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Opened 4 days ago
Closed 3 days ago
#19882 closed defect (duplicate)
Crash in swap_buffers exposing status line during Mac wakeup, macOS 26
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-26.3-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: Bus error
Current thread 0x000000020af43080 (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/graphics/opengl.py", line 248 in swap_buffers
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 561 in swap_buffers
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 166 in status
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 98 in _expose_event
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, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, PIL._imaging, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.dssp._dssp, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw, PIL._avif, PIL._webp, cython.cimports.libc.math, scipy._lib._ccallback_c, 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.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.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct (total: 111)
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"codeSigningTeamID" : "LWV8X224YF",
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
MALLOC_LARGE 667800000-66affc000 [ 56.0M] rw-\/rwx SM=PRV
GAP OF 0x21004000 BYTES
---> commpage (reserved) 68c000000-983400000 [ 11.9G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL 983400000-983800000 [ 4096K] rw-\/rwx SM=PRV ",
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"vmregioninfo" : "0x900001600 is in 0x68c000000-0x983400000; bytes after start: 10536097280 bytes before end: 2202003967
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
MALLOC_LARGE 667800000-66affc000 [ 56.0M] rw-\/rwx SM=PRV
GAP OF 0x21004000 BYTES
---> commpage (reserved) 68c000000-983400000 [ 11.9G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL 983400000-983800000 [ 4096K] rw-\/rwx SM=PRV ",
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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
> open
> /Users/whole.grains/Desktop/16-33a_modelling/head/RealSpaceRefine_2/head_fit_real_space_refined_002.pdb
Chain information for head_fit_real_space_refined_002.pdb #1
---
Chain | Description
A | No description available
> open /Users/whole.grains/Desktop/16-33a_modelling/head/head_sharpened.ccp4
Opened head_sharpened.ccp4 as #2, grid size 600,600,600, pixel 0.59, shown at
level 0.00073, step 4, values float32
> volume #2 level 0.01325
> open
> /Users/whole.grains/Downloads/cryosparc_P1_J1786_006_volume_mask_refine.mrc
Opened cryosparc_P1_J1786_006_volume_mask_refine.mrc as #3, grid size
600,600,600, pixel 0.59, shown at level 5e-05, step 4, values float32
> volume flip #3
Opened cryosparc_P1_J1786_006_volume_mask_refine.mrc z flip as #4, grid size
600,600,600, pixel 0.59, shown at step 1, values float32
> close #3
> volume #4 level 0.632
> volume #4 color #ffffb20d
> volume #4 color #bbbbbb
> volume #4 color #bbbbbb03
> open
> /Users/whole.grains/Desktop/16-33a_modelling/body/RealSpaceRefine_12/body_refined_update_real_space_refined_012_01.pdb
