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Opened 17 hours ago
#20810 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-26.5.2-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00000001edf29d80 (most recent call first):
File "/Applications/ChimeraX-1.11.1.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-1.11.1.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-1.11.1.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, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, PIL._imaging, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, psutil._psutil_osx, psutil._psutil_posix, 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, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, 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._sparsetools, _csparsetools, scipy.sparse._csparsetools, 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.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, kiwisolver._cext (total: 126)
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 1043f8000-1043fc000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.1.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":51385},
"vmregioninfo" : "0x8 is not in any region. Bytes before following region: 4366237688
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: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> close all
> open
> /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE.pdb
Chain information for HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open
> /Users/iktae/PhenixProjects/HpaCas9_J43_validation/LocalRSR_afterISOLDE/20260728_205440/BranchA_PAB8/HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE_BranchA_local_rsr_000.pdb
Chain information for
HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE_BranchA_local_rsr_000.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open
> /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/cryosparc_P7_J43_004_volume_map.mrc
Opened cryosparc_P7_J43_004_volume_map.mrc as #3, grid size 256,256,256, pixel
0.934, shown at level 0.0656, step 1, values float32
> open
> /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/cryosparc_P7_J43_004_volume_map_sharp.mrc
Opened cryosparc_P7_J43_004_volume_map_sharp.mrc as #4, grid size 256,256,256,
pixel 0.934, shown at level 0.0814, step 1, values float32
> volume #4 level 0.2626
> volume #3 level 0.04723
> volume #3 style mesh
> volume #4 level 0.1754
> show #1,2/C:1-22 atoms
> style #1,2/C:1-22 stick
Changed 944 atom styles
> view #1,2/C:1-22
> hide #!3 models
> hide #!4 models
> nucleotides atoms
> style nucleic stick
Changed 5858 atom styles
> nucleotides slab
> style nucleic stick
Changed 5858 atom styles
> nucleotides fill
> style nucleic stick
Changed 5858 atom styles
> show #1,2/C:28-38 atoms
> style #1,2/C:28-38 stick
Changed 440 atom styles
> view #1,2/C:28-38
> show #1,2/C:65-80 atoms
> style #1,2/C:65-80 stick
Changed 682 atom styles
> view #1,2/C:65-80
> color #1,2 bychain
> view
> show #!3 models
> volume #4 style mesh
> show #!4 models
> hide #!3 models
> view #1/B:26
> view
> style #1/B:26 sticks
Expected a keyword
> style #1/B:26 stick
Changed 12 atom styles
> view #1/B:26
>
Unknown command: sequence #1
>
Unknown command: sequence #2
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B #2/B
Alignment identifier is 1
> select #1/B:26 #2/B:26
24 atoms, 24 bonds, 2 residues, 2 models selected
> select #1/B:26 #2/B:26
24 atoms, 24 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [26] RMSD: 0.179
> surface hidePatches sel
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> color sel bynucleotide
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> view
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel tube/slab shape muffler
> surface sel
> hide #!2 models
> select #1/B:22 #2/B:22
24 atoms, 24 bonds, 2 residues, 2 models selected
> select #1/B:22-26 #2/B:22-26
106 atoms, 110 bonds, 10 residues, 2 models selected
1 [ID: 1] region 2 chains [22-26] RMSD: 0.113
> surface hidePatches (#!1 & sel)
> show (#!1 & sel) target ab
> volume #4 level 0.1201
> hide #!4 models
> close all
> open
> /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE.pdb
Chain information for HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open
> /Users/iktae/PhenixProjects/HpaCas9_J43_validation/LocalRSR_afterISOLDE/20260728_205440/BranchA_PAB8/HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE_BranchA_local_rsr_000.pdb
Chain information for
HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE_BranchA_local_rsr_000.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open
> /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/cryosparc_P7_J43_004_volume_map.mrc
Opened cryosparc_P7_J43_004_volume_map.mrc as #3, grid size 256,256,256, pixel
0.934, shown at level 0.0656, step 1, values float32
> open
> /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/cryosparc_P7_J43_004_volume_map_sharp.mrc
Opened cryosparc_P7_J43_004_volume_map_sharp.mrc as #4, grid size 256,256,256,
pixel 0.934, shown at level 0.0814, step 1, values float32
> volume #4 level 0.1284
> info polymers #2/A
physical chain #2/A:1 #2/A:274
physical chain #2/A:289 #2/A:740
physical chain #2/A:762 #2/A:1054
> hide #!3 models
> volume #4 style mesh
> hide #!1 models
> hide #!4 models
> color #2 bychain
> select #2/A:1-274
2226 atoms, 2264 bonds, 274 residues, 1 model selected
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> open /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/input-
> af3-hpacas9-snu-SNUseq_raw.pdb
Chain information for input-af3-hpacas9-snu-SNUseq_raw.pdb #5
---
Chain | Description
A | No description available
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> show #!4 models
> volume #4 level 0.1888
> volume #4 level 0.2223
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> volume #4 color #00fdff
> volume #4
> volume #4 style surface
> volume #4 level 0.1754
> hide #5 models
> hide #!4 models
> close #1-2
> rename #3 id #1
> rename #4 id #2
> close #5
> show #!1 models
> show #!2 models
> open "/Users/iktae/Library/Mobile
> Documents/com~apple~CloudDocs/1.SNU_BPNB/Experiment/002-Anti-CRISPR-
> Cas9/009-AcrIIC6-PCK/4.Structure/Info/itk/hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26/fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif"
Chain information for
fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif #3
---
Chain | Description
A | .
B | .
C | .
> open "/Users/iktae/Library/Mobile
> Documents/com~apple~CloudDocs/1.SNU_BPNB/Experiment/002-Anti-CRISPR-
> Cas9/009-AcrIIC6-PCK/4.Structure/Info/itk/hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26/fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_1.cif"
Chain information for
fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_1.cif #4
---
Chain | Description
A | .
