![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 months ago
Closed 3 months ago
#18220 closed defect (nonchimerax)
Unsupported scale factor detected on Display
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.5-x86_64-i386-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff854fbbdc0 (most recent call first):
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2859 in draw_elements
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1754 in draw
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 857 in _draw_geometry
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 791 in draw_self
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 784 in draw
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1572 in _draw_multiple
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1559 in draw_opaque
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 259 in _draw_scene
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 169 in update_graphics_now
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 153 in resizeEvent
File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 61 in event
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, 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, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, PIL._imaging, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.mlp._mlp, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md (total: 58)
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{
"uptime" : 200000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,3",
"coalitionID" : 545,
"osVersion" : {
"train" : "macOS 15.5",
"build" : "24F74",
"releaseType" : "User"
},
"captureTime" : "2025-07-16 22:26:59.9291 +0300",
"codeSigningMonitor" : 0,
"incident" : "E9C4B1A6-1BD0-42E3-A236-5A0EEE1367D3",
"pid" : 448,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-07-07 16:09:38.1276 +0300",
"procStartAbsTime" : 31385530048,
"procExitAbsTime" : 207922389746244,
"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"},
"storeInfo" : {"deviceIdentifierForVendor":"F4B220C0-9A94-58A8-AA36-FB27CFA9E514","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "5E77A5C3-E224-84D4-9057-DD3C9F3B543E",
"lowPowerMode" : 1,
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["deviceNotCapable"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"bootSessionUUID" : "9F124BF7-9BEA-4CA5-92D1-F7133902A84F",
"wakeTime" : 22,
"bridgeVersion" : {"build":"22P5072","train":"9.5"},
"sleepWakeUUID" : "CB731815-44B7-4F49-A679-EE1E94222C40",
"sip" : "enabled",
"vmRegionInfo" : "0x5bbb0d000 is not in any region. Bytes after previous region: 19083317249 Bytes before following region: 105528492503040\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n VM_ALLOCATE 14a1c8000-14a3c8000 [ 2048K] rw-\/rw- SM=PRV \n---> GAP OF 0x5ffeb5c38000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00000005bbb0d000","rawCodes":[1,24623763456],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000005bbb0d000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":448},
"vmregioninfo" : "0x5bbb0d000 is not in any region. Bytes after previous region: 19083317249 Bytes before following region: 105528492503040\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n VM_ALLOCATE 14a1c8000-14a3c8000 [ 2048K] rw-\/rw- SM=PRV \n---> GAP OF 0x5ffeb5c38000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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"name" : "dyld"
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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.
How to cite UCSF ChimeraX
> open /Users/ioannisliakos/apixaban.sdf
PubChem entry 10182969
> open /Users/ioannisliakos/apixaban.pdbqt