Chain information for body_refined_update_real_space_refined_012_01.pdb #3
---
Chain | Description
A | No description available
B | No description available
> dssp
> open "/Users/whole.grains/Desktop/16-33a_modelling/body/Sharpened
> maps/full_map_sharpened.ccp4"
Opened full_map_sharpened.ccp4 as #5, grid size 600,600,600, pixel 0.59, shown
at level 0.00263, step 4, values float32
> open /Users/whole.grains/Desktop/16-33a_modelling/body/mask.mrc
Opened mask.mrc as #6, grid size 600,600,600, pixel 0.59, shown at level
0.0956, step 4, values float32
> volume #6 level 0.5118
> volume #6 color #bbbbbb
> volume #6 color #bbbbbb03
> volume #5 color #c3c3c3
> color #5 #c3c3c3ff models
> color #6 #cacacaff models
> volume #6 color #cacaca0d
> volume #4 color #bbbbbb0d
> volume #5 level 0.01148
> select add #3
5750 atoms, 5857 bonds, 3 pseudobonds, 716 residues, 2 models selected
> select add #5
5750 atoms, 5857 bonds, 3 pseudobonds, 716 residues, 4 models selected
> select add #6
5750 atoms, 5857 bonds, 3 pseudobonds, 716 residues, 6 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,1,0,0,-47.09,0,1,0,-98.577,0,0,1,5.131,#5,1,0,0,-47.09,0,1,0,-98.577,0,0,1,5.131,#6,1,0,0,-47.09,0,1,0,-98.577,0,0,1,5.131
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.67233,-0.42216,-0.60808,193.31,-0.73887,-0.43289,-0.51641,385.6,-0.045223,0.79649,-0.60296,141.22,#5,0.67233,-0.42216,-0.60808,193.31,-0.73887,-0.43289,-0.51641,385.6,-0.045223,0.79649,-0.60296,141.22,#6,0.67233,-0.42216,-0.60808,193.31,-0.73887,-0.43289,-0.51641,385.6,-0.045223,0.79649,-0.60296,141.22
> view matrix models
> #3,0.55947,-0.54199,-0.62708,238.62,-0.82862,-0.34808,-0.43844,372.25,0.019357,0.76491,-0.64385,142.75,#5,0.55947,-0.54199,-0.62708,238.62,-0.82862,-0.34808,-0.43844,372.25,0.019357,0.76491,-0.64385,142.75,#6,0.55947,-0.54199,-0.62708,238.62,-0.82862,-0.34808,-0.43844,372.25,0.019357,0.76491,-0.64385,142.75
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.55947,-0.54199,-0.62708,232.7,-0.82862,-0.34808,-0.43844,373.81,0.019357,0.76491,-0.64385,187.19,#5,0.55947,-0.54199,-0.62708,232.7,-0.82862,-0.34808,-0.43844,373.81,0.019357,0.76491,-0.64385,187.19,#6,0.55947,-0.54199,-0.62708,232.7,-0.82862,-0.34808,-0.43844,373.81,0.019357,0.76491,-0.64385,187.19
> view matrix models
> #3,0.55947,-0.54199,-0.62708,228.08,-0.82862,-0.34808,-0.43844,387.78,0.019357,0.76491,-0.64385,185.4,#5,0.55947,-0.54199,-0.62708,228.08,-0.82862,-0.34808,-0.43844,387.78,0.019357,0.76491,-0.64385,185.4,#6,0.55947,-0.54199,-0.62708,228.08,-0.82862,-0.34808,-0.43844,387.78,0.019357,0.76491,-0.64385,185.4
> view matrix models
> #3,0.55947,-0.54199,-0.62708,229.43,-0.82862,-0.34808,-0.43844,389.14,0.019357,0.76491,-0.64385,184.99,#5,0.55947,-0.54199,-0.62708,229.43,-0.82862,-0.34808,-0.43844,389.14,0.019357,0.76491,-0.64385,184.99,#6,0.55947,-0.54199,-0.62708,229.43,-0.82862,-0.34808,-0.43844,389.14,0.019357,0.76491,-0.64385,184.99
> open "/Users/whole.grains/Desktop/PDB and
> MRC/fold_vps33a_vps16/fold_vps33a_vps16_model_0.cif"
Chain information for fold_vps33a_vps16_model_0.cif #7
---
Chain | Description
A | .
B | .
