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Opened 101 minutes ago
#19834 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-26.2-arm64-arm-64bit
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
opened "Build Structure" tool
Fatal Python error: Segmentation fault
Current thread 0x00000001f530ec40 (most recent call first):
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 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, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, markupsafe._speedups, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, psutil._psutil_osx, psutil._psutil_posix, PIL._imaging, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 99)
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"procLaunch" : "2026-02-09 15:24:53.6091 -0800",
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"vmRegionInfo" : "0x8 is not in any region. Bytes before following region: 4339957752
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 102ae8000-102aec000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000008","rawCodes":[1,8],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000008"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":4119},
"vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4339957752
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: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/DOCKING/Cyp3A4/P08684/MANUAL/P450-manual-
> sel.cxs
### ViewDock hotkeys on
If clicked into ViewDock dialog or main 3D graphics area, the following keys
are active:
g/m/b/u
Assign good/maybe/bad/(unrated) rating to chosen compounds
up/down arrow
Move up/down compound list*
Escape
Turn hotkeys off (have to use context menu to re-enable)
*Unless in 3D graphics with a selection, in which case normal selection widening/narrowing happens
Log from Wed Feb 19 15:57:43 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/ak87/ownCloud/owncloud/Calculations/P450/RECEPTOR/Cyp3A4/rec-
> minimized-final.pdb
Summary of feedback from opening
/Users/ak87/ownCloud/owncloud/Calculations/P450/RECEPTOR/Cyp3A4/rec-minimized-
final.pdb
---
warnings | CONECT record to nonexistent atom: (4664, 4678)
CONECT record for nonexistent atom: 4678
rec-minimized-final.pdb title:
6MA7 - 5-removed waters [more info...]
Chain information for rec-minimized-final.pdb #1
---
Chain | Description
A | No description available
Non-standard residues in rec-minimized-final.pdb #1
---
ACE — (ACE)
HEM — protoporphyrin IX containing Fe
NMA — (NMA)
> open
> /Users/ak87/ownCloud/owncloud/Calculations/P450/DOCKING/Cyp3A4/P08684/MANUAL/test.mol2.gz
File reader requires uncompressed file;
'/Users/ak87/ownCloud/owncloud/Calculations/P450/DOCKING/Cyp3A4/P08684/MANUAL/test.mol2.gz'
is compressed
> open
> /Users/ak87/ownCloud/owncloud/Calculations/P450/DOCKING/Cyp3A4/P08684/MANUAL/test.mol2
Opened test.mol2 containing 290 structures (11840 atoms, 12550 bonds)
> viewdockx #2.1-290
> hide #2.1-290 models
> show #2.1 models
JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read
properties of undefined (reading 'id')
> hide #2.1 models
JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read
properties of undefined (reading 'id')
> show #2.251 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
42 atoms, 45 bonds, 1 residue, 1 model selected
> select sel : show sel & #!1 atoms
> view sel
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.05
Changed 12770 bond radii
> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> select clear
> save
> /Users/ak87/ownCloud/owncloud/Calculations/P450/DOCKING/Cyp3A4/P08684/MANUAL/P450-manual-
> sel.cxs
> hide #2.251#!1 cartoons
> open 8SPD
Summary of feedback from opening 8SPD fetched from pdb
---
notes | Fetching compressed mmCIF 8spd from http://files.rcsb.org/download/8spd.cif
Fetching CCD CL6 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/6/CL6/CL6.cif
8spd title:
Cytochrome P450 (CYP) 3A4 crystallized with clotrimazole [more info...]
