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Opened 9 hours ago
#20048 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-15.7.4-x86_64-i386-64bit
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.
Fatal Python error: Segmentation fault
Thread 0x0000700012a89000 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007ff84cbea100 (most recent call first):
File "/Applications/ChimeraX-1.10.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-1.10.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-1.10.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, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 59)
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{
"uptime" : 740000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,2",
"coalitionID" : 38279,
"osVersion" : {
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"build" : "24G517",
"releaseType" : "User"
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"captureTime" : "2026-03-22 19:41:36.2664 +0800",
"codeSigningMonitor" : 0,
"incident" : "80CA67DA-1DB4-43F1-B595-1F21E4A78F75",
"pid" : 73224,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2026-03-22 19:39:30.1693 +0800",
"procStartAbsTime" : 744879951891103,
"procExitAbsTime" : 745006007912147,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "C6C3E8A4-6727-9870-8970-EC4AA6F74003",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["deviceNotCapable"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"bootSessionUUID" : "B276BCA6-3E33-4BBB-AA11-99E9A0D1D5A5",
"wakeTime" : 35401,
"bridgeVersion" : {"build":"23P3120","train":"10.3"},
"sleepWakeUUID" : "D7559D67-038E-4B02-A271-8017932DDD2D",
"sip" : "enabled",
"vmRegionInfo" : "0x574f62eabf4e is not in any region. Bytes after previous region: 95992426684239 Bytes before following region: 9554642682034
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
VM_ALLOCATE 167ae3000-1686c6000 [ 11.9M] rw-\/rwx SM=PRV
---> GAP OF 0x5ffe9793a000 BYTES
MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000574f62eabf4e","rawCodes":[1,95998473584462],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000574f62eabf4e"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":73224},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter
VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter
VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter
VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter
VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter
",
"vmregioninfo" : "0x574f62eabf4e is not in any region. Bytes after previous region: 95992426684239 Bytes before following region: 9554642682034
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
VM_ALLOCATE 167ae3000-1686c6000 [ 11.9M] rw-\/rwx SM=PRV
---> GAP OF 0x5ffe9793a000 BYTES
MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"name" : "libsystem_c.dylib"
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Activity Tracing 256K 1
CG image 128K 13
ColorSync 260K 32
CoreAnimation 972K 88
CoreGraphics 20K 3
CoreUI image data 3236K 24
Foundation 16K 1
IOKit 7940K 1
Kernel Alloc Once 8K 1
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MALLOC guard page 48K 12
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mapped file 592.9M 91
shared memory 3536K 32
=========== ======= =======
TOTAL 6.0G 4692
TOTAL, minus reserved VM space 5.9G 4692
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===== Log before crash start =====
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP_hide_RNA.cxs
Log from Sun Mar 22 19:39:27 2026UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP_hide_RNA.cxs
Log from Sun Mar 22 19:38:33 2026UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP_hide_RNA.cxs
Log from Sun Mar 22 19:37:03 2026UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP_hide_RNA.cxs
Log from Sun Mar 22 19:24:28 2026UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP_hide_RNA.cxs
Log from Sun Mar 22 19:23:49 2026UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP_hide_RNA.cxs
Log from Sun Mar 22 19:22:59 2026UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP.cxs
Log from Sun Mar 22 19:20:36 2026UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP.cxs
Log from Sun Mar 22 19:17:00 2026UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP.cxs
Log from Sun Mar 22 18:58:50 2026UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP.cxs
Log from Sun Mar 22 18:57:12 2026UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/zln/Documents/CEMCS/Chen_Lab/Projects/RNase/Structures_AF3_predicted/fold_human_rnase_mrp_predicted/fold_human_rnase_mrp_predicted_model_0.cif
Chain information for fold_human_rnase_mrp_predicted_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
H I | .
J | .
K | .
L | .
> open
> "/Users/zln/Documents/CEMCS/Chen_Lab/Projects/RNase/Structures_published/7C79_yeast
> RNase MRP alone.cif"
7C79_yeast RNase MRP alone.cif title:
Cryo-EM structure of yeast Ribonuclease MRP [more info...]
