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Opened 14 hours ago
#19225 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-15.6-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x000000020a6c20c0 (most recent call first):
File "/Applications/ChimeraX-1.10.1.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-1.10.1.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-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.connect_structure._cs, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw (total: 49)
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{
"uptime" : 7900,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac15,6",
"coalitionID" : 2666,
"osVersion" : {
"train" : "macOS 15.6",
"build" : "24G84",
"releaseType" : "User"
},
"captureTime" : "2025-10-22 13:34:33.8499 +0100",
"codeSigningMonitor" : 1,
"incident" : "BB7C9884-06A9-458A-A22E-8F7203C0ED39",
"pid" : 9401,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-10-22 13:29:48.2159 +0100",
"procStartAbsTime" : 183526734298,
"procExitAbsTime" : 190381369327,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.1","CFBundleVersion":"1.10.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"7402F86B-9DEA-5E38-BB7D-57D332FCCDA6","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "E88225B7-A589-69A2-7948-9F12CCCBC7C9",
"lowPowerMode" : 1,
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "7815F654-1A8C-4B31-9CBB-87779553527D",
"wakeTime" : 1164,
"sleepWakeUUID" : "76433C01-A61E-4016-B0FC-3F90EDF4D474",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"termination" : {"flags":0,"code":6,"namespace":"SIGNAL","indicator":"Abort trap: 6","byProc":"ChimeraX","byPid":9401},
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===== Log before crash start =====
> set bgColor white
> cofr centerOfView
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/c.lewis.2/job036.cif format mmcif
Summary of feedback from opening /Users/c.lewis.2/job036.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for job036.cif #1
---
Chain | Description
A0 | No description available
A1 A2 A4 A5 A6 A8 A9 Ab Ac Ad Ae Af Ag Ai Aj Ak Al Am An Ao Ap As Au Ay Az | No description available
A3 A7 Aaa | No description available
Aa Aa4 Aa6 Aa8 Aab Aad Aae Aaf Aag Aai Aaj Aak Aam Aao Aap Aar Ah Ax | No description available
Aa0 | No description available
Aa1 Aa2 Aax Aay Aaz Ac2 Acm Acp Acq Act Acx Acz | No description available
Aa3 Adc Add Adh Adi | No description available
Aa5 Aal Aan Aaq Aas | No description available
Aa7 Aa9 Aba | No description available
Aac | No description available
Aah | No description available
Aat Ab0 Abd Abe Abh Abi Abj Abn Abr Abx Acg | No description available
Aau Aav Ab1 Ab2 Ab3 Ab4 Ab5 Abc Abf Abg Abk Abl Abm Abo Abp Abq Abs Abt Abu Abv Abw Aby Abz Acf Aci Acj Acl | No description available
Aaw | No description available
Ab6 Ac0 Ac1 Ac6 Ac7 Ac8 Acr Acs Acu Acw | No description available
Ab7 Ab8 Ab9 Ac3 Acn Aco Acv Acy | No description available
Abb | No description available
Ac4 Ac5 Ad1 Ady | No description available
Ac9 | No description available
Aca Acb Adl Adw Adx | No description available
Acc Acd Ad2 Ad3 Ad4 Ad5 Adf Adg Adq Adr Adu | No description available
Ace | No description available
Ach | No description available
Ack | No description available
Ad0 Adm Adt Adv | No description available
Ad6 | No description available
Ad7 | No description available
Ada | No description available
Adb Ads | No description available
Ade | No description available
Adj | No description available
Adk Adn Adp | No description available
Ado Ar Aw | No description available
Adz | No description available
Aq | No description available
At | No description available
Av | No description available
B0 | No description available
B1 | No description available
B2 | No description available
B3 | No description available
B4 | No description available
B5 | No description available
B6 | No description available
B7 | No description available
B8 | No description available
B9 | No description available
Ba | No description available
Ba0 | No description available
Ba1 | No description available
Ba2 | No description available
Ba3 | No description available
Ba4 | No description available