Summary of feedback from opening /Users/ioannisliakos/apixaban.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES COc1ccc(-n2nc(C(N)=O)c3c2C(=O)N(c2ccc(N4CCCCC4=O)cc2)CC3)cc1
Ignored bad PDB record found on line 2
REMARK SMILES IDX 16 1 17 2 7 3 8 4 32 5 31 6 13 7 14 8 15 9 9 10 18 11 19 12
Ignored bad PDB record found on line 3
REMARK SMILES IDX 30 13 20 14 29 15 21 16 22 17 23 18 27 19 24 20 26 21 25 22
Ignored bad PDB record found on line 4
REMARK SMILES IDX 28 23 6 24 5 25 33 26 4 27 34 28 3 29 2 30 1 31 10 32 11 33
Ignored bad PDB record found on line 5
REMARK SMILES IDX 12 34
14 messages similar to the above omitted
Opened apixaban.pdbqt containing 1 structures (36 atoms, 40 bonds)
> close session
> open /Users/ioannisliakos/apixaban.pdbqt format pdbqt
Summary of feedback from opening /Users/ioannisliakos/apixaban.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES COc1ccc(-n2nc(C(N)=O)c3c2C(=O)N(c2ccc(N4CCCCC4=O)cc2)CC3)cc1
Ignored bad PDB record found on line 2
REMARK SMILES IDX 16 1 17 2 7 3 8 4 32 5 31 6 13 7 14 8 15 9 9 10 18 11 19 12
Ignored bad PDB record found on line 3
REMARK SMILES IDX 30 13 20 14 29 15 21 16 22 17 23 18 27 19 24 20 26 21 25 22
Ignored bad PDB record found on line 4
REMARK SMILES IDX 28 23 6 24 5 25 33 26 4 27 34 28 3 29 2 30 1 31 10 32 11 33
Ignored bad PDB record found on line 5
REMARK SMILES IDX 12 34
14 messages similar to the above omitted
Opened apixaban.pdbqt containing 1 structures (36 atoms, 40 bonds)
> close session
> open /Users/ioannisliakos/apixaban.pdbqt
Summary of feedback from opening /Users/ioannisliakos/apixaban.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES COc1ccc(-n2nc(C(N)=O)c3c2C(=O)N(c2ccc(N4CCCCC4=O)cc2)CC3)cc1
Ignored bad PDB record found on line 2
REMARK SMILES IDX 16 1 17 2 7 3 8 4 32 5 31 6 13 7 14 8 15 9 9 10 18 11 19 12
Ignored bad PDB record found on line 3
REMARK SMILES IDX 30 13 20 14 29 15 21 16 22 17 23 18 27 19 24 20 26 21 25 22
Ignored bad PDB record found on line 4
REMARK SMILES IDX 28 23 6 24 5 25 33 26 4 27 34 28 3 29 2 30 1 31 10 32 11 33
Ignored bad PDB record found on line 5
REMARK SMILES IDX 12 34
14 messages similar to the above omitted
Opened apixaban.pdbqt containing 1 structures (36 atoms, 40 bonds)
> open /Users/ioannisliakos/protein.cif
protein.cif title:
Bovine factor xa [more info...]
Chain information for protein.cif #2
---
Chain | Description | UniProt
H | FACTOR XA | FA10_BOVIN 16-251
I | ANTICOAGULANT PEPTIDE | TAP_ORNMO 501-560
L | FACTOR XA | FA10_BOVIN 389-439
> show atoms
> hide atoms
> show atoms
> hbonds reveal true
314 hydrogen bonds found
> coulombic
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
protein.cif #2/I ILE 560 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue UNL (net charge -23) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/p2/v2dkd8912y93gkpm3g51t5xh0000gn/T/tmpcm0_y4qs/ante.in.mol2 -fi
mol2 -o
/var/folders/p2/v2dkd8912y93gkpm3g51t5xh0000gn/T/tmpcm0_y4qs/ante.out.mol2 -fo
mol2 -c bcc -nc -23 -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/p2/v2dkd8912y93gkpm3g51t5xh0000gn/T/tmpcm0_y4qs/ante.in.mol2);
atoms read (36), bonds read (40).`
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(UNL) `Running:
/Applications/ChimeraX-1.10.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-1.10.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(UNL) `Info: Total number of electrons: 242; net charge: -23`
(UNL) ``
(UNL) `Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(UNL) `/Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(UNL) `Cannot properly run
"/Applications/ChimeraX-1.10.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-1.10.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/p2/v2dkd8912y93gkpm3g51t5xh0000gn/T/tmpcm0_y4qs/ante.in.mol2 -fi
mol2 -o