B | .
C | .
> open "/Users/iktae/Library/Mobile
> Documents/com~apple~CloudDocs/1.SNU_BPNB/Experiment/002-Anti-CRISPR-
> Cas9/009-AcrIIC6-PCK/4.Structure/Info/itk/hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26/fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_2.cif"
Chain information for
fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_2.cif #5
---
Chain | Description
A | .
B | .
C | .
> open "/Users/iktae/Library/Mobile
> Documents/com~apple~CloudDocs/1.SNU_BPNB/Experiment/002-Anti-CRISPR-
> Cas9/009-AcrIIC6-PCK/4.Structure/Info/itk/hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26/fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_3.cif"
Chain information for
fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_3.cif #6
---
Chain | Description
A | .
B | .
C | .
> open "/Users/iktae/Library/Mobile
> Documents/com~apple~CloudDocs/1.SNU_BPNB/Experiment/002-Anti-CRISPR-
> Cas9/009-AcrIIC6-PCK/4.Structure/Info/itk/hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26/fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_4.cif"
Chain information for
fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_4.cif #7
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> fitmap #3 inMap #2 search 100
Found 15 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (15 of 100).
Average map values and times found:
0.04864 (1), 0.04822 (1), 0.04815 (1), 0.04705 (1), 0.04393 (1), 0.04385 (1),
0.03923 (1), 0.03817 (1), 0.03805 (1), 0.03709 (1), 0.03641 (1), 0.03629 (1),
0.03607 (1), 0.03599 (1), 0.03291 (1)
Best fit found:
Fit molecule fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif
(#3) to map cryosparc_P7_J43_004_volume_map_sharp.mrc (#2) using 12193 atoms
average map value = 0.04864, steps = 136
shifted from previous position = 1.95
rotated from previous position = 9.65 degrees
atoms outside contour = 10521, contour level = 0.17536
Position of fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif
(#3) relative to cryosparc_P7_J43_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.53421526 -0.52575549 -0.66196319 124.61625561
0.01841852 0.77564049 -0.63090620 112.19412299
0.84514782 -0.34923211 -0.40467536 111.43202151
Axis 0.17313397 -0.92636180 0.33448234
Axis point 37.67263092 0.00000000 112.73145945
Rotation angle (degrees) 125.56492192
Shift along axis -45.08499940
Found 15 fits.
Populating font family aliases took 54 ms. Replace uses of missing font family
"Courier" with one that exists to avoid this cost.
> mmaker #4 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif,
chain A (#3) with
fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_1.cif, chain A (#4),
sequence alignment score = 5391.3
RMSD between 853 pruned atom pairs is 0.943 angstroms; (across all 1054 pairs:
1.826)
> mmaker #5 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif,
chain A (#3) with
fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_2.cif, chain A (#5),
sequence alignment score = 5382.3
RMSD between 893 pruned atom pairs is 0.838 angstroms; (across all 1054 pairs:
2.332)
> mmaker #6 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif,
chain A (#3) with
fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_3.cif, chain A (#6),
sequence alignment score = 5356.5
RMSD between 887 pruned atom pairs is 0.962 angstroms; (across all 1054 pairs:
1.542)
> mmaker #7 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif,
chain A (#3) with
fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_4.cif, chain A (#7),
sequence alignment score = 5381.1
RMSD between 877 pruned atom pairs is 0.762 angstroms; (across all 1054 pairs:
2.636)
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> open
> /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE.pdb
Chain information for HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE.pdb #8
---
Chain | Description
A | No description available
B | No description available
C | No description available
> mmaker #3 to #8
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 HpaCas9_PAB8_AcrIIC6_sgRNAhybrid_afterISOLDE.pdb, chain A (#8) with
fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif, chain A (#3),
sequence alignment score = 4976.3
RMSD between 612 pruned atom pairs is 0.977 angstroms; (across all 1019 pairs:
2.821)
> hide #!8 models
> show #4 models
> mmaker #4 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif,
chain A (#3) with
fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_1.cif, chain A (#4),
sequence alignment score = 5391.3
RMSD between 853 pruned atom pairs is 0.943 angstroms; (across all 1054 pairs:
1.826)
> mmaker #5 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif,
chain A (#3) with
fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_2.cif, chain A (#5),
sequence alignment score = 5382.3
RMSD between 893 pruned atom pairs is 0.838 angstroms; (across all 1054 pairs:
2.332)
> mmaker #6 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif,
chain A (#3) with
fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_3.cif, chain A (#6),
sequence alignment score = 5356.5
RMSD between 887 pruned atom pairs is 0.962 angstroms; (across all 1054 pairs:
1.542)
> mmaker #7 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif,
chain A (#3) with
fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_4.cif, chain A (#7),
sequence alignment score = 5381.1
RMSD between 877 pruned atom pairs is 0.762 angstroms; (across all 1054 pairs:
2.636)
> show #5 models
> show #6 models
> show #7 models
> show #!8 models
> hide #!1 models
> hide #!8 models
> hide #!2 models
> color #3-7 bychain
> close #4-7#8
> show #!2 models
> fitmap #3 inMap #2 search 100
Found 18 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (18 of 100).
Average map values and times found:
0.0488 (1), 0.04646 (1), 0.04524 (1), 0.04423 (1), 0.04077 (1), 0.04077 (1),
0.04059 (1), 0.03987 (1), 0.03694 (1), 0.03642 (1), 0.03614 (1), 0.03583 (1),
0.03556 (1), 0.03549 (1), 0.03482 (1), 0.03396 (1), 0.03288 (1), 0.03171 (1)
Best fit found:
Fit molecule fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif
(#3) to map cryosparc_P7_J43_004_volume_map_sharp.mrc (#2) using 12193 atoms
average map value = 0.0488, steps = 268
shifted from previous position = 2.32
rotated from previous position = 5.96 degrees
atoms outside contour = 10524, contour level = 0.17536
Position of fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif
(#3) relative to cryosparc_P7_J43_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.71239231 -0.65770712 -0.24478277 140.51639191
0.05689133 0.29352948 -0.95425570 108.23587887
0.69947173 -0.69373042 -0.17169030 122.84264202
Axis 0.21486733 -0.77877066 0.58936262
Axis point 60.89458733 0.00000000 131.98979156
Rotation angle (degrees) 142.68138405
Shift along axis 18.30031667
Found 18 fits.