Chain information for 8spd #3
---
Chain | Description | UniProt
A | Cytochrome P450 3A4 | CP3A4_HUMAN 24-503
Non-standard residues in 8spd #3
---
CL6 — 1-[(2-chlorophenyl)(diphenyl)methyl]-1H-imidazole (clotrimazole)
HEM — protoporphyrin IX containing Fe (HEME)
> mmaker #3 to #1
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
Desktop color scheme is dark
Desktop color scheme is light
Desktop color scheme is dark
Desktop color scheme is light
> ui windowfill toggle
> open smiles:C12C3C4C5C1C1C6C2C2C3C3C4C4C5C1C1C6C2C3C41
Translated SMILES to 3D structure via NCI web service (SMILES:
C12C3C4C5C1C1C6C2C2C3C3C4C4C5C1C1C6C2C3C41)
Drag select of 40 atoms, 50 bonds
> select clear
> select HC
28772 atoms, 1656 residues, 1656 models selected
> delete atoms (#5#3.4 & sel)
> delete bonds (#5#3.4 & sel)
Drag select of 20 atoms, 30 bonds
> ui mousemode right "translate selected models"
> view matrix models #5,1,0,0,-17.198,0,1,0,-16.063,0,0,1,-16.994
> view matrix models #5,1,0,0,-18.738,0,1,0,-18.248,0,0,1,-8.5941
> view matrix models #5,1,0,0,-19.436,0,1,0,-21.881,0,0,1,-9.7245
> ui windowfill toggle
> hide #!3 models
> ui windowfill toggle
> view matrix models #5,1,0,0,-20.164,0,1,0,-21.647,0,0,1,-9.7962
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.99914,0.036516,0.019576,-20.164,-0.036651,0.99931,0.0066042,-21.647,-0.019322,-0.007316,0.99979,-9.7963
> view matrix models
> #5,0.9998,0.011987,-0.016128,-20.164,-0.014308,0.9882,-0.15248,-21.648,0.01411,0.15268,0.98818,-9.7956
> view matrix models
> #5,0.80576,-0.47257,0.35696,-20.165,0.58889,0.70334,-0.39815,-21.648,-0.062911,0.53103,0.84502,-9.7947
> view matrix models
> #5,0.95901,-0.16352,0.23142,-20.164,0.25945,0.8351,-0.48508,-21.648,-0.11394,0.52524,0.84329,-9.7949
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.95901,-0.16352,0.23142,-20.296,0.25945,0.8351,-0.48508,-21.884,-0.11394,0.52524,0.84329,-9.1598
> view sel
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.06
Changed 30 bond radii
> view matrix models
> #5,0.95901,-0.16352,0.23142,-20.243,0.25945,0.8351,-0.48508,-21.969,-0.11394,0.52524,0.84329,-9.1426
> select clear
> ui tool show Distances
> select #2/A:602@C7
1 atom, 1 residue, 1 model selected
> select add #5/?:1@C9
2 atoms, 2 residues, 2 models selected
> distance #2/A:602@C7 #5/?:1@C9
Distance between xtal-lig.pdb #2/A TPF 602 C7 and
smiles:C12C3C4C5C1C1C6C2C2C3C3C4C4C5C1C1C6C2C3C41 #5/? UNL 1 C9: 0.519Å
> select clear
> select add #5/?:1@C1
1 atom, 1 bond, 1 residue, 2 models selected
> select #2/A:602@C6
1 atom, 1 residue, 1 model selected
> select add #5/?:1@C1
2 atoms, 2 residues, 2 models selected
> distance #2/A:602@C6 #5/?:1@C1
Distance between xtal-lig.pdb #2/A TPF 602 C6 and
smiles:C12C3C4C5C1C1C6C2C2C3C3C4C4C5C1C1C6C2C3C41 #5/? UNL 1 C1: 0.943Å
> select clear
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
4615 atoms, 4708 bonds, 472 residues, 1 model selected
> hide sel atoms
> select clear
> hide #5 models
Drag select of 4 atoms, 5 bonds
> ui tool show "Build Structure"
2 models">hide #2.232 models
> show #2.233 models
> hide #2.233 models
> show #2.234 models
> hide #2.234 models
> show #2.235 models
> hide #2.235 models
> show #2.236 models
> hide #2.236 models
> show #2.237 models
> hide #2.237 models
> show #2.238 models
> hide #2.238 models
> show #2.239 models
> hide #2.239 models
> show #2.240 models
> hide #2.240 models
> show #2.1 models
> hide #!4 models
> open 3NXU
3nxu title:
Crystal structure of human cytochrome P4503A4 bound to an inhibitor ritonavir
[more info...]
