaz1_ypk9_yeast_shortyeast_model_2.cif, chain B (#3) with
fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2), sequence
alignment score = 2454.1
RMSD between 387 pruned atom pairs is 1.137 angstroms; (across all 1130 pairs:
19.908)
> hide #1 models
> hide #2 models
> open
> /Users/casano0002/Downloads/fold_fly_oaz1_atp13a3_shorteraz1_shortera3-2/fold_fly_oaz1_atp13a3_shorteraz1_shortera3_model_2.cif
Chain information for fold_fly_oaz1_atp13a3_shorteraz1_shortera3_model_2.cif
#4
---
Chain | Description
A | .
B | .
Computing secondary structure
> matchmaker #2 to #4
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 fold_fly_oaz1_atp13a3_shorteraz1_shortera3_model_2.cif, chain A
(#4) with fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2),
sequence alignment score = 2596.7
RMSD between 727 pruned atom pairs is 1.203 angstroms; (across all 1146 pairs:
18.869)
> show #2 models
> matchmaker #2 to #4
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 fold_fly_oaz1_atp13a3_shorteraz1_shortera3_model_2.cif, chain A
(#4) with fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2),
sequence alignment score = 2596.7
RMSD between 727 pruned atom pairs is 1.203 angstroms; (across all 1146 pairs:
18.869)
> matchmaker #2 to #3
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 fold_oaz1_ypk9_yeast_shortyeast_model_2.cif, chain B (#3) with
fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2), sequence
alignment score = 2454.1
RMSD between 387 pruned atom pairs is 1.137 angstroms; (across all 1130 pairs:
19.908)
> matchmaker #3 ro #4
Expected a keyword
> matchmaker #3 to #4
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 fold_fly_oaz1_atp13a3_shorteraz1_shortera3_model_2.cif, chain A
(#4) with fold_oaz1_ypk9_yeast_shortyeast_model_2.cif, chain B (#3), sequence
alignment score = 2553.6
RMSD between 395 pruned atom pairs is 0.973 angstroms; (across all 1215 pairs:
19.189)
> matchmaker #1 to #4
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 fold_fly_oaz1_atp13a3_shorteraz1_shortera3_model_2.cif, chain A
(#4) with fold_catp6_oaz1_celegans_shortaz1_model_3.cif, chain A (#1),
sequence alignment score = 2967.9
RMSD between 737 pruned atom pairs is 1.072 angstroms; (across all 1169 pairs:
16.160)
> matchmaker #2 to #4
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 fold_fly_oaz1_atp13a3_shorteraz1_shortera3_model_2.cif, chain A
(#4) with fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2),
sequence alignment score = 2596.7
RMSD between 727 pruned atom pairs is 1.203 angstroms; (across all 1146 pairs:
18.869)
> hide #2 models
> hide #4 models
> hide #3 models
> show #4 models
> select #4/B:1-212
1671 atoms, 1710 bonds, 212 residues, 1 model selected
> color #4/B:1-212 #f99c1c
> select #4/A:1-1416
11277 atoms, 11554 bonds, 1416 residues, 1 model selected
> select #4/A:1-1416
11277 atoms, 11554 bonds, 1416 residues, 1 model selected
> select #4/A:1-1416, color #8195d
Expected a keyword
> select #4/A:1-1416, color #8195ddff
Expected a keyword
> hide #4 models
> show #2 models
> hide #2 models
> show #4 models
> select #4/A:1-1416, color #8195d
Expected a keyword
> show target m
> hide target m
> show #4 models
> color sel #718bdeff
> hide #4 models
> show #2 models
> select add #4
12948 atoms, 13264 bonds, 1628 residues, 1 model selected
> select subtract #4
Nothing selected
> select #2/A
9456 atoms, 9644 bonds, 1203 residues, 1 model selected
> color sel #718bdeff
> hide #2 models
> show #3 models
> hide #3 models
> show #4 models
> show #3 models
> hide #4 models
> select #3A
Expected an objects specifier or a keyword
> select #3/A
2399 atoms, 2451 bonds, 292 residues, 1 model selected
> show #4 models
> color sel #ffa81eff
> hide #4 models
> select #3/A, color#3/A #f99c1c
Expected a keyword
> select #3/A, color sel #f99c1c
Expected a keyword
> show #4 models
> hide #4 models
> show #2 models
> color sel #f0961bff
> color sel #d38418ff
> color sel #d18318ff
> select #3/A, color sel #f99c1c
Expected a keyword
> select #3/A, color #f99c1c
Expected a keyword
> color sel #f99c1c
> hide #2 models
