![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 hours ago
#20185 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-26.3.1-arm64-arm-64bit
ChimeraX Version: 1.12.dev202602272329 (2026-02-27 23:29:28 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 240000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac16,12",
"coalitionID" : 22669,
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"build" : "25D771280a",
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"captureTime" : "2026-04-18 00:25:18.1368 +0800",
"codeSigningMonitor" : 2,
"incident" : "5DBCDD2C-6D39-4059-88A2-513FDA11FD58",
"pid" : 32961,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-04-18 00:21:15.6462 +0800",
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"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "BE64E9E1-898A-A967-633B-6B4CC5D02D8E",
"lowPowerMode" : 1,
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["assetIsNotReady","notOptedIn"]},
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"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
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"wakeTime" : 14867,
"sleepWakeUUID" : "ECEEBE94-3EB7-4114-BEFB-32D9D9B3E362",
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"vmRegionInfo" : "0x609c3d is not in any region. Bytes before following region: 4335428547
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 102ca0000-102ca4000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000609c3d","rawCodes":[1,6331453],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000609c3d"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":32961},
"vmregioninfo" : "0x609c3d is not in any region. Bytes before following region: 4335428547
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
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===== Log before crash start =====
UCSF ChimeraX version: 1.12.dev202602272329 (2026-02-27)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/donna/Downloads/SMLo203_446925.sdf
> ui tool show "Minimize Structure"
> minimize #1
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Deleting residues with incomplete backbones
Summary of feedback from adding hydrogens to SMLo203_446925.sdf #1
---
notes | Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
42 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue UNL (net charge +0) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/lt/lzx73w3j113f2gjdvdzckrfc0000gn/T/tmpuy0279tn/ante.in.mol2 -fi
mol2 -o
/var/folders/lt/lzx73w3j113f2gjdvdzckrfc0000gn/T/tmpuy0279tn/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n
(UNL) ``
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`
(UNL) ``
(UNL) `Info: Finished reading file
(/var/folders/lt/lzx73w3j113f2gjdvdzckrfc0000gn/T/tmpuy0279tn/ante.in.mol2);
atoms read (82), bonds read (81).`
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(UNL) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(UNL) ``
(UNL) ``
(UNL) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(UNL) `Info: Total number of electrons: 282; net charge: 0`
(UNL) ``
(UNL) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(UNL) `/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(UNL) `Cannot properly run
"/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`
Charges failed to converge using fast method; re-running using slower more
stable method
Running ANTECHAMBER command:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/lt/lzx73w3j113f2gjdvdzckrfc0000gn/T/tmpuy0279tn/ante.in.mol2 -fi
mol2 -o
/var/folders/lt/lzx73w3j113f2gjdvdzckrfc0000gn/T/tmpuy0279tn/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n
(UNL) ``
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`
(UNL) ``
(UNL) `Info: Finished reading file
(/var/folders/lt/lzx73w3j113f2gjdvdzckrfc0000gn/T/tmpuy0279tn/ante.in.mol2);
atoms read (82), bonds read (81).`
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(UNL) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(UNL) ``
(UNL) ``
(UNL) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(UNL) `Info: Total number of electrons: 282; net charge: 0`
(UNL) ``
(UNL) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =101