> fitmap #3 inMap #2 search 500
Found 86 unique fits from 500 random placements having fraction of points
inside contour >= 0.100 (86 of 500).
Average map values and times found:
0.05878 (1), 0.05087 (1), 0.04773 (1), 0.04748 (1), 0.04735 (1), 0.0455 (1),
0.0454 (1), 0.04492 (1), 0.0449 (1), 0.04468 (1), 0.04435 (1), 0.04341 (1),
0.04328 (1), 0.04273 (1), 0.04262 (1), 0.04261 (1), 0.04246 (1), 0.04238 (1),
0.04225 (1), 0.04188 (1), 0.04123 (1), 0.04107 (1), 0.04072 (1), 0.04061 (1),
0.04052 (1), 0.04035 (1), 0.04021 (1), 0.03981 (1), 0.0396 (1), 0.03932 (1),
0.03895 (1), 0.03889 (1), 0.03883 (1), 0.03852 (1), 0.03814 (1), 0.03811 (1),
0.03805 (1), 0.03773 (1), 0.03767 (1), 0.03767 (1), 0.03757 (1), 0.03757 (1),
0.03754 (1), 0.03735 (1), 0.03696 (1), 0.03674 (1), 0.0366 (1), 0.03657 (1),
0.0365 (1), 0.03645 (1), 0.03624 (1), 0.0362 (1), 0.03614 (1), 0.03613 (1),
0.03584 (1), 0.03583 (1), 0.03574 (1), 0.03573 (1), 0.03568 (1), 0.03548 (1),
0.03528 (1), 0.03519 (1), 0.03504 (1), 0.03459 (1), 0.03437 (1), 0.03432 (1),
0.03429 (1), 0.03426 (1), 0.03422 (1), 0.03401 (1), 0.03389 (1), 0.03376 (1),
0.03357 (1), 0.03355 (1), 0.03315 (1), 0.03284 (1), 0.03269 (1), 0.03268 (1),
0.03263 (1), 0.0325 (1), 0.03228 (1), 0.03215 (1), 0.03202 (1), 0.03193 (1),
0.03182 (1), 0.03058 (1)
Best fit found:
Fit molecule fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif
(#3) to map cryosparc_P7_J43_004_volume_map_sharp.mrc (#2) using 12193 atoms
average map value = 0.05878, steps = 280
shifted from previous position = 7.98
rotated from previous position = 19 degrees
atoms outside contour = 10051, contour level = 0.17536
Position of fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif
(#3) relative to cryosparc_P7_J43_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-0.17818556 -0.53481697 -0.82596659 120.60722532
-0.98363881 0.07416627 0.16417716 115.03215752
-0.02654588 0.84170676 -0.53928205 123.76489008
Axis 0.59433316 -0.70125679 -0.39370929
Axis point 86.50756224 0.00000000 64.15074726
Rotation angle (degrees) 145.25037350
Shift along axis -57.71359512
Found 86 fits.
> fitmap #3 inMap #1 search 100
Found 92 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (96 of 100).
Average map values and times found:
0.1082 (4), 0.05659 (1), 0.05494 (2), 0.05474 (1), 0.05177 (1), 0.05133 (1),
0.04992 (1), 0.04876 (1), 0.0485 (1), 0.04822 (1), 0.04777 (1), 0.04756 (1),
0.04748 (1), 0.04732 (1), 0.04685 (1), 0.04664 (1), 0.04652 (1), 0.04638 (1),
0.04627 (1), 0.04605 (1), 0.04604 (1), 0.04591 (1), 0.04582 (1), 0.04571 (1),
0.0457 (1), 0.0457 (1), 0.04562 (1), 0.04513 (1), 0.04482 (1), 0.04449 (1),
0.04432 (1), 0.04373 (1), 0.04344 (1), 0.04308 (1), 0.04303 (1), 0.04286 (1),
0.04281 (1), 0.04249 (1), 0.04243 (1), 0.04219 (1), 0.04216 (1), 0.04213 (1),
0.04198 (1), 0.04179 (1), 0.0417 (1), 0.04135 (1), 0.04134 (1), 0.04132 (1),
0.04094 (1), 0.04083 (1), 0.04076 (1), 0.04055 (1), 0.04036 (1), 0.03951 (1),
0.03945 (1), 0.03932 (1), 0.03879 (1), 0.03801 (1), 0.03791 (1), 0.03776 (1),
0.03749 (1), 0.03746 (1), 0.03741 (1), 0.03735 (1), 0.03727 (1), 0.03725 (1),
0.03709 (1), 0.03701 (1), 0.03656 (1), 0.03626 (1), 0.03601 (1), 0.03587 (1),
0.03529 (1), 0.03528 (1), 0.03513 (1), 0.03503 (1), 0.03479 (1), 0.03444 (1),
0.03326 (1), 0.03325 (1), 0.03323 (1), 0.03264 (1), 0.03022 (1), 0.03011 (1),
0.03 (1), 0.02964 (1), 0.0293 (1), 0.0281 (1), 0.02785 (1), 0.02724 (1),
0.01914 (1), 0.01896 (1)
Best fit found:
Fit molecule fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif
(#3) to map cryosparc_P7_J43_004_volume_map.mrc (#1) using 12193 atoms
average map value = 0.1082, steps = 876
shifted from previous position = 62.4
rotated from previous position = 63.5 degrees
atoms outside contour = 4237, contour level = 0.065555
Position of fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif
(#3) relative to cryosparc_P7_J43_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.33919257 -0.26230761 -0.90340643 125.17077408
-0.91427917 0.13415173 -0.38222635 117.76073271
0.22145441 0.95561399 -0.19431914 124.37948944
Axis 0.71713755 -0.60297176 -0.34948362
Axis point 0.00000000 56.17476383 141.85909093
Rotation angle (degrees) 111.13013240
Shift along axis -24.71032764
Found 92 fits.