Chain information for 3nxu #5
---
Chain | Description | UniProt
A B | Cytochrome P450 3A4 | CP3A4_HUMAN 25-503
Non-standard residues in 3nxu #5
---
DMS — dimethyl sulfoxide
HEM — protoporphyrin IX containing Fe (HEME)
RIT — ritonavir (A-84538)
3nxu mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> mmaker #5 to #1
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker rec-minimized-final.pdb, chain A (#1) with 3nxu, chain A (#5),
sequence alignment score = 2362.1
RMSD between 374 pruned atom pairs is 0.875 angstroms; (across all 457 pairs:
1.714)
> hide #2.1#!1,5 cartoons
> hide #2.1 models
> show #2.2 models
> hide #2.2 models
> show #2.3 models
> hide #2.3 models
> show #2.4 models
> hide #2.4 models
> show #2.5 models
> hide #2.5 models
> show #2.6 models
> hide #2.6 models
> show #2.7 models
> hide #2.7 models
> show #2.8 models
> hide #2.8 models
> show #2.9 models
> hide #2.9 models
> show #2.10 models
> hide #2.10 models
> show #2.11 models
> hide #2.11 models
> show #2.10 models
> hide #2.10 models
> show #2.11 models
> hide #2.11 models
> show #2.11 models
> hide #2.11 models
> show #2.11 models
> open 4D6Z
Summary of feedback from opening 4D6Z fetched from pdb
---
notes | Fetching compressed mmCIF 4d6z from http://files.rcsb.org/download/4d6z.cif
Fetching CCD GOL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GOL/GOL.cif
Fetching CCD IMD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/IMD/IMD.cif
Fetching CCD PK9 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/9/PK9/PK9.cif
4d6z title:
Cytochrome P450 3A4 bound to imidazole and an inhibitor [more info...]
Chain information for 4d6z #6
---
Chain | Description | UniProt
A | CYTOCHROME P450 3A4 | CP3A4_HUMAN 23-503
Non-standard residues in 4d6z #6
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
HEM — protoporphyrin IX containing Fe (HEME)
IMD — imidazole
PK9 — tert-butyl {6-oxo-6-[(pyridin-3-ylmethyl)amino]hexyl}carbamate
53 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> mmaker #6 to #1
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker rec-minimized-final.pdb, chain A (#1) with 4d6z, chain A (#6),
sequence alignment score = 2377.1
RMSD between 449 pruned atom pairs is 0.366 angstroms; (across all 460 pairs:
0.618)
> hide #!5 models
> hide #2.11#!1,6 cartoons
> show #!5 models
> hide #!6 models
> hide #2.11 models
> show #2.1 models
> hide #2.1 models
> show #2.2 models
> hide #2.2 models
> show #2.3 models
> hide #2.3 models
> show #2.4 models
> hide #2.4 models
> show #2.5 models
> hide #2.5 models
> show #2.1 models
> hide #2.1 models
> show #2.21 models
> hide #2.21 models
> show #2.21 models
> hide #2.21 models
> show #2.21 models
> show #!6 models
> hide #!5 models
> hide #2.21 models
> show #2.20 models
> hide #2.20 models
> show #2.21 models
> hide #2.21 models
> show #2.20 models
> hide #2.20 models
> show #2.16 models
> hide #2.16 models
> show #2.17 models
> hide #2.17 models
> show #2.20 models
> hide #2.20 models
> show #2.21 models
> hide #2.21 models
> show #2.22 models
> hide #2.22 models
> show #2.24 models
> hide #2.24 models
> show #2.25 models
> hide #2.25 models
> show #2.19 models
> hide #2.19 models
> show #2.22 models
> hide #2.22 models
> show #2.31 models
> hide #2.31 models
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> hide #2.32 models
> show #2.41 models
> hide #2.41 models
> show #2.41 models
> hide #2.41 models
> show #2.41 models
> hide #2.41 models
> show #2.41 models
> hide #2.41 models
> show #2.41 models
> hide #2.41 models
> show #2.41 models
> hide #2.41 models
> show #2.41 models
> open 4D75
Summary of feedback from opening 4D75 fetched from pdb
---
note | Fetching compressed mmCIF 4d75 from http://files.rcsb.org/download/4d75.cif
4d75 title:
Cytochrome P450 3A4 bound to an inhibitor [more info...]