Ba5 | No description available
Ba6 | No description available
Ba7 | No description available
Ba8 | No description available
Ba9 | No description available
Baa | No description available
Bab | No description available
Bac | No description available
Bad | No description available
Bae | No description available
Baf | No description available
Bag | No description available
Bah | No description available
Bai | No description available
Baj | No description available
Bak | No description available
Bal | No description available
Bam | No description available
Ban | No description available
Bao | No description available
Bap | No description available
Baq | No description available
Bar | No description available
Bas | No description available
Bat | No description available
Bau | No description available
Bav | No description available
Baw | No description available
Bax | No description available
Bay | No description available
Baz | No description available
Bb | No description available
Bb0 | No description available
Bb1 | No description available
Bb2 | No description available
Bb3 | No description available
Bb4 | No description available
Bb5 | No description available
Bb6 | No description available
Bb7 | No description available
Bb8 | No description available
Bb9 | No description available
Bba | No description available
Bbb | No description available
Bbc | No description available
Bbd | No description available
Bbe | No description available
Bbf | No description available
Bbg | No description available
Bbh | No description available
Bbi | No description available
Bbj | No description available
Bbk | No description available
Bbl | No description available
Bbm | No description available
Bbn | No description available
Bbo | No description available
Bbp | No description available
Bbq | No description available
Bbr | No description available
Bbs | No description available
Bbt | No description available
Bbu | No description available
Bbv | No description available
Bbw | No description available
Bbx | No description available
Bby | No description available
Bbz | No description available
Bc | No description available
Bc0 | No description available
Bc1 | No description available
Bc2 | No description available
Bc3 | No description available
Bc4 | No description available
Bc5 | No description available
Bc6 | No description available
Bc7 | No description available
Bc8 Biv | No description available
Bc9 | No description available
Bca | No description available
Bcb | No description available
Bcc | No description available
Bcd | No description available
Bce | No description available
Bcf | No description available
Bcg | No description available
Bch | No description available
Bci Bd4 | No description available
Bcj | No description available
Bck | No description available
Bcl | No description available
Bcm | No description available
Bcn | No description available
Bco | No description available
Bcp | No description available
Bcq | No description available
Bcr | No description available
Bcs | No description available
Bct | No description available
Bcu | No description available
Bcv | No description available
Bcw | No description available
Bcx | No description available
Bcy | No description available
Bcz | No description available
Bd | No description available
Bd0 | No description available
Bd1 | No description available
Bd2 | No description available
Bd3 | No description available
Bd5 | No description available
Bd6 | No description available
Bd7 | No description available
Bd8 | No description available
Bd9 | No description available
Bda | No description available
Bdb | No description available
Bdc | No description available
Bdd | No description available
Bde | No description available
Bdf | No description available
Bdg | No description available
Bdh | No description available
Bdi | No description available
Bdj | No description available
Bdk | No description available
Bdl | No description available
Bdm | No description available
Bdn | No description available
Bdo | No description available
Bdp | No description available
Bdq | No description available
Bdr | No description available
Bds | No description available
Bdt | No description available
Bdu | No description available