> show #!1 models
> fitmap #3 inMap #1 resolution 3.2 metric correlation
Opened fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif map 3.2
as #4, grid size 116,156,111, pixel 1.07, shown at level 0.112, step 1, values
float32
Fit map fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif map
3.2 in map cryosparc_P7_J43_004_volume_map.mrc using 114926 points
correlation = 0.4462, correlation about mean = 0.003041, overlap = 3170
steps = 216, shift = 14.6, angle = 22.4 degrees
Position of fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif
map 3.2 (#4) relative to cryosparc_P7_J43_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.19524616 -0.65599666 -0.72907296 126.50585638
0.11731941 0.72242014 -0.68142891 112.44004804
0.97371205 -0.21858079 -0.06408864 126.03166979
Axis 0.24024299 -0.88383673 0.40139251
Axis point 21.21672085 0.00000000 144.79583287
Rotation angle (degrees) 105.57248907
Shift along axis -18.39832990
> close #4
> open /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/input-
> af3-hpacas9-snu-SNUseq_raw.pdb
Chain information for input-af3-hpacas9-snu-SNUseq_raw.pdb #4
---
Chain | Description
A | No description available
> mmaker #3 to #4
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 input-af3-hpacas9-snu-SNUseq_raw.pdb, chain A (#4) with
fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif, chain A (#3),
sequence alignment score = 5288.7
RMSD between 871 pruned atom pairs is 0.778 angstroms; (across all 1054 pairs:
2.942)
> hide #!1 models
> hide #!2 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> show #!1 models
> volume #1 style mesh
> open
> /Users/iktae/PhenixProjects/HpaCas9_SNU_J43_validation/input/fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif
Chain information for
fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif #5
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> close #5
>
Unknown command: sequence #3
>
Unknown command: sequence #3
>
Unknown command: sequence #3/C
>
Unknown command: sequence #3.C
> ui tool show "Show Sequence Viewer"
> sequence chain #3/C
Alignment identifier is 3/C
> close #4
> open /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/01_guide20/NewAF_guide24to20_5OH_SNUproject.cxc
> close all
> open /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/00_raw/fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif
Chain information for
fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> save /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/00_raw/NewAF_original_142nt.pdb models #1
> save /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/01_guide20/before_guide_edit.cxs
> info chains #1
chain id /A chain_id A
chain id /B chain_id B
chain id /C chain_id C
> info polymers #1/C
physical chain /C:1 /C:142
> sequence chain #1/C
Alignment identifier is 1/C
> delete atoms #1/C:1-4
> renumber #1/C start 1 relative false
138 residues renumbered
> swapna #1/C:1-20 G,G,A,A,A,U,U,A,G,G,U,G,C,G,C,U,U,G,G,C preserve true
> delete atoms #1/C:1@P,OP1,OP2
> show #1/C:1-24 atoms
> style #1/C:1-24 stick
Changed 515 atom styles
> view #1/C:1-24
> info polymers #1/C
physical chain /C:1 /C:138
> distance #1/C:20@O3' #1/C:21@P
Distance between /C C 20 O3' and G 21 P: 1.588Å
> sequence chain #1/C
Destroying pre-existing alignment with identifier 1/C
Alignment identifier is 1/C
> save /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/01_guide20/NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH.pdb
> models #1
> save /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/01_guide20/after_guide_edit.cxs
executed NewAF_guide24to20_5OH_SNUproject.cxc
> info chains #1
chain id /A chain_id A
chain id /B chain_id B
chain id /C chain_id C
> info polymers #1/A
physical chain /A:1 /A:1054
> info polymers #1/B
physical chain /B:1 /B:76
> info polymers #1/C
physical chain /C:1 /C:138
> sequence chain #1/C
Destroying pre-existing alignment with identifier 1/C
Alignment identifier is 1/C
> distance #1/C:20@O3' #1/C:21@P
Distance already exists; modify distance properties with 'distance style'
> nucleotides atoms
> style nucleic stick
Changed 2929 atom styles
> nucleotides fill
> style nucleic stick
Changed 2929 atom styles
> nucleotides slab
> style nucleic stick
Changed 2929 atom styles
> color bynucleotide
> nucleotides atoms
> style nucleic stick
Changed 2929 atom styles
> close all
> open /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/01_guide20/NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH.pdb
Chain information for NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> info chains #1
chain id /A chain_id A
chain id /B chain_id B
chain id /C chain_id C
> info polymers #1/C
physical chain /C:1 /C:138
> sequence chain #1/C
Alignment identifier is 1/C
> distance #1/C:20@O3' #1/C:21@P
Distance between /C C 20 O3' and G 21 P: 1.588Å
> open /Users/iktae/Downloads/emd_34919.map
Opened emd_34919.map as #3, grid size 184,184,184, pixel 1.04, shown at level
0.0297, step 1, values float32
> select add #3
2 models selected
> select subtract #3
Nothing selected
> volume #3 level 0.03792
> close #3
> info polymers #1/B
physical chain /B:1 /B:76
> info polymers #1/A
physical chain /A:1 /A:1054
> close all
> open /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/01_guide20/NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH.pdb
Chain information for NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open "/Users/iktae/Library/Mobile
> Documents/com~apple~CloudDocs/1.SNU_BPNB/Experiment/002-Anti-CRISPR-
> Cas9/009-AcrIIC6-PCK/3.Cryo-EM/4.Phenix/input/fitted_model_J43.cif"
Summary of feedback from opening /Users/iktae/Library/Mobile
Documents/com~apple~CloudDocs/1.SNU_BPNB/Experiment/002-Anti-CRISPR-
Cas9/009-AcrIIC6-PCK/3.Cryo-EM/4.Phenix/input/fitted_model_J43.cif
---
warnings | Unknown polymer entity '1' on line 106
Missing or incorrect sequence information. Inferred polymer connectivity.