/var/folders/p2/v2dkd8912y93gkpm3g51t5xh0000gn/T/tmpcm0_y4qs/ante.out.mol2 -fo
mol2 -c bcc -nc -23 -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/p2/v2dkd8912y93gkpm3g51t5xh0000gn/T/tmpcm0_y4qs/ante.in.mol2);
atoms read (36), bonds read (40).`
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(UNL) `Running:
/Applications/ChimeraX-1.10.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-1.10.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(UNL) `Info: Total number of electrons: 242; net charge: -23`
(UNL) ``
(UNL) `Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(UNL) `/Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(UNL) `Cannot properly run
"/Applications/ChimeraX-1.10.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 = 87
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| 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 = 138
| QMMM: diag iterations used for timing = 10
| QMMM:
| QMMM: Internal diag routine = 0.046114 seconds
| QMMM: Dspev diag routine = 0.045616 seconds
| QMMM: Dspevd diag routine = 0.035222 seconds
| QMMM: Dspevx diag routine = 0.147825 seconds
| QMMM: Dsyev diag routine = 0.047784 seconds
| QMMM: Dsyevd diag routine = 0.037968 seconds
| QMMM: Dsyevr diag routine = 0.040192 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.019469 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 O 1.2870 0.2980 0.3540
QMMM: 2 2 N -0.1430 0.1640 -1.5100
QMMM: 3 3 N 3.6330 -0.1240 -1.4430
QMMM: 4 4 N 4.3330 -0.2460 -2.5640
QMMM: 5 5 C 0.8320 -0.2980 -3.7820
QMMM: 6 6 C -0.2230 0.4710 -2.9550
QMMM: 7 7 C 2.1690 -0.2720 -3.0990
QMMM: 8 8 C 2.3170 -0.1370 -1.7470
QMMM: 9 9 C 1.1560 0.1040 -0.8840
QMMM: 10 10 C 3.4640 -0.3590 -3.5930
QMMM: 11 11 C -1.3420 0.1240 -0.7090
QMMM: 12 12 C -2.3750 1.0550 -0.9160
QMMM: 13 13 C -1.4970 -0.8580 0.2840
QMMM: 14 14 C -3.5360 1.0080 -0.1400
QMMM: 15 15 C -2.6580 -0.9040 1.0600
QMMM: 16 16 C -3.6820 0.0310 0.8570
QMMM: 17 17 N -4.8790 -0.0280 1.6520
QMMM: 18 18 C -5.7760 -1.1780 1.4660
QMMM: 19 19 C -5.2950 1.1210 2.4240
QMMM: 20 20 C -6.7330 -1.3530 2.6470
QMMM: 21 21 C -6.4690 1.0410 3.3590
QMMM: 22 22 C -7.4610 -0.0420 2.9360
QMMM: 23 23 O -4.6160 2.1840 2.3980
QMMM: 24 24 C 4.2450 -0.0150 -0.1510
QMMM: 25 25 C 5.2690 0.9170 0.0620
QMMM: 26 26 C 3.8820 -0.8860 0.8870
QMMM: 27 27 C 5.8960 1.0080 1.3080
QMMM: 28 28 C 4.5070 -0.7960 2.1340
QMMM: 29 29 C 5.5140 0.1500 2.3580
QMMM: 30 30 O 6.1090 0.2030 3.6270
QMMM: 31 31 C 7.1400 1.1140 3.9940
QMMM: 32 32 C 3.8980 -0.5190 -4.9930
QMMM: 33 33 N 3.0580 -1.1310 -5.9730
QMMM: 34 34 O 5.0520 -0.1390 -5.3230
QMMM: 35 35 H 2.1940 -1.6470 -5.7020
QMMM: 36 36 H 3.3660 -1.1720 -6.9700
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
iter sqm energy rms gradient
---- ------------------- -----------------------
xmin 10 14313.8072 kcal/mol 47.2185 kcal/(mol*A)
xmin 20 13572.6741 kcal/mol 30.9471 kcal/(mol*A)
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.8137E+06 DeltaE = 0.1581E+03 DeltaP = 0.3720E+00
QMMM: Smallest DeltaE = 0.3492E-09 DeltaP = 0.1505E-05 Step = 3
Failure running ANTECHAMBER for residue UNL Check reply log for details
> ui tool show ViewDockX
No suitable models found for ViewDockX
> ui tool show "Cage Builder"
> select add #1
36 atoms, 40 bonds, 1 residue, 1 model selected
> select add #2
2792 atoms, 2866 bonds, 314 pseudobonds, 353 residues, 3 models selected
> select subtract #2
36 atoms, 40 bonds, 1 residue, 1 model selected
> select add #2
2792 atoms, 2866 bonds, 314 pseudobonds, 353 residues, 3 models selected
> style sel ball
Changed 2792 atom styles
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
Errors may have occurred when running pip:
pip standard error:
\---
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.