> select #3/B, color sel #f99c1c
Expected a keyword
> select #3/B
11504 atoms, 11782 bonds, 1440 residues, 1 model selected
> color sel #718bdeff
> hide #3 models
> show #3 models
> show #4 models
> show #2 models
> show #1 models
> hide #1 models
> hide #2 models
> hide #3 models
> select add #3
13903 atoms, 14233 bonds, 1732 residues, 1 model selected
> select subtract #3
Nothing selected
> show #3 models
> cartoon style width 1.5 thickness 0.5
> lighting soft
> lighting shadows true intensity 0.5
> graphics silhouettes true width 8
> set bgColor white
> show #1 models
> show #2 models
> hide #2 models
> hide #3 models
> hide #4 models
> save /Users/casano0002/ATP13A3_canonicalOrganismsCATP5.png width 6000 height
> 6000 supersample 3
> hide #1 models
> show #2 models
> save /Users/casano0002/ATP13A3_canonicalOrganismsCATP5.png width 6000 height
> 6000 supersample 3
> show #1 models
> hide #2 models
> hide #1 models
> show #3 models
> hide #3 models
> show #1 models
> save /Users/casano0002/ATP13A3_canonicalOrganismsCATP6.png width 6000 height
> 6000 supersample 3
> hide #1 models
> show #3 models
> save /Users/casano0002/ATP13A3_canonicalOrganismsYEAST.png width 6000 height
> 6000 supersample 3
> hide #3 models
> show #4 models
> show #3 models
> show #2 models
> show #1 models
> hide #1 models
> hide #2 models
> hide #3 models
> save /Users/casano0002/ATP13A3_canonicalOrganismsfly.png width 6000 height
> 6000 supersample 3
> hide #4 models
> show #1 models
> select /B:1-121
3829 atoms, 3927 bonds, 484 residues, 4 models selected
> color sel #f99c1c
> select add #1
13814 atoms, 14125 bonds, 1751 residues, 4 models selected
> select subtract #1
2853 atoms, 2923 bonds, 363 residues, 3 models selected
> show #2 models
> show #3 models
> hide #3 models
> hide #2 models
> save /Users/casano0002/ATP13A3_canonicalOrganismsCATP6.png width 6000 height
> 6000 supersample 3
> open /Users/casano0002/Downloads/A3_full-OAZ1_N-trunc_0009_best.pdb
Summary of feedback from opening /Users/casano0002/Downloads/A3_full-OAZ1_N-
trunc_0009_best.pdb
---
warnings | Ignored bad PDB record found on line 21726
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 21727
#BEGIN_POSE_ENERGIES_TABLE A3_full-OAZ1_N-trunc_0009.pdb
Ignored bad PDB record found on line 21728
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega fa_dun
p_aa_pp yhh_planarity ref rama_prepro cart_bonded total
Ignored bad PDB record found on line 21729
weights 1 0.55 1 0.005 1 1 1 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 0.5 NA
Ignored bad PDB record found on line 21730
pose -8342.82 835.552 4700.04 18.9827 228.62 -212.212 -2635.55 -623.123
-300.969 -262.172 -242.384 -0.93833 19.7511 1352.03 -288.768 1.81732 655.338
-99.8253 675.911 -4520.72
1367 messages similar to the above omitted
Chain information for A3_full-OAZ1_N-trunc_0009_best.pdb #5
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> matchmakee #1 #5
Unknown command: matchmakee #1 #5
> matchmakee #1, #5
Unknown command: matchmakee #1, #5
> matchmakee #1 and #5
Unknown command: matchmakee #1 and #5
> matchmaker #1 and #5
Expected a keyword
> matchmaker #1 #5
Missing required "to" argument
> matchmaker #1, #5
Missing or invalid "matchAtoms" argument: only initial part "#1" of atom
specifier valid
> matchmaker #2 to #5
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 A3_full-OAZ1_N-trunc_0009_best.pdb, chain A (#5) with
fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2), sequence
alignment score = 2693.2
RMSD between 699 pruned atom pairs is 1.229 angstroms; (across all 1113 pairs:
5.931)
> matchmaker #2 to #5
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 A3_full-OAZ1_N-trunc_0009_best.pdb, chain A (#5) with
fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2), sequence
alignment score = 2693.2
RMSD between 699 pruned atom pairs is 1.229 angstroms; (across all 1113 pairs:
5.931)
> matchmaker #2 to #4
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 fold_fly_oaz1_atp13a3_shorteraz1_shortera3_model_2.cif, chain A
(#4) with fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2),