Chain information for 4d75 #7
---
Chain | Description | UniProt
A | CYTOCHROME P450 3A4 | CP3A4_HUMAN 23-503
Non-standard residues in 4d75 #7
---
HEM — protoporphyrin IX containing Fe (HEME)
PK9 — tert-butyl {6-oxo-6-[(pyridin-3-ylmethyl)amino]hexyl}carbamate
3 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!6 models
> mmaker #7 to #1
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker rec-minimized-final.pdb, chain A (#1) with 4d75, chain A (#7),
sequence alignment score = 2329.7
RMSD between 451 pruned atom pairs is 0.438 angstroms; (across all 460 pairs:
0.607)
> hide #2.41#!1,7 cartoons
> hide #2.41 models
> show #2.42 models
> hide #2.42 models
> show #2.43 models
> hide #2.43 models
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> show #2.44 models
> hide #2.44 models
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> show #2.50 models
> hide #2.50 models
> show #2.41 models
> hide #2.41 models
> show #2.51 models
> hide #2.51 models
> show #2.51 models
> open 4I4G
Summary of feedback from opening 4I4G fetched from pdb
---
notes | Fetching compressed mmCIF 4i4g from http://files.rcsb.org/download/4i4g.cif
Fetching CCD Z8Z from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/Z8Z/Z8Z.cif
4i4g title:
Crystal structure of CYP3A4 ligated to oxazole-substituted desoxyritonavir
[more info...]
Chain information for 4i4g #8
---
Chain | Description | UniProt
A | Cytochrome P450 3A4 | CP3A4_HUMAN 21-503
Non-standard residues in 4i4g #8
---
HEM — protoporphyrin IX containing Fe (HEME)
Z8Z —
N~2~-(methyl{[2-(propan-2-yl)-1,3-thiazol-4-yl]methyl}carbamoyl)-N-[(2R,5R)-5-{[(1,3-oxazol-5-ylmethoxy)carbonyl]amino}-1,6-diphenylhexan-2-yl]-L-valinamide
4i4g mmCIF Assemblies
---
1| author_defined_assembly
2| software_defined_assembly
> mmaker #8 to #1
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker rec-minimized-final.pdb, chain A (#1) with 4i4g, chain A (#8),
sequence alignment score = 2343.5
RMSD between 390 pruned atom pairs is 0.738 angstroms; (across all 459 pairs:
1.498)
> hide #2.51#!1,7-8 cartoons
> hide #!7 models
> hide #2.51 models
> show #2.52 models
> hide #2.52 models
> show #2.53 models
> hide #2.53 models
> show #2.54 models
> hide #2.54 models
> show #2.55 models
> hide #2.55 models
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> hide #2.56 models
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> show #2.60 models
> hide #2.60 models
> show #2.61 models
> hide #2.61 models
> show #2.51 models
> hide #2.51 models
> show #2.61 models
> hide #2.61 models
> show #2.61 models
> open 4I4H
Summary of feedback from opening 4I4H fetched from pdb
---
notes | Fetching compressed mmCIF 4i4h from http://files.rcsb.org/download/4i4h.cif
Fetching CCD Z9Z from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/Z9Z/Z9Z.cif
4i4h title:
Crystal structure of CYP3A4 ligated to pyridine-substituted desoxyritonavir
[more info...]
Chain information for 4i4h #9
---
Chain | Description | UniProt
A | Cytochrome P450 3A4 | CP3A4_HUMAN 21-503
Non-standard residues in 4i4h #9
---
HEM — protoporphyrin IX containing Fe (HEME)
Z9Z — pyridin-3-ylmethyl
[(2R,5S)-5-{[N-(methyl{[2-(propan-2-yl)-1,3-thiazol-4-yl]methyl}carbamoyl)-D-valyl]amino}-1,6-diphenylhexan-2-yl]carbamate
4i4h mmCIF Assemblies
---
1| author_defined_assembly
2| software_defined_assembly
> mmaker #9 to #1
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker rec-minimized-final.pdb, chain A (#1) with 4i4h, chain A (#9),
sequence alignment score = 2326.7
RMSD between 386 pruned atom pairs is 0.772 angstroms; (across all 457 pairs:
1.531)
> hide #!8 models
> hide #2.61#!1,9 cartoons
> save
> /Users/ak87/ownCloud/owncloud/Calculations/P450/DOCKING/Cyp3A4/P08684/MANUAL/P450-manual-
> sel.cxs
> hide #2.61 models
> show #2.62 models
> hide #2.62 models
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> hide #2.64 models
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> hide #2.101 models
> show #2.101 models
> hide #2.101 models
> show #2.101 models
> hide #2.101 models
> show #2.101 models
> open 4NY4
4ny4 title:
Crystal structure of CYP3A4 in complex with an inhibitor [more info...]