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-09 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-06
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 202
| QMMM: diag iterations used for timing = 4
| QMMM:
| QMMM: Internal diag routine = 0.054608 seconds
| QMMM: Dspev diag routine = 0.046360 seconds
| QMMM: Dspevd diag routine = 0.036300 seconds
| QMMM: Dspevx diag routine = 0.161682 seconds
| QMMM: Dsyev diag routine = 0.050421 seconds
| QMMM: Dsyevd diag routine = 0.038188 seconds
| QMMM: Dsyevr diag routine = 0.043460 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.026265 seconds
| QMMM:
| QMMM: Using dspevd routine (diag_routine=3).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 C 4.6740 -5.6080 0.0000
QMMM: 2 2 C 15.9190 -6.1170 0.0000
QMMM: 3 3 C 8.1280 -5.6080 0.0000
QMMM: 4 4 C 12.4390 -6.1170 0.0000
QMMM: 5 5 C 5.5310 -6.1170 0.0000
QMMM: 6 6 C 15.0360 -5.6080 0.0000
QMMM: 7 7 C 1.1930 -5.6080 0.0000
QMMM: 8 8 C 19.3730 -6.1170 0.0000
QMMM: 9 9 C 7.2710 -6.1170 0.0000
QMMM: 10 10 C 13.3220 -5.6080 0.0000
QMMM: 11 11 C 3.7910 -6.1170 0.0000
QMMM: 12 12 C 16.7760 -5.6080 0.0000
QMMM: 13 13 C 6.3880 -5.6080 0.0000
QMMM: 14 14 C 14.1790 -6.1170 0.0000
QMMM: 15 15 C 8.9850 -6.1170 0.0000
QMMM: 16 16 C 11.5820 -5.6080 0.0000
QMMM: 17 17 C 2.0770 -6.1170 0.0000
QMMM: 18 18 C 18.4900 -5.6080 0.0000
QMMM: 19 19 C 2.9340 -5.6080 0.0000
QMMM: 20 20 C 17.6330 -6.1170 0.0000
QMMM: 21 21 C 9.8410 -5.6080 0.0000
QMMM: 22 22 C 10.7250 -6.1170 0.0000
QMMM: 23 23 C 0.3370 -6.1170 0.0000
QMMM: 24 24 C 20.2030 -5.6080 0.0000
QMMM: 25 25 C -0.5200 -5.6080 0.0000
QMMM: 26 26 C 21.0600 -6.1170 0.0000
QMMM: 27 27 C 4.6740 -4.6170 0.0000
QMMM: 28 28 C 15.9190 -7.1070 0.0000
QMMM: 29 29 C 8.1280 -4.6170 0.0000
QMMM: 30 30 C 12.4390 -7.1070 0.0000
QMMM: 31 31 C 1.1930 -4.6170 0.0000
QMMM: 32 32 C 19.3730 -7.1070 0.0000
QMMM: 33 33 C -1.3770 -6.1170 0.0000
QMMM: 34 34 C 21.9170 -5.6080 0.0000
QMMM: 35 35 C -2.2610 -5.6080 0.0000
QMMM: 36 36 C 22.8000 -6.1170 0.0000
QMMM: 37 37 C -3.1170 -6.1170 0.0000
QMMM: 38 38 C 23.6570 -5.6080 0.0000
QMMM: 39 39 C -2.2610 -4.6170 0.0000
QMMM: 40 40 C 22.8000 -7.1070 0.0000
QMMM: 41 41 H 5.5310 -7.1970 0.0000
QMMM: 42 42 H 15.0290 -4.5280 0.0000
QMMM: 43 43 H 7.2780 -7.1970 0.0000
QMMM: 44 44 H 13.3290 -4.5280 0.0000
QMMM: 45 45 H 3.7830 -7.1970 0.0000
QMMM: 46 46 H 16.7760 -4.5280 0.0000
QMMM: 47 47 H 6.3800 -4.5280 0.0000
QMMM: 48 48 H 14.1790 -7.1970 0.0000
QMMM: 49 49 H 8.9850 -7.1970 0.0000
QMMM: 50 50 H 11.5820 -4.5280 0.0000
QMMM: 51 51 H 2.0840 -7.1970 0.0000
QMMM: 52 52 H 18.4820 -4.5280 0.0000
QMMM: 53 53 H 2.9340 -4.5280 0.0000
QMMM: 54 54 H 17.6330 -7.1970 0.0000
QMMM: 55 55 H 9.8340 -4.5280 0.0000
QMMM: 56 56 H 10.7320 -7.1970 0.0000
QMMM: 57 57 H 0.3370 -7.1970 0.0000
QMMM: 58 58 H 20.1960 -4.5280 0.0000
QMMM: 59 59 H -0.5200 -4.5280 0.0000
QMMM: 60 60 H 21.0600 -7.1970 0.0000
QMMM: 61 61 H -1.3700 -7.1970 0.0000
QMMM: 62 62 H 21.9100 -4.5280 0.0000
QMMM: 63 63 H 5.6090 -4.0770 -0.0000
QMMM: 64 64 H 3.7390 -4.0770 0.0000
QMMM: 65 65 H 14.9840 -7.6470 -0.0000
QMMM: 66 66 H 16.8550 -7.6470 0.0000
QMMM: 67 67 H 7.1930 -4.0770 0.0000
QMMM: 68 68 H 9.0630 -4.0770 -0.0000
QMMM: 69 69 H 13.3740 -7.6470 0.0000
QMMM: 70 70 H 11.5030 -7.6470 -0.0000
QMMM: 71 71 H 2.1290 -4.0770 -0.0000
QMMM: 72 72 H 0.2580 -4.0770 0.0000
QMMM: 73 73 H 18.4380 -7.6470 -0.0000
QMMM: 74 74 H 20.3090 -7.6470 0.0000
QMMM: 75 75 H -3.1040 -7.1970 0.0000
QMMM: 76 76 H -4.0590 -5.5880 -0.0000
QMMM: 77 77 H 23.6440 -4.5280 0.0000
QMMM: 78 78 H 24.5990 -6.1370 -0.0000
QMMM: 79 79 H -1.3250 -4.0770 -0.0000
QMMM: 80 80 H -3.1960 -4.0770 0.0000
QMMM: 81 81 H 21.8650 -7.6470 -0.0000
QMMM: 82 82 H 23.7360 -7.6470 0.0000
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
iter sqm energy rms gradient
---- ------------------- -----------------------
xmin 10 1633.2016 kcal/mol 35.7562 kcal/(mol*A)
xmin 20 846.0589 kcal/mol 3.8322 kcal/(mol*A)
xmin 30 762.0414 kcal/mol 2.1330 kcal/(mol*A)
xmin 40 730.5680 kcal/mol 2.2927 kcal/(mol*A)
xmin 50 671.5491 kcal/mol 6.7086 kcal/(mol*A)
xmin 60 629.5589 kcal/mol 1.8236 kcal/(mol*A)
xmin 70 626.6628 kcal/mol 0.1957 kcal/(mol*A)