Unknown polymer entity '1' on line 8883
Missing or incorrect sequence information. Inferred polymer connectivity.
Unknown polymer entity '1' on line 9637
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for fitted_model_J43.cif
---
Chain | Description
2.1/A | No description available
2.2/B | No description available
2.3/C | No description available
Computing secondary structure
> mmaker #2 to #1
No matrix compatible with both reference structure and all match structures
> matchmaker #2 to #1
No matrix compatible with both reference structure and all match structures
> open /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/maps/cryosparc_P7_J43_004_volume_map_sharp.mrc
Opened cryosparc_P7_J43_004_volume_map_sharp.mrc as #3, grid size 256,256,256,
pixel 0.934, shown at level 0.0814, step 1, values float32
> matchmaker #1 to #2
Specify a single 'to' model only
> matchmaker #1/A to #2.1/A
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 fitted_model_J43.cif, chain A (#2.1) with
NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH.pdb, chain A (#1), sequence alignment
score = 5273.8
RMSD between 871 pruned atom pairs is 0.778 angstroms; (across all 1054 pairs:
2.942)
> volume #3 level 0.37
> hide #!2 models
> volume #3 level 0.1687
> view #3
> show #!2 models
> hide #!3 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #2 models
> show #!3 models
> fitmap #1/A inMap #3 resolution 3.2 moveWholeMolecules true
Opened NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH.pdb map 3.2 as #4, grid size
111,113,99, pixel 1.07, shown at level 0.104, step 1, values float32
Fit map NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH.pdb map 3.2 in map
cryosparc_P7_J43_004_volume_map_sharp.mrc using 83296 points
correlation = 0.4734, correlation about mean = 0.1765, overlap = 6203
steps = 52, shift = 0.498, angle = 1.28 degrees
Position of NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH.pdb map 3.2 (#4) relative
to cryosparc_P7_J43_004_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.33857473 -0.27000738 -0.90136739 125.19961221
-0.91587880 0.12504575 -0.38148340 117.92280308
0.21571549 0.95470392 -0.20495671 123.88670167
Axis 0.71933522 -0.60138055 -0.34770429
Axis point 0.00000000 56.86598985 140.96411150
Rotation angle (degrees) 111.75682757
Shift along axis -23.93192622
> show #!4 models
> view #1/A
> hide #!4 models
> view #1/B
> color #1 bychain
> view #1/C:1-20
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> view #1/C:21-138
> volume #3 level 0.1217
> save /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/03_J43_rigidfit/NewAF_HpaCas9_AcrIIC6_sgRNA20_J43_rigidfit.pdb
> models #1
> save /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/03_J43_rigidfit/NewAF_HpaCas9_AcrIIC6_sgRNA20_J43_rigidfit.cxs
> close all
> open /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/03_J43_rigidfit/NewAF_HpaCas9_AcrIIC6_sgRNA20_J43_rigidfit.pdb
Chain information for NewAF_HpaCas9_AcrIIC6_sgRNA20_J43_rigidfit.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> info chains #1
chain id /A chain_id A
chain id /B chain_id B
chain id /C chain_id C
> info polymers #1/A
physical chain /A:1 /A:1054
> info polymers #1/B
physical chain /B:1 /B:76
> info polymers #1/C
physical chain /C:1 /C:138
> sequence chain #1/C
Alignment identifier is 1/C
> select clear
> open /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/01_guide20/NewAF_guide24to20_stage1_unfixed.cxc
> close all
> open /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/00_raw/fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif
Chain information for
fold_hpacas9_rnp_acriic6_tdna_snurna_8hnt24guide_26_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> save /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/00_raw/NewAF_original_142nt.pdb models #1
> save /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/01_guide20/before_guide_edit.cxs
> delete atoms #1/C:1-4
> renumber #1/C start 1 relative false
138 residues renumbered
> swapna #1/C:1-20 G,G,A,A,A,U,U,A,G,G,U,G,C,G,C,U,U,G,G,C preserve true
> delete atoms #1/C:1@P,OP1,OP2
> info chains #1
chain id /A chain_id A
chain id /B chain_id B
chain id /C chain_id C
> info polymers #1/C
physical chain /C:1 /C:138
> distance #1/C:20@O3' #1/C:21@P
Distance between /C C 20 O3' and G 21 P: 1.588Å
> show #1/C:1-24 atoms
> style #1/C:1-24 stick
Changed 515 atom styles
> view #1/C:1-24
> save /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/01_guide20/NewAF_HpaCas9_AcrIIC6_sgRNA20_EDITED_COORDS_UNFIXED_SEQRES.pdb
> models #1
> save /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/01_guide20/after_guide_edit_unfixed.cxs
executed NewAF_guide24to20_stage1_unfixed.cxc
> ui tool show "Show Sequence Viewer"
> sequence chain /C
Alignment identifier is 1/C
> close all
> open /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/01_guide20/NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH_SEQRESfixed.pdb
Chain information for NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH_SEQRESfixed.pdb
#1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> info polymers #1/C
physical chain /C:1 /C:138
> sequence chain #1/C
Alignment identifier is 1/C
> open "/Users/iktae/Library/Mobile
> Documents/com~apple~CloudDocs/1.SNU_BPNB/Experiment/002-Anti-CRISPR-
> Cas9/009-AcrIIC6-PCK/3.Cryo-EM/4.Phenix/input/fitted_model_J43.cif"
Summary of feedback from opening /Users/iktae/Library/Mobile
Documents/com~apple~CloudDocs/1.SNU_BPNB/Experiment/002-Anti-CRISPR-
Cas9/009-AcrIIC6-PCK/3.Cryo-EM/4.Phenix/input/fitted_model_J43.cif
---
warnings | Unknown polymer entity '1' on line 106
Missing or incorrect sequence information. Inferred polymer connectivity.