Chain information for 4ny4 #10
---
Chain | Description | UniProt
A | Cytochrome P450 3A4 | CP3A4_HUMAN 25-503
Non-standard residues in 4ny4 #10
---
2QH —
(8R)-3,3-difluoro-8-[4-fluoro-3-(pyridin-3-yl)phenyl]-8-(4-methoxy-3-methylphenyl)-2,3,4,8-tetrahydroimidazo[1,5-a]pyrimidin-6-amine
HEM — protoporphyrin IX containing Fe (HEME)
4ny4 mmCIF Assemblies
---
1| author_defined_assembly
2| software_defined_assembly
> hide #!9 models
> mmaker #10 to #1
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker rec-minimized-final.pdb, chain A (#1) with 4ny4, chain A (#10),
sequence alignment score = 2359.1
RMSD between 446 pruned atom pairs is 0.561 angstroms; (across all 460 pairs:
0.833)
> hide #2.101#!1,10 cartoons
> hide #2.101 models
> show #2.71 models
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> hide #2.83 models
> show #2.95 models
> hide #2.95 models
> show #2.191 models
> hide #2.191 models
> show #2.191 models
> open 5TE8
Summary of feedback from opening 5TE8 fetched from pdb
---
notes | Fetching compressed mmCIF 5te8 from http://files.rcsb.org/download/5te8.cif
Fetching CCD 08J from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/J/08J/08J.cif
5te8 title:
Crystal structure of the midazolam-bound human CYP3A4 [more info...]
Chain information for 5te8 #11
---
Chain | Description | UniProt
A B C | Cytochrome P450 3A4 | CP3A4_HUMAN 1-503
Non-standard residues in 5te8 #11
---
08J —
8-chloro-6-(2-fluorophenyl)-1-methyl-4H-imidazo[1,5-a][1,4]benzodiazepine
(Midazolam)
HEM — protoporphyrin IX containing Fe (HEME)
5te8 mmCIF Assemblies
---
1| author_and_software_defined_assembly
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> mmaker #11 to #1
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker rec-minimized-final.pdb, chain A (#1) with 5te8, chain A (#11),
sequence alignment score = 2328.5
RMSD between 403 pruned atom pairs is 0.880 angstroms; (across all 466 pairs:
1.969)
> hide #2.191#!1,10-11 cartoons
> hide #!10 models
> hide #2.191 models
> show #2.192 models
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> show #2.221 models
> hide #2.221 models
> show #2.221 models
> open 6MA6
Summary of feedback from opening 6MA6 fetched from pdb
---
warning | Cannot find consistent set of bond orders for ring system containing atom N1 in residue MYT /A:603
notes | Fetching compressed mmCIF 6ma6 from http://files.rcsb.org/download/6ma6.cif
Fetching CCD MYT from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/MYT/MYT.cif
6ma6 title:
Human CYP3A4 bound to an inhibitor metyrapone [more info...]
Chain information for 6ma6 #12
---
Chain | Description | UniProt
A | Cytochrome P450 3A4 | CP3A4_HUMAN 23-503
Non-standard residues in 6ma6 #12
---
EDO — 1,2-ethanediol (ethylene glycol)
GOL — glycerol (glycerin; propane-1,2,3-triol)
HEM — protoporphyrin IX containing Fe (HEME)
MYT — metyrapone
6ma6 mmCIF Assemblies
---
1| author_defined_assembly
2| software_defined_assembly
94 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> mmaker #12 to #1
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker rec-minimized-final.pdb, chain A (#1) with 6ma6, chain A (#12),
sequence alignment score = 2410.7
RMSD between 460 pruned atom pairs is 0.367 angstroms; (across all 466 pairs:
0.538)
> hide #2.221#!1,11-12 cartoons
> hide #!11 models
> hide #2.221 models
> show #2.222 models
> hide #2.222 models
> show #2.223 models
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> show #2.211 models
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> hide #2.220 models
> show #2.231 models
> hide #2.231 models
> show #2.241 models
> hide #!12 models
> hide #2.241 models
> show #2.241 models
> open 8SO1
Summary of feedback from opening 8SO1 fetched from pdb
---
notes | Fetching compressed mmCIF 8so1 from http://files.rcsb.org/download/8so1.cif
Fetching CCD CFF from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/CFF/CFF.cif
8so1 title:
Human CYP3A4 bound to three caffeine molecules [more info...]