sequence alignment score = 2596.7
RMSD between 727 pruned atom pairs is 1.203 angstroms; (across all 1146 pairs:
18.869)
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_catp6_oaz1_celegans_shortaz1_model_3.cif, chain A (#1) with
fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2), sequence
alignment score = 3396.8
RMSD between 948 pruned atom pairs is 0.860 angstroms; (across all 1124 pairs:
4.359)
> show #2 models
> show #3 models
> show #4 models
> hide #1 models
> hide #2 models
> hide #3 models
> hide #4 models
> show #4 models
> matchmaker #4 to #5
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 A3_full-OAZ1_N-trunc_0009_best.pdb, chain A (#5) with
fold_fly_oaz1_atp13a3_shorteraz1_shortera3_model_2.cif, chain A (#4), sequence
alignment score = 3007.7
RMSD between 547 pruned atom pairs is 1.077 angstroms; (across all 1173 pairs:
10.910)
> show #3 models
> show #1 models
> show #2 models
> matchmaker #4 to #2
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 fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2) with
fold_fly_oaz1_atp13a3_shorteraz1_shortera3_model_2.cif, chain A (#4), sequence
alignment score = 2596.7
RMSD between 727 pruned atom pairs is 1.203 angstroms; (across all 1146 pairs:
18.869)
> matchmaker #5 to #2
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 fold_catp5_oaz1_celegans_shortaz1_model_1.cif, chain A (#2) with
A3_full-OAZ1_N-trunc_0009_best.pdb, chain A (#5), sequence alignment score =
2693.2
RMSD between 699 pruned atom pairs is 1.229 angstroms; (across all 1113 pairs:
5.931)
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> hide #1 models
> select add #2
12309 atoms, 12567 bonds, 1566 residues, 3 models selected
> select add #3
25280 atoms, 25845 bonds, 3177 residues, 3 models selected
> select add #4
37283 atoms, 38145 bonds, 4684 residues, 3 models selected
> select subtract #4
24335 atoms, 24881 bonds, 3056 residues, 2 models selected
> select subtract #3
10432 atoms, 10648 bonds, 1324 residues, 1 model selected
> select subtract #2
Nothing selected
> show #1 models
> show #2 models
> show #3 models
> show #4 models
> show #5 models
> hide #1 models
> show #1 models
> hide #4 models
> hide #3 models
> hide #2 models
> hide #1 models
> select #5/A:1-1226
19526 atoms, 19751 bonds, 1226 residues, 1 model selected
> color #5 #718bdeff
> select add #5
21713 atoms, 21961 bonds, 1364 residues, 1 model selected
> select subtract #5
Nothing selected
> select #5/B:1-138
2187 atoms, 2210 bonds, 138 residues, 1 model selected
> color sel #f99c1c
> select add #5
21713 atoms, 21961 bonds, 1364 residues, 1 model selected
> select subtract #5
Nothing selected
> cartoon style width 1.5 thickness 0.5
> lighting soft
> lighting shadows true intensity 0.5
> graphics silhouettes true width 8
> set bgColor white
> save /Users/casano0002/ATP13A3_canonicalOrganismshuman.png width 6000 height
> 6000 supersample 3
Unsupported scale factor (0.000000) detected on Display0
[Repeated 5 time(s)]
Unsupported scale factor (0.000000) detected on Display1
[Repeated 5 time(s)]Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
> save /Users/casano0002/Models_ATP13A3-AZ1_yeast_worm_fly.cxs
——— End of log from Mon Jun 8 08:35:03 2026 ———
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,7
Model Number: Z1AF001PSSM/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 Performance and 6 Efficiency)
Memory: 18 GB
System Firmware Version: 18000.101.7
OS Loader Version: 18000.101.7
Software:
System Software Overview:
System Version: macOS 26.4 (25E246)
Kernel Version: Darwin 25.4.0
Time since boot: 28 days, 1 hour, 32 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 4
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
P27q-30:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 70.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
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: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
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: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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