Bdv | No description available
Bdw | No description available
Bdx | No description available
Bdy | No description available
Bdz | No description available
Be | No description available
Be0 | No description available
Be1 | No description available
Be2 | No description available
Be3 | No description available
Be4 | No description available
Be5 | No description available
Be6 | No description available
Be7 | No description available
Be8 | No description available
Be9 | No description available
Bea | No description available
Beb | No description available
Bec | No description available
Bed | No description available
Bee | No description available
Bef | No description available
Beg | No description available
Beh | No description available
Bei | No description available
Bej | No description available
Bek | No description available
Bel | No description available
Bem | No description available
Ben | No description available
Beo | No description available
Bep | No description available
Beq | No description available
Ber | No description available
Bes | No description available
Bet | No description available
Beu | No description available
Bev | No description available
Bew | No description available
Bex | No description available
Bey | No description available
Bez | No description available
Bf | No description available
Bf0 | No description available
Bf1 | No description available
Bf2 | No description available
Bf3 | No description available
Bf4 Bg7 Bhi | No description available
Bf6 | No description available
Bf7 | No description available
Bf8 | No description available
Bfa | No description available
Bfb | No description available
Bfc | No description available
Bfd | No description available
Bfe | No description available
Bff | No description available
Bfg | No description available
Bfh | No description available
Bfi Bfw | No description available
Bfj | No description available
Bfk | No description available
Bfl | No description available
Bfm | No description available
Bfn | No description available
Bfo | No description available
Bfp | No description available
Bfr | No description available
Bfs | No description available
Bft | No description available
Bfu | No description available
Bfv | No description available
Bfx | No description available
Bfy | No description available
Bfz | No description available
Bg | No description available
Bg0 | No description available
Bg1 | No description available
Bg2 | No description available
Bg3 | No description available
Bg4 | No description available
Bg5 | No description available
Bg6 | No description available
Bg8 | No description available
Bg9 | No description available
Bga | No description available
Bgb | No description available
Bgc | No description available
Bgd | No description available
Bge | No description available
Bgf | No description available
Bgg | No description available
Bgh | No description available
Bgi | No description available
Bgj | No description available
Bgk Biz | No description available
Bgl | No description available
Bgm | No description available
Bgn | No description available
Bgo | No description available
Bgp | No description available
Bgq | No description available
Bgr | No description available
Bgs | No description available
Bgt | No description available
Bgu | No description available
Bgv | No description available
Bgw | No description available
Bgx | No description available
Bgy | No description available
Bgz Bht | No description available
Bh | No description available
Bh0 | No description available
Bh1 | No description available
Bh2 | No description available
Bh3 | No description available
Bh4 | No description available
Bh5 | No description available
Bh6 | No description available
Bh7 | No description available
Bh8 | No description available
Bh9 Bhw Bie | No description available
Bha | No description available
Bhb | No description available
Bhc | No description available
Bhd | No description available
Bhe | No description available
Bhf | No description available
Bhg | No description available
Bhh | No description available
Bhj | No description available
Bhk | No description available
Bhl | No description available
Bhm | No description available
Bhn | No description available