Chain information for 8so1 #13
---
Chain | Description | UniProt
A | Cytochrome P450 3A4 | CP3A4_HUMAN 1-503
Non-standard residues in 8so1 #13
---
CFF — caffeine (3,7-dihydro-1,3,7-trimethyl-1H-purine-2,6-dione)
HEM — protoporphyrin IX containing Fe (HEME)
8so1 mmCIF Assemblies
---
1| author_defined_assembly
14 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> mmaker #13 to #1
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker rec-minimized-final.pdb, chain A (#1) with 8so1, chain A (#13),
sequence alignment score = 2392.7
RMSD between 463 pruned atom pairs is 0.385 angstroms; (across all 467 pairs:
0.571)
> hide #2.241#!1,13 cartoons
> hide #2.241 models
> show #2.242 models
> hide #2.242 models
> show #2.243 models
> hide #2.243 models
> show #2.244 models
> hide #2.244 models
> show #2.245 models
> hide #2.245 models
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> hide #2.246 models
> show #2.247 models
> hide #2.247 models
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> hide #2.248 models
> show #2.249 models
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> show #2.250 models
> hide #2.250 models
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> hide #2.271 models
> show #2.250 models
> hide #2.250 models
> show #2.251 models
> hide #2.251 models
> show #2.251 models
> hide #2.251 models
> show #2.251 models
> open 8SPD
8spd title:
Cytochrome P450 (CYP) 3A4 crystallized with clotrimazole [more info...]
Chain information for 8spd #14
---
Chain | Description | UniProt
A | Cytochrome P450 3A4 | CP3A4_HUMAN 24-503
Non-standard residues in 8spd #14
---
CL6 — 1-[(2-chlorophenyl)(diphenyl)methyl]-1H-imidazole (clotrimazole)
HEM — protoporphyrin IX containing Fe (HEME)
> mmaker #14 to #1
Computing secondary structure
[Repeated 1 time(s)] Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker rec-minimized-final.pdb, chain A (#1) with 8spd, chain A (#14),
sequence alignment score = 2311.7
RMSD between 410 pruned atom pairs is 0.665 angstroms; (across all 454 pairs:
1.406)
> hide #2.251#!1,13-14 cartoons
> hide #!13 models
> hide #2.251 models
> show #2.261 models
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> show #2.281 models
> hide #2.281 models
> show #2.272 models
> hide #2.272 models
> show #2.262 models
> hide #2.262 models
> show #2.251 models
JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read
properties of undefined (reading 'id')
> hide #2.251 models
> show #2.273 models
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> show #2.260 models
> save
> /Users/ak87/ownCloud/owncloud/Calculations/P450/DOCKING/Cyp3A4/P08684/MANUAL/P450-manual-
> sel.cxs
——— End of log from Wed Feb 19 15:57:43 2025 ———
> view name session-start
opened ChimeraX session
> show #!7 models
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Desktop color scheme is dark
Desktop color scheme is light
> show #!5 models
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> hide #!5 models
Desktop color scheme is dark
Desktop color scheme is light
> hide #!2 models
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> show #!12 models
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> hide #!10 models
> show #!10 models
> select clear
> select #10/A:602@N32
1 atom, 1 residue, 1 model selected
> getcrd sel
Atom #10/A:602@N32 -17.703 -22.119 -9.320
> open
> /Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/RECEPTOR/Cyp3A4/dockfiles/matching_spheres.xyz
opened matching_spheres.xyz as an XYZ coordinate file
> select #15/a:1@O23
1 atom, 1 residue, 1 model selected
> getcrd sel
Atom #15/a:1@O23 -18.133 -22.477 -9.298
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/DOCKING/Cyp3A4/CHEMBL/p450_chembl_actives.cxs
### ViewDock hotkeys on
If clicked into ViewDock dialog or main 3D graphics area, the following keys
are active:
g/m/b/u
Assign good/maybe/bad/(unrated) rating to chosen compounds
up/down arrow
Move up/down compound list*
Escape
Turn hotkeys off (have to use context menu to re-enable)
*Unless in 3D graphics with a selection, in which case normal selection widening/narrowing happens
Log from Mon Feb 9 15:27:24 2026UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/DOCKING/Cyp3A4/CHEMBL/p450_chembl_actives.cxs
### ViewDock hotkeys on
If clicked into ViewDock dialog or main 3D graphics area, the following keys
are active:
g/m/b/u
Assign good/maybe/bad/(unrated) rating to chosen compounds
up/down arrow
Move up/down compound list*
Escape
Turn hotkeys off (have to use context menu to re-enable)
*Unless in 3D graphics with a selection, in which case normal selection widening/narrowing happens
Log from Sat Feb 7 13:45:05 2026UCSF ChimeraX version: 1.11 (2025-12-17)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/RECEPTOR/Cyp3A4/rec-
> minimized-final.pdb
Summary of feedback from opening
/Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/RECEPTOR/Cyp3A4/rec-
minimized-final.pdb
---
warnings | CONECT record to nonexistent atom: (4664, 4678)
CONECT record for nonexistent atom: 4678
rec-minimized-final.pdb title:
6MA7 - 5-removed waters [more info...]