nptyping 2.5.0 requires numpy=1.20.0; python_version >= "3.8", but you
have numpy 2.2.6 which is incompatible.
chimerax-bundlebuilder 1.5.1 requires numpy==1.26.4, but you have numpy 2.2.6
which is incompatible.
\---
pip standard output:
\---
\---
pyKVFinder module installed from PyPi repository.
No structures chosen
> close session
> open /Users/ioannisliakos/protein.cif format mmcif
protein.cif title:
Bovine factor xa [more info...]
Chain information for protein.cif #1
---
Chain | Description | UniProt
H | FACTOR XA | FA10_BOVIN 16-251
I | ANTICOAGULANT PEPTIDE | TAP_ORNMO 501-560
L | FACTOR XA | FA10_BOVIN 389-439
> open /Users/ioannisliakos/apixaban.pdbqt
Summary of feedback from opening /Users/ioannisliakos/apixaban.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES COc1ccc(-n2nc(C(N)=O)c3c2C(=O)N(c2ccc(N4CCCCC4=O)cc2)CC3)cc1
Ignored bad PDB record found on line 2
REMARK SMILES IDX 16 1 17 2 7 3 8 4 32 5 31 6 13 7 14 8 15 9 9 10 18 11 19 12
Ignored bad PDB record found on line 3
REMARK SMILES IDX 30 13 20 14 29 15 21 16 22 17 23 18 27 19 24 20 26 21 25 22
Ignored bad PDB record found on line 4
REMARK SMILES IDX 28 23 6 24 5 25 33 26 4 27 34 28 3 29 2 30 1 31 10 32 11 33
Ignored bad PDB record found on line 5
REMARK SMILES IDX 12 34
14 messages similar to the above omitted
Opened apixaban.pdbqt containing 1 structures (36 atoms, 40 bonds)
> close session
> open /Users/ioannisliakos/apixaban.sdf format sdf
PubChem entry 10182969
> open /Users/ioannisliakos/protein.cif
protein.cif title:
Bovine factor xa [more info...]
Chain information for protein.cif #2
---
Chain | Description | UniProt
H | FACTOR XA | FA10_BOVIN 16-251
I | ANTICOAGULANT PEPTIDE | TAP_ORNMO 501-560
L | FACTOR XA | FA10_BOVIN 389-439
> select add #1
59 atoms, 63 bonds, 1 residue, 1 model selected
> select add #2
2815 atoms, 2889 bonds, 353 residues, 2 models selected
> select subtract #1
2756 atoms, 2826 bonds, 352 residues, 1 model selected
> select subtract #2
Nothing selected
> color resist & C gold target al
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color resist & C gold target al
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color resist & C gold target al
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color resist & C gold target al
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> view #1 clip false
> log metadata #1
The model has no metadata
> log chains #1
> hide #1 target m
> close #1
> hide target m
> show target m
> view clip false
> close session
> open /Users/ioannisliakos/protein.cif format mmcif
protein.cif title:
Bovine factor xa [more info...]