Bho Bhv | No description available
Bhp | No description available
Bhq | No description available
Bhr | No description available
Bhs | No description available
Bhu | No description available
Bhx | No description available
Bhy | No description available
Bhz | No description available
Bi | No description available
Bi0 | No description available
Bi1 | No description available
Bi2 | No description available
Bi3 | No description available
Bi4 | No description available
Bi5 | No description available
Bi6 | No description available
Bi7 | No description available
Bi8 | No description available
Bi9 Bja Bjb Bje Bjf Bji Bjj | No description available
Bia | No description available
Bib | No description available
Bic | No description available
Bid | No description available
Bif | No description available
Big | No description available
Bih | No description available
Bii | No description available
Bij | No description available
Bik Bin | No description available
Bil | No description available
Bim | No description available
Bio | No description available
Bip | No description available
Biq | No description available
Bir | No description available
Bis | No description available
Bit | No description available
Biu | No description available
Biw | No description available
Bix | No description available
Biy | No description available
Bj | No description available
Bjc | No description available
Bjd | No description available
Bjg | No description available
Bjh | No description available
Bjk | No description available
Bjl | No description available
Bjm | No description available
Bk | No description available
Bl | No description available
Bm | No description available
Bn | No description available
Bo | No description available
Bp | No description available
Bq | No description available
Br | No description available
Bs | No description available
Bt | No description available
Bu | No description available
Bv | No description available
Bw | No description available
Bx | No description available
By | No description available
Bz | No description available
Cannot find consistent set of bond orders for ring system containing atom CG
in residue PHE /Bcf:487
Cannot find consistent set of bond orders for ring system containing atom CD2
in residue TRP /Be:384
> show surfaces
Alignment identifier is 1
Computing secondary structure
Alignment identifier is 1/Ba
Alignment identifier is 2
Alignment identifier is 1/Bb
Alignment identifier is 1/Aq
Alignment identifier is 3
Alignment identifier is 1/At
Alignment identifier is 1/Av
Alignment identifier is 1/Bc
Alignment identifier is 1/Bd
Alignment identifier is 1/Be
Alignment identifier is 1/Bf
Alignment identifier is 1/Bg
Alignment identifier is 1/Bh
Alignment identifier is 1/Bi
Alignment identifier is 1/Bj
Alignment identifier is 1/Bk
Alignment identifier is 1/Bl
Alignment identifier is 1/Bm
Alignment identifier is 1/Bn
Alignment identifier is 1/Bo
Alignment identifier is 1/Bp
Alignment identifier is 1/Bq
Alignment identifier is 1/Br
Alignment identifier is 1/Bs
Alignment identifier is 1/Bt
Alignment identifier is 1/Bu
Alignment identifier is 1/Bv
Alignment identifier is 1/Bw
Alignment identifier is 1/Bx
Alignment identifier is 1/By
Alignment identifier is 1/Bz
Alignment identifier is 1/B0
Alignment identifier is 1/B1
Alignment identifier is 1/B2
Alignment identifier is 1/B3
Alignment identifier is 1/B4
Alignment identifier is 1/B5
Alignment identifier is 1/B6
Alignment identifier is 1/B7
Alignment identifier is 1/B8
Alignment identifier is 1/B9
Alignment identifier is 1/Baa
Alignment identifier is 1/Bab
Alignment identifier is 1/Bac
Alignment identifier is 1/Bad
Alignment identifier is 1/Bae
Alignment identifier is 1/Baf
Alignment identifier is 1/Bag
Alignment identifier is 1/Bah
Alignment identifier is 1/Bai
Alignment identifier is 1/Baj
Alignment identifier is 1/Bak
Alignment identifier is 1/Bal
Alignment identifier is 1/Bam
Alignment identifier is 1/Ban
Alignment identifier is 1/Bao
Alignment identifier is 1/Bap
Alignment identifier is 1/Baq
Alignment identifier is 1/Bar
Alignment identifier is 1/Bas
Alignment identifier is 1/Bat
Alignment identifier is 1/Bau
Alignment identifier is 1/Bav
Alignment identifier is 1/Baw
Alignment identifier is 1/Bax