Unknown polymer entity '1' on line 8883
Missing or incorrect sequence information. Inferred polymer connectivity.
Unknown polymer entity '1' on line 9637
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for fitted_model_J43.cif
---
Chain | Description
2.1/A | No description available
2.2/B | No description available
2.3/C | No description available
Computing secondary structure
> matchmaker #1/A to #2.1/A
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 fitted_model_J43.cif, chain A (#2.1) with
NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH_SEQRESfixed.pdb, chain A (#1),
sequence alignment score = 5273.8
RMSD between 871 pruned atom pairs is 0.778 angstroms; (across all 1054 pairs:
2.942)
> open /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/maps/cryosparc_P7_J43_004_volume_map_sharp.mrc
Opened cryosparc_P7_J43_004_volume_map_sharp.mrc as #3, grid size 256,256,256,
pixel 0.934, shown at level 0.0814, step 1, values float32
> view #3
> fitmap #1/A inMap #3 resolution 3.2 moveWholeMolecules true
Opened NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH_SEQRESfixed.pdb map 3.2 as #4,
grid size 111,113,99, pixel 1.07, shown at level 0.104, step 1, values float32
Fit map NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH_SEQRESfixed.pdb map 3.2 in map
cryosparc_P7_J43_004_volume_map_sharp.mrc using 83296 points
correlation = 0.4734, correlation about mean = 0.1765, overlap = 6203
steps = 52, shift = 0.498, angle = 1.28 degrees
Position of NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH_SEQRESfixed.pdb map 3.2
(#4) relative to cryosparc_P7_J43_004_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.33857473 -0.27000738 -0.90136739 125.19961221
-0.91587880 0.12504575 -0.38148340 117.92280308
0.21571549 0.95470392 -0.20495671 123.88670167
Axis 0.71933522 -0.60138055 -0.34770429
Axis point 0.00000000 56.86598985 140.96411150
Rotation angle (degrees) 111.75682757
Shift along axis -23.93192622
> save /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/03_J43_rigidfit/NewAF_HpaCas9_AcrIIC6_sgRNA20_J43_rigidfit_SEQRESfixed.pdb
> models #1
> show #!4 models
> hide #!4 models
> hide #2.1 models
> hide #2.2 models
> hide #2.3 models
> hide #!2 models
> hide #!3 models
> color #1 bychain
> show #!3 models
> volume #3 style mesh
> volume #3 level 0.1781
> open /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/PredictAndBuildCryoEM_4/PredictAndBuild_4_overall_best.pdb
Chain information for PredictAndBuild_4_overall_best.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
Computing secondary structure
> info #4
2 models
#4, NewAF_HpaCas9_AcrIIC6_sgRNA20_clean_5OH_SEQRESfixed.pdb map 3.2, hidden
size 111,113,99, step 1, voxel size 1.0667, level 0.1035, value range 0 -
2.6513, value type float32, 0 symmetry operators
#4.1, surface, shown, 228360 triangles
> info chains #4
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> volume #3 level 0.116
> open /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/PredictAndBuildCryoEM_4/PredictAndBuild_4_overall_best_superposed_predicted_models.pdb
Chain information for
PredictAndBuild_4_overall_best_superposed_predicted_models.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
Computing secondary structure
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> color #5 by chain
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #5 bychain
> hide #6 models
> hide #!3 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> select #5/B
609 atoms, 621 bonds, 76 residues, 1 model selected
> show sel atoms
> show #6 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #6 models
> hide #1 models
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> select clear
> nucleotides #!5 atoms
> style nucleic & #!5 stick
Changed 2134 atom styles
> show #1 models
> select #1/B
623 atoms, 636 bonds, 76 residues, 1 model selected
> show sel atoms
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> select #5/B
609 atoms, 621 bonds, 76 residues, 1 model selected
> hide sel atoms
> show #6 models
> hide #6 models
> close #6#5
> show #1 models
> close #2
> rename #3 id #2
> rename #4 id #3
> open /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/PredictAndBuildCryoEM_5/PredictAndBuild_5_overall_best.pdb
Chain information for PredictAndBuild_5_overall_best.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
Computing secondary structure
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> color #4 bychain
> show #!3 models
> hide #!3 models
> show #!2 models
> volume #2 level 0.2196
> show #1 models
> hide #!2 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> open /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/PredictAndBuildCryoEM_5/PredictAndBuild_5_CarryOn/PredictAndBuild_5_rebuilt_3_cycle_1.pdb
Chain information for PredictAndBuild_5_rebuilt_3_cycle_1.pdb #5
---
Chain | Description
C | No description available
Computing secondary structure
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!4 models
> hide #5 models