xmin 80 625.1995 kcal/mol 0.1411 kcal/(mol*A)
xmin 90 624.2291 kcal/mol 0.4960 kcal/(mol*A)
xmin 100 621.5184 kcal/mol 1.0584 kcal/(mol*A)
xmin 110 617.4799 kcal/mol 0.8248 kcal/(mol*A)
xmin 120 596.1212 kcal/mol 8.6728 kcal/(mol*A)
xmin 130 533.2602 kcal/mol 0.9423 kcal/(mol*A)
xmin 140 530.4349 kcal/mol 0.2842 kcal/(mol*A)
xmin 150 530.1604 kcal/mol 0.2357 kcal/(mol*A)
xmin 160 530.0195 kcal/mol 0.1657 kcal/(mol*A)
xmin 170 529.9881 kcal/mol 0.1197 kcal/(mol*A)
xmin 180 529.8287 kcal/mol 0.2995 kcal/(mol*A)
xmin 190 529.6802 kcal/mol 0.0872 kcal/(mol*A)
xmin 200 529.5337 kcal/mol 0.1256 kcal/(mol*A)
xmin 210 529.4721 kcal/mol 0.1244 kcal/(mol*A)
xmin 220 529.4255 kcal/mol 0.1028 kcal/(mol*A)
xmin 230 529.3477 kcal/mol 0.0626 kcal/(mol*A)
Failure running ANTECHAMBER for residue UNL
Check reply log for details
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.12.dev202602272329 (2026-02-27)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PySide6 6.10.1, Qt 6.10.1
Qt runtime version: 6.10.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac16,12
Model Number: MC6T4PP/A
Chip: Apple M4
Total Number of Cores: 10 (4 Performance and 6 Efficiency)
Memory: 16 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3.1 (a) (25D771280a)
Kernel Version: Darwin 25.3.0
Time since boot: 8 days, 1 hour, 24 minutes
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
accessible-pygments: 0.0.5
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: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.1.0
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: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
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: 1.64.1
ChimeraX-AtomicLibrary: 14.2.3
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: 1.4.1
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: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12.dev202602272329
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: 1.2
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: 1.8.2
ChimeraX-Label: 1.3
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
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: 0.2.0
ChimeraX-MDcrds: 2.18
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.5
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
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: 1.0.1
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: 1.15.4
ChimeraX-OpenFold: 1.0
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: 1.5.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8
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: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.5
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-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
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: 1.50.3
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.1
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: 7.13.4
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.20
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: 7.1.0
ipython: 9.9.0
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: 8.8.0
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: 6.7.1
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: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.6
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: 4.9.2
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: 2.13.1
pydantic_core: 2.41.5
pydata-sphinx-theme: 0.16.1
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.0
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
PySide6: 6.10.1
PySide6_Addons: 6.10.1
PySide6_Essentials: 6.10.1
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.22
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.1
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
shiboken6: 6.10.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
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: 3.3.2
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: 0.41.0
wcwidth: 0.6.0
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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