Chain information for protein.cif #1
---
Chain | Description | UniProt
H | FACTOR XA | FA10_BOVIN 16-251
I | ANTICOAGULANT PEPTIDE | TAP_ORNMO 501-560
L | FACTOR XA | FA10_BOVIN 389-439
> open /Users/ioannisliakos/apixaban.pdbqt
Summary of feedback from opening /Users/ioannisliakos/apixaban.pdbqt
---
warnings | Ignored bad PDB record found on line 1
REMARK SMILES COc1ccc(-n2nc(C(N)=O)c3c2C(=O)N(c2ccc(N4CCCCC4=O)cc2)CC3)cc1
Ignored bad PDB record found on line 2
REMARK SMILES IDX 16 1 17 2 7 3 8 4 32 5 31 6 13 7 14 8 15 9 9 10 18 11 19 12
Ignored bad PDB record found on line 3
REMARK SMILES IDX 30 13 20 14 29 15 21 16 22 17 23 18 27 19 24 20 26 21 25 22
Ignored bad PDB record found on line 4
REMARK SMILES IDX 28 23 6 24 5 25 33 26 4 27 34 28 3 29 2 30 1 31 10 32 11 33
Ignored bad PDB record found on line 5
REMARK SMILES IDX 12 34
14 messages similar to the above omitted
Opened apixaban.pdbqt containing 1 structures (36 atoms, 40 bonds)
> select add #1
2756 atoms, 2826 bonds, 352 residues, 1 model selected
> select add #2
2792 atoms, 2866 bonds, 353 residues, 2 models selected
> hbonds sel reveal true
314 hydrogen bonds found
> hbonds sel reveal true
314 hydrogen bonds found
> hbonds sel reveal true
314 hydrogen bonds found
> hbonds sel reveal true
314 hydrogen bonds found
> hbonds sel reveal true
314 hydrogen bonds found
> hbonds sel reveal true
314 hydrogen bonds found
> select add #3
2792 atoms, 2866 bonds, 314 pseudobonds, 353 residues, 3 models selected
> log metadata #1
Metadata for protein.cif #1
---
Title | Bovine factor xa
Citation | Wei, A., Alexander, R.S., Duke, J., Ross, H., Rosenfeld, S.A., Chang, C.H. (1998). Unexpected binding mode of tick anticoagulant peptide complexed to bovine factor Xa. J.Mol.Biol., 283, 147-154. PMID: 9761680. DOI: 10.1006/jmbi.1998.2069
Gene sources | Bos taurus (cattle)
Ornithodoros moubata
Experimental method | X-ray diffraction
Resolution | 3.0Å
> log chains #1
Chain information for protein.cif #1
---
Chain | Description | UniProt
H | FACTOR XA | FA10_BOVIN 16-251
I | ANTICOAGULANT PEPTIDE | TAP_ORNMO 501-560
L | FACTOR XA | FA10_BOVIN 389-439
> log metadata #2
The model has no metadata
> log chains #2
> ui tool show "Selection Inspector"
> ui tool show AlphaFold
> ui tool show "Model Loops"
Populating font family aliases took 139 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
No alignments chosen for modeling
> mlp sel
Map values for surface "protein.cif_H SES surface": minimum -28.3, mean
-5.656, maximum 23.86
Map values for surface "protein.cif_I SES surface": minimum -24.89, mean
-5.436, maximum 22.79
Map values for surface "protein.cif_L SES surface": minimum -28.46, mean
-6.549, maximum 22.48
To also show corresponding color key, enter the above mlp command and add key
true
> mlp sel
Map values for surface "protein.cif_H SES surface": minimum -28.3, mean
-5.656, maximum 23.86
Map values for surface "protein.cif_I SES surface": minimum -24.89, mean
-5.436, maximum 22.79
Map values for surface "protein.cif_L SES surface": minimum -28.46, mean
-6.549, maximum 22.48
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
protein.cif #1/I ILE 560 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue UNL (net charge -23) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/p2/v2dkd8912y93gkpm3g51t5xh0000gn/T/tmpge1j8mc_/ante.in.mol2 -fi
mol2 -o
/var/folders/p2/v2dkd8912y93gkpm3g51t5xh0000gn/T/tmpge1j8mc_/ante.out.mol2 -fo
mol2 -c bcc -nc -23 -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/p2/v2dkd8912y93gkpm3g51t5xh0000gn/T/tmpge1j8mc_/ante.in.mol2);
atoms read (36), bonds read (40).`
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(UNL) `Running:
/Applications/ChimeraX-1.10.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-1.10.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(UNL) `Info: Total number of electrons: 242; net charge: -23`
(UNL) ``
(UNL) `Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(UNL) `/Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(UNL) `Cannot properly run
"/Applications/ChimeraX-1.10.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-1.10.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/p2/v2dkd8912y93gkpm3g51t5xh0000gn/T/tmpge1j8mc_/ante.in.mol2 -fi
mol2 -o
/var/folders/p2/v2dkd8912y93gkpm3g51t5xh0000gn/T/tmpge1j8mc_/ante.out.mol2 -fo
mol2 -c bcc -nc -23 -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/p2/v2dkd8912y93gkpm3g51t5xh0000gn/T/tmpge1j8mc_/ante.in.mol2);
atoms read (36), bonds read (40).`
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(UNL) `Running:
/Applications/ChimeraX-1.10.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-1.10.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(UNL) `Info: Total number of electrons: 242; net charge: -23`
(UNL) ``
(UNL) `Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(UNL) `/Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`
(UNL) `Cannot properly run
"/Applications/ChimeraX-1.10.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 = 87
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| 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 = 138
| QMMM: diag iterations used for timing = 10
| QMMM:
| QMMM: Internal diag routine = 0.047597 seconds
| QMMM: Dspev diag routine = 0.045833 seconds
| QMMM: Dspevd diag routine = 0.036427 seconds
| QMMM: Dspevx diag routine = 0.162946 seconds
| QMMM: Dsyev diag routine = 0.049110 seconds
| QMMM: Dsyevd diag routine = 0.040425 seconds
| QMMM: Dsyevr diag routine = 0.042580 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.021267 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 O 1.2870 0.2980 0.3540
QMMM: 2 2 N -0.1430 0.1640 -1.5100
QMMM: 3 3 N 3.6330 -0.1240 -1.4430
QMMM: 4 4 N 4.3330 -0.2460 -2.5640
QMMM: 5 5 C 0.8320 -0.2980 -3.7820
QMMM: 6 6 C -0.2230 0.4710 -2.9550
QMMM: 7 7 C 2.1690 -0.2720 -3.0990
QMMM: 8 8 C 2.3170 -0.1370 -1.7470
QMMM: 9 9 C 1.1560 0.1040 -0.8840
QMMM: 10 10 C 3.4640 -0.3590 -3.5930
QMMM: 11 11 C -1.3420 0.1240 -0.7090
QMMM: 12 12 C -2.3750 1.0550 -0.9160
QMMM: 13 13 C -1.4970 -0.8580 0.2840
QMMM: 14 14 C -3.5360 1.0080 -0.1400
QMMM: 15 15 C -2.6580 -0.9040 1.0600
QMMM: 16 16 C -3.6820 0.0310 0.8570
QMMM: 17 17 N -4.8790 -0.0280 1.6520
QMMM: 18 18 C -5.7760 -1.1780 1.4660
QMMM: 19 19 C -5.2950 1.1210 2.4240
QMMM: 20 20 C -6.7330 -1.3530 2.6470
QMMM: 21 21 C -6.4690 1.0410 3.3590
QMMM: 22 22 C -7.4610 -0.0420 2.9360
QMMM: 23 23 O -4.6160 2.1840 2.3980
QMMM: 24 24 C 4.2450 -0.0150 -0.1510
QMMM: 25 25 C 5.2690 0.9170 0.0620
QMMM: 26 26 C 3.8820 -0.8860 0.8870
QMMM: 27 27 C 5.8960 1.0080 1.3080
QMMM: 28 28 C 4.5070 -0.7960 2.1340
QMMM: 29 29 C 5.5140 0.1500 2.3580
QMMM: 30 30 O 6.1090 0.2030 3.6270
QMMM: 31 31 C 7.1400 1.1140 3.9940
QMMM: 32 32 C 3.8980 -0.5190 -4.9930
QMMM: 33 33 N 3.0580 -1.1310 -5.9730
QMMM: 34 34 O 5.0520 -0.1390 -5.3230
QMMM: 35 35 H 2.1940 -1.6470 -5.7020
QMMM: 36 36 H 3.3660 -1.1720 -6.9700
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
iter sqm energy rms gradient
---- ------------------- -----------------------
xmin 10 14313.8072 kcal/mol 47.2185 kcal/(mol*A)
xmin 20 13572.6741 kcal/mol 30.9471 kcal/(mol*A)
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.8137E+06 DeltaE = 0.1581E+03 DeltaP = 0.3720E+00
QMMM: Smallest DeltaE = 0.3492E-09 DeltaP = 0.1505E-05 Step = 3
Failure running ANTECHAMBER for residue UNL Check reply log for details
> rainbow sel
> color bfactor sel
2792 atoms, 353 residues, 3 surfaces, atom bfactor range 0 to 20
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select add #1