> show #5 models
> show #!4 models
> show #1 models
> hide #!4 models
> open /Users/iktae/PhenixProjects/SNU-HpaCas9-AcrIIC6-J43-validation/
'/Users/iktae/PhenixProjects/SNU-HpaCas9-AcrIIC6-J43-validation/' has no
suffix
> 04_PredictAndBuild/PAB5_clean_audit/00_prepared/inputs/
Unknown command: 04_PredictAndBuild/PAB5_clean_audit/00_prepared/inputs/
> PAB5_full_untrimmed_rebuilt_ABC.pdb
Unknown command: PAB5_full_untrimmed_rebuilt_ABC.pdb
> open /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/04_PredictAndBuild/PAB5_clean_audit/00_prepared/inputs/PAB5_full_untrimmed_rebuilt_ABC.pdb
Chain information for PAB5_full_untrimmed_rebuilt_ABC.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
Computing secondary structure
> hide #5 models
> hide #1 models
> select #7/B
Nothing selected
> select #7.B
Expected an objects specifier or a keyword
> select #6/B
609 atoms, 621 bonds, 76 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B #4/B #6/B
Alignment identifier is 1
> select #1/B:41-49,54-65,69-74 #4/B:41-49,54-65,69-74 #6/B:41-49,54-65,69-74
666 atoms, 672 bonds, 81 residues, 3 models selected
> select #1/B:26 #4/B:26 #6/B:26
36 atoms, 36 bonds, 3 residues, 3 models selected
> select #1/B:26-34 #4/B:26-34 #6/B:26-34
210 atoms, 216 bonds, 27 residues, 3 models selected
1 [ID: 1] region 3 chains [26-34] RMSD: 2.130
> select add #1
12253 atoms, 12778 bonds, 1286 residues, 3 models selected
> select subtract #1
134 atoms, 138 bonds, 18 residues, 2 models selected
> select add #4
11265 atoms, 11709 bonds, 4 pseudobonds, 1208 residues, 3 models selected
> select subtract #4
67 atoms, 69 bonds, 9 residues, 1 model selected
> select add #6
12109 atoms, 12629 bonds, 1268 residues, 1 model selected
> select subtract #6
Nothing selected
> hide #6 models
> show #6 models
> select add #6
12109 atoms, 12629 bonds, 1268 residues, 1 model selected
> select subtract #6
Nothing selected
> select #1/B:26-27 #4/B:26-27 #6/B:26-27
60 atoms, 60 bonds, 6 residues, 3 models selected
> select #1/B:26-34 #4/B:26-34 #6/B:26-34
210 atoms, 216 bonds, 27 residues, 3 models selected
1 [ID: 1] region 3 chains [26-34] RMSD: 2.130
> close all
> open /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/04_PredictAndBuild/PAB5_clean_audit/00_prepared/inputs/PAB5_full_untrimmed_rebuilt_ABC.pdb
Chain information for PAB5_full_untrimmed_rebuilt_ABC.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
Computing secondary structure
> open /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/04_PredictAndBuild/PAB5_clean_audit/00_prepared/inputs/PAB5_full_superposed_predicted_reference.pdb
Chain information for PAB5_full_superposed_predicted_reference.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open
> /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/cryosparc_P7_J43_004_volume_map_sharp.mrc
Opened cryosparc_P7_J43_004_volume_map_sharp.mrc as #3, grid size 256,256,256,
pixel 0.934, shown at level 0.0814, step 1, values float32
> open
> /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/cryosparc_P7_J43_004_volume_map.mrc
Opened cryosparc_P7_J43_004_volume_map.mrc as #4, grid size 256,256,256, pixel
0.934, shown at level 0.0656, step 1, values float32
Computing secondary structure
> volume #3 level 0.1687
> hide #!4 models
> hide #!3 models
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
> hide #1 atoms
> hide #2 atoms
> show #1/B:19-38 atoms
> show #2/B:19-38 atoms
> style #1/B:19-38 stick
Changed 157 atom styles
> style #2/B:19-38 stick
Changed 171 atom styles
> color #1/B:19-38 cyan
> color #2/B:19-38 magenta
> show #1/A:250,444,446,464 atoms
> show #1/C:9 atoms
> style #1/A:250,444,446,464 stick
Changed 40 atom styles
> style #1/C:9 stick
Changed 23 atom styles
> select #1/B:19-38 | #2/B:19-38 | #1/A:250,444,446,464 | #1/C:9
391 atoms, 400 bonds, 45 residues, 2 models selected
> view sel
> volume zone #3 nearAtoms #1/B:19-38 range 4
> volume zone #4 nearAtoms #1/B:19-38 range 4
> show #!3 models
> show #!4 models
> volume #3 style mesh
> volume #4 style mesh
> distance #1/B:24@C #1/B:25@N
Distance between PAB5_full_untrimmed_rebuilt_ABC.pdb #1/B ASN 24 C and HIS 25
N: 3.292Å
> distance #1/B:29@C #1/B:30@N
Distance between PAB5_full_untrimmed_rebuilt_ABC.pdb #1/B ASN 29 C and ILE 30
N: 4.884Å
> distance #2/B:24@C #2/B:25@N
Distance between PAB5_full_superposed_predicted_reference.pdb #2/B ASN 24 C
and HIS 25 N: 1.337Å
> distance #2/B:29@C #2/B:30@N
Distance between PAB5_full_superposed_predicted_reference.pdb #2/B ASN 29 C
and ILE 30 N: 1.331Å
> distance #1/A:464@OE1 #1/B:26@CE2
Distance between PAB5_full_untrimmed_rebuilt_ABC.pdb #1/A GLU 464 OE1 and /B
TYR 26 CE2: 0.913Å
> distance #1/B:27@OD2 #1/C:9@OP1
Distance between PAB5_full_untrimmed_rebuilt_ABC.pdb #1/B ASP 27 OD2 and /C G
9 OP1: 0.901Å
> distance #1/B:18@C #1/B:19@N
Distance between PAB5_full_untrimmed_rebuilt_ABC.pdb #1/B THR 18 C and PHE 19
N: 1.333Å
> distance #1/B:38@C #1/B:39@N
Distance between PAB5_full_untrimmed_rebuilt_ABC.pdb #1/B LYS 38 C and LEU 39