Alignment identifier is 1/Bay
Alignment identifier is 1/Baz
Alignment identifier is 1/Ba0
Alignment identifier is 1/Ba1
Alignment identifier is 1/Ba2
Alignment identifier is 1/Ba3
Alignment identifier is 1/Ba4
Alignment identifier is 1/Ba5
Alignment identifier is 1/Ba6
Alignment identifier is 1/Ba7
Alignment identifier is 1/Ba8
Alignment identifier is 1/Ba9
Alignment identifier is 1/Bba
Alignment identifier is 1/Bbb
Alignment identifier is 1/Bbc
Alignment identifier is 1/Bbd
Alignment identifier is 1/Bbe
Alignment identifier is 1/Bbf
Alignment identifier is 1/Bbg
Alignment identifier is 1/Bbh
Alignment identifier is 1/Bbi
Alignment identifier is 1/Bbj
Alignment identifier is 1/Bbk
Alignment identifier is 1/Bbl
Alignment identifier is 1/Bbm
Alignment identifier is 1/Bbn
Alignment identifier is 1/Bbo
Alignment identifier is 1/Bbp
Alignment identifier is 1/Bbq
Alignment identifier is 1/Bbr
Alignment identifier is 1/Bbs
Alignment identifier is 1/Bbt
Alignment identifier is 1/Bbu
Alignment identifier is 1/Bbv
Alignment identifier is 1/Bbw
Alignment identifier is 1/Bbx
Alignment identifier is 1/Bby
Alignment identifier is 1/Bbz
Alignment identifier is 1/Bb0
Alignment identifier is 1/Bb1
Alignment identifier is 1/Bb2
Alignment identifier is 1/Bb3
Alignment identifier is 1/Bb4
Alignment identifier is 1/Bb5
Alignment identifier is 1/Bb6
Alignment identifier is 1/Bb7
Alignment identifier is 1/Bb8
Alignment identifier is 1/Bb9
Alignment identifier is 1/Bca
Alignment identifier is 1/Bcb
Alignment identifier is 1/Bcc
Alignment identifier is 1/Bcd
Alignment identifier is 1/Bce
Alignment identifier is 1/Bcf
Alignment identifier is 1/Bcg
Alignment identifier is 1/Bch
Alignment identifier is 4
Alignment identifier is 1/Bcj
Alignment identifier is 1/Bck
Alignment identifier is 1/Bcl
Alignment identifier is 1/Bcm
Alignment identifier is 1/Bcn
Alignment identifier is 1/Bco
Alignment identifier is 1/Bcp
Alignment identifier is 1/Bcq
Alignment identifier is 1/Bcr
Alignment identifier is 1/Bcs
Alignment identifier is 1/Bct
Alignment identifier is 1/Bcu
Alignment identifier is 1/Bcv
Alignment identifier is 1/Bcw
Alignment identifier is 1/Bcx
Alignment identifier is 1/Bcy
Alignment identifier is 1/Bcz
Alignment identifier is 1/Bc0
Alignment identifier is 1/Bc1
Alignment identifier is 1/Bc2
Alignment identifier is 1/Bc3
Alignment identifier is 1/Bc4
Alignment identifier is 1/Bc5
Alignment identifier is 1/Bc6
Alignment identifier is 1/Bc7
Alignment identifier is 5
Alignment identifier is 1/Bc9
Alignment identifier is 1/Bda
Alignment identifier is 1/Bdb
Alignment identifier is 1/Bdc
Alignment identifier is 1/Bdd
Alignment identifier is 1/Bde
Alignment identifier is 1/Bdf
Alignment identifier is 1/Bdg
Alignment identifier is 1/Bdh
Alignment identifier is 1/Bdi
Alignment identifier is 1/Bdj
Alignment identifier is 1/Bdk
Alignment identifier is 1/Bdl
Alignment identifier is 1/Bdm
Alignment identifier is 1/Bdn
Alignment identifier is 1/Bdo
Alignment identifier is 1/Bdp
Alignment identifier is 1/Bdq
Alignment identifier is 1/Bdr
Alignment identifier is 1/Bds
Alignment identifier is 1/Bdt
Alignment identifier is 1/Bdu
Alignment identifier is 1/Bdv
Alignment identifier is 1/Bdw
Alignment identifier is 1/A0
Alignment identifier is 6
Alignment identifier is 1/Bdx
Alignment identifier is 1/Bdy
Alignment identifier is 1/Bdz
Alignment identifier is 1/Aac
Alignment identifier is 1/Aah
Alignment identifier is 7
Alignment identifier is 8
Alignment identifier is 9
Alignment identifier is 1/Bd0
Alignment identifier is 1/Bd1
Alignment identifier is 1/Bd2
Alignment identifier is 1/Bd3
Alignment identifier is 1/Bd5
Alignment identifier is 1/Bd6
Alignment identifier is 1/Bd7
Alignment identifier is 1/Bd8
Alignment identifier is 1/Bd9
Alignment identifier is 1/Bea
Alignment identifier is 1/Beb
Alignment identifier is 1/Bec
Alignment identifier is 1/Bed
Alignment identifier is 1/Bee
Alignment identifier is 1/Bef
Alignment identifier is 1/Beg
Alignment identifier is 1/Beh
Alignment identifier is 1/Bei
Alignment identifier is 1/Aaw
Alignment identifier is 1/Bej
Alignment identifier is 1/Bek
Alignment identifier is 1/Bel
Alignment identifier is 10
Alignment identifier is 1/Aa0