Chain information for 7C79_yeast RNase MRP alone.cif #2
---
Chain | Description | UniProt
A | Ribonuclease MRP RNA subunit NME1 |
B | Ribonucleases P/MRP protein subunit POP1 | POP1_YEAST 1-875
C | Ribonucleases P/MRP protein subunit POP3 | POP3_YEAST 1-195
D | RNases MRP/P 32.9 kDa subunit | POP4_YEAST 1-279
E | Ribonuclease P/MRP protein subunit POP5 | POP5_YEAST 1-173
F | Ribonucleases P/MRP protein subunit POP6 | POP6_YEAST 1-158
G | Ribonucleases P/MRP protein subunit POP7 | POP7_YEAST 1-140
H | Ribonucleases P/MRP protein subunit POP8 | POP8_YEAST 1-133
I J | Ribonuclease P/MRP protein subunit RPP1 | RPP1_YEAST 1-293
K | Ribonuclease MRP protein subunit SNM1 | RMRP_YEAST 1-198
L | Ribonuclease MRP protein subunit RMP1 | RMP1_YEAST 1-201
Non-standard residues in 7C79_yeast RNase MRP alone.cif #2
---
MG — magnesium ion
ZN — zinc ion
> open
> "/Users/zln/Documents/CEMCS/Chen_Lab/Projects/RNase/Structures_published/6AHR_Atomic
> model of human RNase P holoenzyme.cif"
6AHR_Atomic model of human RNase P holoenzyme.cif title:
Cryo-EM structure of human Ribonuclease P [more info...]
Chain information for 6AHR_Atomic model of human RNase P holoenzyme.cif #3
---
Chain | Description | UniProt
A | H1 RNA |
B | Ribonucleases P/MRP protein subunit POP1 | POP1_HUMAN 1-1024
C | Ribonuclease P protein subunit p38 | RPP38_HUMAN 1-283
D | Ribonuclease P protein subunit p29 | RPP29_HUMAN 1-220
E | Ribonuclease P/MRP protein subunit POP5 | POP5_HUMAN 1-163
F | Ribonuclease P protein subunit p25 | RPP25_HUMAN 1-199
G | Ribonuclease P protein subunit p20 | POP7_HUMAN 1-140
H | Ribonuclease P protein subunit p14 | RPP14_HUMAN 1-124
I J | Ribonuclease P protein subunit p30 | RPP30_HUMAN 1-268
K | Ribonuclease P protein subunit p21 | RPP21_HUMAN 1-154
L | Ribonuclease P protein subunit p40 | RPP40_HUMAN 1-363
Non-standard residues in 6AHR_Atomic model of human RNase P holoenzyme.cif #3
---
ZN — zinc ion
> show cartoons
Computing secondary structure
> hide atoms
> view
> ui tool show Matchmaker
> 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_human_rnase_mrp_predicted_model_0.cif, chain L (#1) with
7C79_yeast RNase MRP alone.cif, chain A (#2), sequence alignment score =
1136.5
RMSD between 27 pruned atom pairs is 1.213 angstroms; (across all 264 pairs:
36.419)
> set bgColor white
> graphics silhouettes true
> save /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP.cxs
——— End of log from Sun Mar 22 18:57:12 2026 ———
> view name session-start
opened ChimeraX session
> ui tool show Matchmaker
> matchmaker #!3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_human_rnase_mrp_predicted_model_0.cif, chain A (#1) with
6AHR_Atomic model of human RNase P holoenzyme.cif, chain B (#3), sequence
alignment score = 4594.2
RMSD between 517 pruned atom pairs is 1.204 angstroms; (across all 774 pairs:
3.265)
> color #1 white
> color #3 #fffb00ff
> color #2 #0096ffff
> hide #!3 models
> save /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP.cxs
——— End of log from Sun Mar 22 18:58:50 2026 ———
> view name session-start
opened ChimeraX session
> hide #!2 models
> show #!3 models
> open
> /Users/zln/Documents/CEMCS/Chen_Lab/Projects/RNase/Structures_AF3_predicted/fold_human_rnase_p_predicted/fold_human_rnase_p_predicted_model_0.cif
Chain information for fold_human_rnase_p_predicted_model_0.cif #4
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
H | .