N: 1.329Å
> distance #2/B:18@C #2/B:19@N
Distance between PAB5_full_superposed_predicted_reference.pdb #2/B THR 18 C
and PHE 19 N: 1.323Å
> distance #2/B:38@C #2/B:39@N
Distance between PAB5_full_superposed_predicted_reference.pdb #2/B LYS 38 C
and LEU 39 N: 1.320Å
> hide #2 models
> volume #3 style surface
> volume #3 style mesh
> hide #!4 models
> show #2 models
> hide #2 models
> hide #!3 models
> show #!3 models
> show #2 models
> hide #1 models
> close all
> open /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/04_PredictAndBuild/PAB5_clean_audit/03_local_repair/PAB5_fullABC_B19-38_reference_graft_raw_v1.pdb
Chain information for PAB5_fullABC_B19-38_reference_graft_raw_v1.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
Computing secondary structure
> open
> /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/cryosparc_P7_J43_004_volume_map_sharp.mrc
Opened cryosparc_P7_J43_004_volume_map_sharp.mrc as #2, grid size 256,256,256,
pixel 0.934, shown at level 0.0814, step 1, values float32
> open
> /Users/iktae/PhenixProjects/HpaCas9_J43_validation/input/cryosparc_P7_J43_004_volume_map.mrc
Opened cryosparc_P7_J43_004_volume_map.mrc as #3, grid size 256,256,256, pixel
0.934, shown at level 0.0656, step 1, values float32
> hide #!2 models
> hide #!3 models
> show #!2 models
> volume #2 level 0.1955
> volume #2 style image region 0,0,127,255,255,127 step 1 showOutlineBox true
> volume #2 region 0,0,0,255,255,255 step 1
> volume #2 style mesh region 0,0,0,255,255,255 step 1
> volume #2 change image level -0.02881,0 level 0.1865,0.8 level 1.841,1
> volume #2 level 0.1754
> hide #1 atoms
> show #1/B:17-40 atoms
> style #1/B:17-40 stick
Changed 200 atom styles
> select #1/B:17-40
200 atoms, 205 bonds, 24 residues, 1 model selected
> view sel
> volume zone #2 nearAtoms #1/B:17-40 range 4
> volume zone #3 nearAtoms #1/B:17-40 range 4
> distance #1/B:18@C #1/B:19@N
Distance between /B THR 18 C and PHE 19 N: 1.224Å
> distance #1/B:24@C #1/B:25@N
Distance between /B ASN 24 C and HIS 25 N: 1.337Å
> distance #1/B:29@C #1/B:30@N
Distance between /B ASN 29 C and ILE 30 N: 1.331Å
> distance #1/B:38@C #1/B:39@N
Distance between /B LYS 38 C and LEU 39 N: 1.276Å
> distance #1/A:464@OE1 #1/B:26@CE2
Distance between /A GLU 464 OE1 and /B TYR 26 CE2: 3.865Å
> distance #1/B:27@OD2 #1/C:9@OP1
Distance between /B ASP 27 OD2 and /C G 9 OP1: 1.635Å
> open /Users/iktae/PhenixProjects/SNU-
> HpaCas9-AcrIIC6-J43-validation/04_PredictAndBuild/PAB5_clean_audit/03_local_repair/PAB5_fullABC_B19-38_fromReference_v1.pdb
Chain information for PAB5_fullABC_B19-38_fromReference_v1.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
Computing secondary structure
> rename #5 id #6
> hide #1 models
> hide #!2 models
> hide #!4 models
> hide #4.1 models
> distance #6/B:18@C #6/B:19@N
Distance between PAB5_fullABC_B19-38_fromReference_v1.pdb #6/B THR 18 C and
PHE 19 N: 1.224Å
> distance #6/B:24@C #6/B:25@N
Distance between PAB5_fullABC_B19-38_fromReference_v1.pdb #6/B ASN 24 C and
HIS 25 N: 1.337Å
> distance #6/B:29@C #6/B:30@N
Distance between PAB5_fullABC_B19-38_fromReference_v1.pdb #6/B ASN 29 C and
ILE 30 N: 1.331Å
> distance #6/B:38@C #6/B:39@N
Distance between PAB5_fullABC_B19-38_fromReference_v1.pdb #6/B LYS 38 C and
LEU 39 N: 1.276Å
> distance #6/A:464@OE1 #6/B:26@CE2
Distance between PAB5_fullABC_B19-38_fromReference_v1.pdb #6/A GLU 464 OE1 and
/B TYR 26 CE2: 3.865Å
> distance #6/B:27@OD2 #6/C:9@OP1
Distance between PAB5_fullABC_B19-38_fromReference_v1.pdb #6/B ASP 27 OD2 and
/C G 9 OP1: 1.635Å
> close all
> open PAB5_fullABC_B19-38_fromReference_v1.pdb
No such file/path: PAB5_fullABC_B19-38_fromReference_v1.pdb
> open cryosparc_P7_J43_004_volume_map.mrc
No such file/path: cryosparc_P7_J43_004_volume_map.mrc
> open cryosparc_P7_J43_004_volume_map_sharp.mrc
No such file/path: cryosparc_P7_J43_004_volume_map_sharp.mrc
> addh #1
No structures specified
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde select #1
Missing or invalid "model" argument: Must specify exactly one atomic
structure, got 0 for #1.
> clipper associate #2 toModel #1
Invalid "toModel" argument: Must specify 1 model, got 0
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4 Max
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: Mac16,5
Model Number: MX303LL/A
Chip: Apple M4 Max
Total Number of Cores: 14 (10 Performance and 4 Efficiency)
Memory: 36 GB
System Firmware Version: 18000.121.3
OS Loader Version: 18000.121.3
Software:
System Software Overview:
System Version: macOS 26.5.2 (25F84)
Kernel Version: Darwin 25.5.0
Time since boot: 8 days, 11 minutes
Graphics/Displays:
Apple M4 Max:
Chipset Model: Apple M4 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 32
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
2777M:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.26.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ISOLDE: 1.11.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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