Alignment identifier is 1/Bem
Alignment identifier is 1/Ben
Alignment identifier is 1/Beo
Alignment identifier is 1/Bep
Alignment identifier is 1/Beq
Alignment identifier is 1/Ber
Alignment identifier is 1/Bes
Alignment identifier is 1/Bet
Alignment identifier is 1/Beu
Alignment identifier is 1/Bev
Alignment identifier is 1/Bew
Alignment identifier is 1/Bex
Alignment identifier is 1/Bey
Alignment identifier is 11
Alignment identifier is 1/Bez
Alignment identifier is 1/Be0
Alignment identifier is 1/Be1
Alignment identifier is 1/Be2
Alignment identifier is 1/Be3
Alignment identifier is 1/Be4
Alignment identifier is 12
Alignment identifier is 1/Abb
Alignment identifier is 1/Be5
Alignment identifier is 1/Be6
Alignment identifier is 1/Be7
Alignment identifier is 1/Be8
Alignment identifier is 1/Be9
Alignment identifier is 1/Bfa
Alignment identifier is 1/Bfb
Alignment identifier is 1/Bfc
Alignment identifier is 13
Alignment identifier is 14
Alignment identifier is 1/Bfd
Alignment identifier is 1/Bfe
Alignment identifier is 1/Bff
Alignment identifier is 1/Bfg
Alignment identifier is 1/Bfh
Alignment identifier is 15
Alignment identifier is 1/Bfj
Alignment identifier is 1/Bfk
Alignment identifier is 1/Bfl
Alignment identifier is 1/Bfm
Alignment identifier is 1/Bfn
Alignment identifier is 1/Bfo
Alignment identifier is 1/Bfp
Alignment identifier is 1/Bfr
Alignment identifier is 1/Bfs
Alignment identifier is 1/Bft
Alignment identifier is 16
Alignment identifier is 1/Bfu
Alignment identifier is 1/Bfv
Alignment identifier is 1/Bfx
Alignment identifier is 1/Bfy
Alignment identifier is 1/Bfz
Alignment identifier is 1/Bf0
Alignment identifier is 1/Bf1
Alignment identifier is 1/Bf2
Alignment identifier is 1/Bf3
Alignment identifier is 17
Alignment identifier is 1/Bf6
Alignment identifier is 1/Bf7
Alignment identifier is 1/Bf8
Alignment identifier is 1/Bga
Alignment identifier is 1/Bgb
Alignment identifier is 1/Bgc
Alignment identifier is 1/Bgd
Alignment identifier is 1/Bge
Alignment identifier is 1/Bgf
Alignment identifier is 1/Bgg
Alignment identifier is 18
Alignment identifier is 1/Bgh
Alignment identifier is 1/Bgi
Alignment identifier is 1/Bgj
Alignment identifier is 19
Alignment identifier is 1/Bgl
Alignment identifier is 1/Bgm
Alignment identifier is 1/Bgn
Alignment identifier is 1/Bgo
Alignment identifier is 1/Bgp
Alignment identifier is 1/Bgq
Alignment identifier is 1/Bgr
Alignment identifier is 1/Bgs
Alignment identifier is 1/Bgt
Alignment identifier is 1/Bgu
Alignment identifier is 1/Bgv
Alignment identifier is 1/Bgw
Alignment identifier is 1/Ace
Alignment identifier is 1/Bgx
Alignment identifier is 1/Bgy
Alignment identifier is 20
Alignment identifier is 1/Bg0
Alignment identifier is 1/Bg1
Alignment identifier is 1/Ach
Alignment identifier is 1/Ack
Alignment identifier is 1/Bg2
Alignment identifier is 1/Bg3
Alignment identifier is 1/Bg4
Alignment identifier is 1/Bg5
Alignment identifier is 1/Bg6
Alignment identifier is 1/Bg8
Alignment identifier is 1/Bg9
Alignment identifier is 1/Bha
Alignment identifier is 1/Bhb
Alignment identifier is 1/Bhc
Alignment identifier is 1/Bhd
Alignment identifier is 1/Bhe
Alignment identifier is 1/Bhf
Alignment identifier is 1/Bhg
Alignment identifier is 1/Bhh
Alignment identifier is 1/Bhj
Alignment identifier is 1/Bhk
Alignment identifier is 1/Bhl
Alignment identifier is 1/Bhm
Alignment identifier is 1/Bhn
Alignment identifier is 21
Alignment identifier is 1/Bhp
Alignment identifier is 1/Bhq
Alignment identifier is 1/Bhr
Alignment identifier is 1/Bhs
Alignment identifier is 1/Bhu
Alignment identifier is 22
Alignment identifier is 1/Bhx
Alignment identifier is 1/Bhy
Alignment identifier is 23
Alignment identifier is 1/Bhz
Alignment identifier is 1/Bh0
Alignment identifier is 1/Bh1
Alignment identifier is 1/Bh2
Alignment identifier is 1/Bh3
Alignment identifier is 1/Ac9
Alignment identifier is 1/Bh4
Alignment identifier is 1/Bh5
Alignment identifier is 1/Bh6
Alignment identifier is 1/Bh7
Alignment identifier is 1/Bh8
Alignment identifier is 1/Bia
Alignment identifier is 1/Bib
Alignment identifier is 1/Ada
Alignment identifier is 24
Alignment identifier is 1/Bic
Alignment identifier is 1/Bid
Alignment identifier is 1/Bif