I | .
J | .
K | .
L | .
> show #1,4#!3 cartoons
Computing secondary structure
> show #1,4#!3 cartoons
> hide #1,4#!3 atoms
> color #4 #d4fb79ff
> color #4 #7a81ffff
> save /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP.cxs
——— End of log from Sun Mar 22 19:17:00 2026 ———
> view name session-start
opened ChimeraX session
> open
> "/Users/zln/Documents/CEMCS/Chen_Lab/Projects/RNase/Structures_published/7C79_yeast
> RNase MRP alone.cif"
7C79_yeast RNase MRP alone.cif title:
Cryo-EM structure of yeast Ribonuclease MRP [more info...]
Chain information for 7C79_yeast RNase MRP alone.cif #5
---
Chain | Description | UniProt
A | Ribonuclease MRP RNA subunit NME1 |
B | Ribonucleases P/MRP protein subunit POP1 | POP1_YEAST 1-875
C | Ribonucleases P/MRP protein subunit POP3 | POP3_YEAST 1-195
D | RNases MRP/P 32.9 kDa subunit | POP4_YEAST 1-279
E | Ribonuclease P/MRP protein subunit POP5 | POP5_YEAST 1-173
F | Ribonucleases P/MRP protein subunit POP6 | POP6_YEAST 1-158
G | Ribonucleases P/MRP protein subunit POP7 | POP7_YEAST 1-140
H | Ribonucleases P/MRP protein subunit POP8 | POP8_YEAST 1-133
I J | Ribonuclease P/MRP protein subunit RPP1 | RPP1_YEAST 1-293
K | Ribonuclease MRP protein subunit SNM1 | RMRP_YEAST 1-198
L | Ribonuclease MRP protein subunit RMP1 | RMP1_YEAST 1-201
Non-standard residues in 7C79_yeast RNase MRP alone.cif #5
---
MG — magnesium ion
ZN — zinc ion
> color #5 #ff8ad8ff
> show #1,4#!3,5 cartoons
> hide #1,4#!3,5 atoms
> ui tool show Matchmaker
> matchmaker #!5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_human_rnase_mrp_predicted_model_0.cif, chain L (#1) with
7C79_yeast RNase MRP alone.cif, chain A (#5), sequence alignment score =
1136.5
RMSD between 27 pruned atom pairs is 1.213 angstroms; (across all 264 pairs:
36.419)
> save /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP.cxs
——— End of log from Sun Mar 22 19:20:36 2026 ———
> view name session-start
opened ChimeraX session
> close #5
> save /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP.cxs
> save /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP_hide_RNA.cxs
——— End of log from Sun Mar 22 19:22:59 2026 ———
> view name session-start
opened ChimeraX session
> hide #!3 models
> hide #4 models
> hide #1/L cartoons
> save /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP_hide_RNA.cxs
> hide #1 models
> show #!2 models
> hide #2/A cartoons
> save /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP_hide_RNA.cxs
——— End of log from Sun Mar 22 19:23:49 2026 ———
> view name session-start
opened ChimeraX session
> show #!3 models
> hide #!2 models
> hide #3/A cartoons
> save /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP_hide_RNA.cxs
——— End of log from Sun Mar 22 19:24:28 2026 ———
> view name session-start
opened ChimeraX session
> ui tool show Matchmaker
> matchmaker #4 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_human_rnase_mrp_predicted_model_0.cif, chain A (#1) with
fold_human_rnase_p_predicted_model_0.cif, chain F (#4), sequence alignment
score = 5190
RMSD between 728 pruned atom pairs is 0.610 angstroms; (across all 1024 pairs:
18.331)
> hide #4/L cartoons
> save /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP_hide_RNA.cxs
——— End of log from Sun Mar 22 19:37:03 2026 ———
> view name session-start
opened ChimeraX session
> open
> "/Users/zln/Documents/CEMCS/Chen_Lab/Projects/RNase/Structures_published/6AGB_Atomic
> model of yeast Ribonuclease P.cif"
6AGB_Atomic model of yeast Ribonuclease P.cif title:
Cryo-EM structure of yeast Ribonuclease P [more info...]