Chain information for rec-minimized-final.pdb #1
---
Chain | Description
A | No description available
Non-standard residues in rec-minimized-final.pdb #1
---
ACE — (ACE)
HEM — protoporphyrin IX containing Fe
NMA — (NMA)
3759 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> open
> /Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/RECEPTOR/Cyp3A4/xtal-
> lig.pdb
> open
> /Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/DOCKING/Cyp3A4/CHEMBL/p450_chembl_actives.mol2
Opened p450_chembl_actives.mol2 containing 1655 structures (74072 atoms, 78160
bonds)
### ViewDock hotkeys on
If clicked into ViewDock dialog or main 3D graphics area, the following keys
are active:
g/m/b/u
Assign good/maybe/bad/(unrated) rating to chosen compounds
up/down arrow
Move up/down compound list*
Escape
Turn hotkeys off (have to use context menu to re-enable)
*Unless in 3D graphics with a selection, in which case normal selection widening/narrowing happens
> ui windowfill toggle
> view
> save
> /Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/DOCKING/Cyp3A4/CHEMBL/p450_chembl_actives.cxs
——— End of log from Sat Feb 7 13:45:05 2026 ———
> view name session-start
opened ChimeraX session
> ui windowfill toggle
> select ::name="UNL"
74072 atoms, 78160 bonds, 1655 residues, 1655 models selected
> select sel :< 4 & ~sel
489 atoms, 485 bonds, 4 pseudobonds, 43 residues, 3 models selected
> show sel atoms
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.06
Changed 485 bond radii
> label (#2#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> view sel
> save
> /Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/DOCKING/Cyp3A4/CHEMBL/p450_chembl_actives.cxs
> select clear
> hide #3.1#!1-2 cartoons
Drag select of 196 atoms, 5 pseudobonds, 196 bonds
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.06
Changed 196 bond radii
> select clear
> select ::name="HEM"
43 atoms, 46 bonds, 4 pseudobonds, 1 residue, 2 models selected
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.2
Changed 46 bond radii
> select clear
> save
> /Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/DOCKING/Cyp3A4/CHEMBL/p450_chembl_actives.cxs
——— End of log from Mon Feb 9 15:27:24 2026 ———
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,1
Model Number: MK193LL/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 13822.61.10
OS Loader Version: 13822.61.10
Software:
System Software Overview:
System Version: macOS 26.2 (25C56)
Kernel Version: Darwin 25.2.0
Time since boot: 31 день, 19 годин і 48 хвилин
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-clix: 0.2.5
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.11
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
narwhals: 2.16.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 2.4.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
plotly: 6.5.2
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: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pyKVFinder: 0.9.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.5
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pytz: 2025.2
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.0.0
roman-numerals-py: 4.0.0
rpds-py: 0.30.0
scipy: 1.14.0
Send2Trash: 1.8.3
SEQCROW: 1.9.7
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.0.4
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tomlkit: 0.14.0
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.3
urllib3: 2.6.2
uvicorn: 0.38.0
wcwidth: 0.2.14
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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