Alignment identifier is 1/Ade
Alignment identifier is 1/Adj
Alignment identifier is 1/Big
Alignment identifier is 1/Bih
Alignment identifier is 1/Bii
Alignment identifier is 25
Alignment identifier is 1/Bij
Alignment identifier is 26
Alignment identifier is 1/Bil
Alignment identifier is 1/Bim
Alignment identifier is 1/Bio
Alignment identifier is 1/Bip
Alignment identifier is 1/Biq
Alignment identifier is 27
Alignment identifier is 1/Bir
Alignment identifier is 1/Bis
Alignment identifier is 1/Bit
Alignment identifier is 1/Biu
Alignment identifier is 1/Biw
Alignment identifier is 1/Bix
Alignment identifier is 1/Adz
Alignment identifier is 1/Biy
Alignment identifier is 1/Bi0
Alignment identifier is 1/Bi1
Alignment identifier is 1/Bi2
Alignment identifier is 1/Bi3
Alignment identifier is 1/Bi4
Alignment identifier is 1/Bi5
Alignment identifier is 1/Bi6
Alignment identifier is 1/Bi7
Alignment identifier is 1/Bi8
Alignment identifier is 28
Alignment identifier is 1/Bjc
Alignment identifier is 1/Bjd
Alignment identifier is 1/Ad6
Alignment identifier is 1/Bjg
Alignment identifier is 1/Bjh
Alignment identifier is 1/Bjk
Alignment identifier is 1/Bjl
Alignment identifier is 1/Bjm
Alignment identifier is 1/Ad7
===== Log before crash end =====
Log:
> set bgColor white
> cofr centerOfView
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/c.lewis.2/Desktop/VP2
> paper/Focused_class/VS4_peptide/CC/run_it025_class001.mrc"
Opened run_it025_class001.mrc as #1, grid size 200,200,200, pixel 3.12, shown
at level 7.89e-06, step 1, values float32
> open "/Users/c.lewis.2/Desktop/VP2
> paper/Focused_class/VS4_peptide/CC/run_it025_class002.mrc"
Opened run_it025_class002.mrc as #2, grid size 200,200,200, pixel 3.12, shown
at level 1.62e-05, step 1, values float32
> open "/Users/c.lewis.2/Desktop/VP2
> paper/Focused_class/VS4_peptide/CC/run_it025_class003.mrc"
Opened run_it025_class003.mrc as #3, grid size 200,200,200, pixel 3.12, shown
at level 8.28e-06, step 1, values float32
> open "/Users/c.lewis.2/Desktop/VP2
> paper/Focused_class/VS4_peptide/CC/run_it025_class004.mrc"
Opened run_it025_class004.mrc as #4, grid size 200,200,200, pixel 3.12, shown
at level 1.4e-06, step 1, values float32
> open "/Users/c.lewis.2/Desktop/VP2
> paper/Focused_class/VS4_peptide/CC/run_it025_class005.mrc"
Opened run_it025_class005.mrc as #5, grid size 200,200,200, pixel 3.12, shown
at level 2.84e-06, step 1, values float32
> open "/Users/c.lewis.2/Desktop/VP2
> paper/Focused_class/VS4_peptide/CC/run_it025_class006.mrc"
Opened run_it025_class006.mrc as #6, grid size 200,200,200, pixel 3.12, shown
at level 1.84e-05, step 1, values float32
> open "/Users/c.lewis.2/Desktop/VP2
> paper/Focused_class/VS4_peptide/CC/run_it025_class007.mrc"
Opened run_it025_class007.mrc as #7, grid size 200,200,200, pixel 3.12, shown
at level 2.04e-05, step 1, values float32
> open "/Users/c.lewis.2/Desktop/VP2
> paper/Focused_class/VS4_peptide/CC/run_it025_class008.mrc"
Opened run_it025_class008.mrc as #8, grid size 200,200,200, pixel 3.12, shown
at level 5.79e-06, step 1, values float32
> open "/Users/c.lewis.2/Desktop/VP2
> paper/Focused_class/VS4_peptide/CC/run_it025_class009.mrc"
Opened run_it025_class009.mrc as #9, grid size 200,200,200, pixel 3.12, shown
at level 8.44e-06, step 1, values float32
> open "/Users/c.lewis.2/Desktop/VP2
> paper/Focused_class/VS4_peptide/CC/run_it025_class010.mrc"
Opened run_it025_class010.mrc as #10, grid size 200,200,200, pixel 3.12, shown
at level 1.91e-05, step 1, values float32
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: Z1AU001HUB/A
Chip: Apple M3 Pro
Total Number of Cores: 11 (5 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6 (24G84)
Kernel Version: Darwin 24.6.0
Time since boot: 5 hours, 4 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
HP Z24n G3:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
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
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
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: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
MolecularDynamicsViewer: 1.6
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
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