2756 atoms, 2826 bonds, 314 pseudobonds, 352 residues, 2 models selected
> select add #2
2792 atoms, 2866 bonds, 314 pseudobonds, 353 residues, 6 models selected
> color resist & C gold target al
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> gtgtgtterw
Unknown command: gtgtgtterw
> gtgtgtterwmodels
Unknown command: gtgtgtterwmodels
> alphafold match #1/H
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Fetching compressed AlphaFold P00743 from
https://alphafold.ebi.ac.uk/files/AF-P00743-F1-model_v3.cif
1 AlphaFold model found using UniProt identifier: P00743 (chain H)
AlphaFold prediction matching protein.cif
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
H | P00743 | FA10_BOVIN | 3.37 | 241 | 241 | 100
Opened 1 AlphaFold model
> alphafold match #1/H
1 AlphaFold model found using UniProt identifier: P00743 (chain H)
AlphaFold prediction matching protein.cif
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
H | P00743 | FA10_BOVIN | 3.37 | 241 | 241 | 100
Opened 1 AlphaFold model
> alphafold match #1/H
1 AlphaFold model found using UniProt identifier: P00743 (chain H)
AlphaFold prediction matching protein.cif
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
H | P00743 | FA10_BOVIN | 3.37 | 241 | 241 | 100
Opened 1 AlphaFold model
> alphafold predict #1/H
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
> alphafold predict #1/H
Running AlphaFold prediction
Alphafold prediction send sequence to Google Colab returned: None
Running AlphaFold prediction
> alphafold predict #1/H
Running AlphaFold prediction
No alignments chosen for modeling
Unsupported scale factor (0.000000) detected on Display0
Unsupported scale factor (0.000000) detected on Display1
===== Log before crash end =====
Log:
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-23.0.26
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.
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: MacBookPro16,3
Processor Name: Quad-Core Intel Core i5
Processor Speed: 1.4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2075.120.2.0.0 (iBridge: 22.16.15072.0.0,0)
OS Loader Version: 583~1350
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 9 ημέρες, 6 ώρες, 19 λεπτά
Graphics/Displays:
Intel Iris Plus Graphics 645:
Chipset Model: Intel Iris Plus Graphics 645
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea6
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:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
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: 14.1.18
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
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: 1.1.2
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: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
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: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
narwhals: 1.47.0
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: 2.2.6
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
plotly: 6.0.1
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
pyelftools: 0.32
Pygments: 2.18.0
pyKVFinder: 0.8.1
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
tomlkit: 0.13.2
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
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
Change History (2)
comment:1 by , 3 months ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Unsupported scale factor detected on Display |
comment:2 by , 3 months ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
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The crash was a typical Apple Intel graphics driver crash. I don't think is related to the unsupported display scale factor warnings which are a long-standing Qt bug but not one that seems to cause crashes.