Chain information for 6AGB_Atomic model of yeast Ribonuclease P.cif #5
---
Chain | Description | UniProt
A | Ribonuclease P RNA |
B | Ribonucleases P/MRP protein subunit POP1 | POP1_YEAST 1-875
C | Ribonucleases P/MRP protein subunit POP3 | POP3_YEAST 1-195
D | RNases MRP/P 32.9 kDa subunit | POP4_YEAST 1-279
E | Ribonuclease P/MRP protein subunit POP5 | POP5_YEAST 1-173
F | Ribonucleases P/MRP protein subunit POP6 | POP6_YEAST 1-158
G | Ribonucleases P/MRP protein subunit POP7 | POP7_YEAST 1-140
H | Ribonucleases P/MRP protein subunit POP8 | POP8_YEAST 1-133
I J | Ribonuclease P/MRP protein subunit RPP1 | RPP1_YEAST 1-293
K | Ribonuclease P protein subunit RPR2 | RPR2_YEAST 1-144
Non-standard residues in 6AGB_Atomic model of yeast Ribonuclease P.cif #5
---
ZN — zinc ion
> color #5 #ff8ad8ff
> show #!3,5 cartoons
> hide #!3,5 atoms
> undo
[Repeated 1 time(s)]
> hide #!3 models
> view
> show #!5 cartoons
> hide #!5 atoms
> save /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP_hide_RNA.cxs
——— End of log from Sun Mar 22 19:38:33 2026 ———
> view name session-start
opened ChimeraX session
> hide #5/A cartoons
> save /Users/zln/Desktop/Predicted_AF3_Human_RNase_MRP_hide_RNA.cxs
——— End of log from Sun Mar 22 19:39:27 2026 ———
> view name session-start
opened ChimeraX session
> ui tool show Matchmaker
> matchmaker #!5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_human_rnase_mrp_predicted_model_0.cif, chain L (#1) with
6AGB_Atomic model of yeast Ribonuclease P.cif, chain A (#5), sequence
alignment score = 1093.3
RMSD between 3 pruned atom pairs is 1.237 angstroms; (across all 265 pairs:
76.149)
> show #1 models
> ui tool show Matchmaker
> matchmaker #!5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_human_rnase_mrp_predicted_model_0.cif, chain L (#1) with
6AGB_Atomic model of yeast Ribonuclease P.cif, chain A (#5), sequence
alignment score = 1093.3
RMSD between 3 pruned atom pairs is 1.237 angstroms; (across all 265 pairs:
76.149)
> view
> select add #5
27190 atoms, 28468 bonds, 311 pseudobonds, 2774 residues, 4 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.15905,-0.6674,-0.72752,219.67,-0.31736,0.73235,-0.60245,74.989,0.93487,0.13506,-0.32829,-137.69
> view matrix models
> #5,0.46648,-0.88453,-0.00084201,26.91,-0.33422,-0.17538,-0.92603,278.17,0.81896,0.43226,-0.37744,-157.66
> view matrix models
> #5,0.13569,0.58569,0.7991,-285.35,-0.8636,0.46523,-0.19434,146.01,-0.48558,-0.66373,0.56892,90.816
> view matrix models
> #5,-0.12308,0.56332,0.81702,-239.77,-0.56463,0.63729,-0.52446,120.49,-0.81612,-0.52586,0.23963,179.94
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.12308,0.56332,0.81702,-212.33,-0.56463,0.63729,-0.52446,71.882,-0.81612,-0.52586,0.23963,195.75
> select subtract #5
Nothing selected
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-23.7.4
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
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: MacBookPro15,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.8 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2094.80.5.0.0 (iBridge: 23.16.13120.0.0,0)
OS Loader Version: 583~2317
Software:
System Software Overview:
System Version: macOS 15.7.4 (24G517)
Kernel Version: Darwin 24.6.0
Time since boot: 20天11小时24分钟
Graphics/Displays:
Intel Iris Plus Graphics 655:
Chipset Model: Intel Iris Plus Graphics 655
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea5
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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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