Computing secondary structure
> select subtract #3
4 models selected
> select subtract #5
2 models selected
> select subtract #6
Nothing selected
> select add #7
11424 atoms, 11657 bonds, 1435 residues, 1 model selected
> view matrix models #7,1,0,0,111.09,0,1,0,0.97154,0,0,1,1.9178
> view matrix models #7,1,0,0,128,0,1,0,146.37,0,0,1,98.093
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.095869,0.9635,0.24995,128.21,-0.90859,0.017854,-0.41732,142.78,-0.40655,-0.26711,0.87371,96.849
> view matrix models
> #7,-0.43931,0.89781,0.030766,128.34,-0.87019,-0.4168,-0.26277,140.41,-0.22309,-0.14221,0.96437,97.26
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.43931,0.89781,0.030766,117.59,-0.87019,-0.4168,-0.26277,154.81,-0.22309,-0.14221,0.96437,191.09
> view matrix models
> #7,-0.43931,0.89781,0.030766,141.81,-0.87019,-0.4168,-0.26277,124.28,-0.22309,-0.14221,0.96437,196.1
> view matrix models
> #7,-0.43931,0.89781,0.030766,136.37,-0.87019,-0.4168,-0.26277,128.21,-0.22309,-0.14221,0.96437,203.2
> matchmaker #7 to #4
No 'to' model specified
> view matrix models
> #7,-0.43931,0.89781,0.030766,135.82,-0.87019,-0.4168,-0.26277,125.98,-0.22309,-0.14221,0.96437,209.09
> matchmaker #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 body_refined_update_real_space_refined_012_01.pdb, chain B (#3)
with fold_vps33a_vps16_model_0.cif, chain B (#7), sequence alignment score =
2750
RMSD between 462 pruned atom pairs is 1.114 angstroms; (across all 566 pairs:
1.625)
> select subtract #7
Nothing selected
> select add #1
4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 2 models selected
> select add #2
4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 4 models selected
> select add #4
4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 6 models selected
> view matrix models
> #1,1,0,0,-1.0779,0,1,0,3.1558,0,0,1,13.734,#2,1,0,0,-1.0779,0,1,0,3.1558,0,0,1,13.734,#4,1,0,0,-1.0779,0,1,0,3.1558,0,0,1,13.734
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.54767,0.043536,-0.83556,216.12,0.12617,0.98293,0.13391,-39.307,0.82712,-0.17876,0.53283,-17.32,#2,0.54767,0.043536,-0.83556,216.12,0.12617,0.98293,0.13391,-39.307,0.82712,-0.17876,0.53283,-17.32,#4,0.54767,0.043536,-0.83556,216.12,0.12617,0.98293,0.13391,-39.307,0.82712,-0.17876,0.53283,-17.32
> view matrix models
> #1,0.37601,0.37658,-0.84665,190.11,-0.21291,0.92436,0.31658,-2.1319,0.90182,0.061224,0.42775,-53.576,#2,0.37601,0.37658,-0.84665,190.11,-0.21291,0.92436,0.31658,-2.1319,0.90182,0.061224,0.42775,-53.576,#4,0.37601,0.37658,-0.84665,190.11,-0.21291,0.92436,0.31658,-2.1319,0.90182,0.061224,0.42775,-53.576
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.37601,0.37658,-0.84665,206.09,-0.21291,0.92436,0.31658,-33.67,0.90182,0.061224,0.42775,-1.5982,#2,0.37601,0.37658,-0.84665,206.09,-0.21291,0.92436,0.31658,-33.67,0.90182,0.061224,0.42775,-1.5982,#4,0.37601,0.37658,-0.84665,206.09,-0.21291,0.92436,0.31658,-33.67,0.90182,0.061224,0.42775,-1.5982
> hide #!2 models
> view matrix models
> #1,0.37601,0.37658,-0.84665,206.11,-0.21291,0.92436,0.31658,-34.084,0.90182,0.061224,0.42775,-3.949,#2,0.37601,0.37658,-0.84665,206.11,-0.21291,0.92436,0.31658,-34.084,0.90182,0.061224,0.42775,-3.949,#4,0.37601,0.37658,-0.84665,206.11,-0.21291,0.92436,0.31658,-34.084,0.90182,0.061224,0.42775,-3.949
> view matrix models
> #1,0.37601,0.37658,-0.84665,213.05,-0.21291,0.92436,0.31658,-37.733,0.90182,0.061224,0.42775,-21.783,#2,0.37601,0.37658,-0.84665,213.05,-0.21291,0.92436,0.31658,-37.733,0.90182,0.061224,0.42775,-21.783,#4,0.37601,0.37658,-0.84665,213.05,-0.21291,0.92436,0.31658,-37.733,0.90182,0.061224,0.42775,-21.783
> view matrix models
> #1,0.37601,0.37658,-0.84665,211.14,-0.21291,0.92436,0.31658,-39.986,0.90182,0.061224,0.42775,-24.759,#2,0.37601,0.37658,-0.84665,211.14,-0.21291,0.92436,0.31658,-39.986,0.90182,0.061224,0.42775,-24.759,#4,0.37601,0.37658,-0.84665,211.14,-0.21291,0.92436,0.31658,-39.986,0.90182,0.061224,0.42775,-24.759
> view matrix models
> #1,0.37601,0.37658,-0.84665,208.95,-0.21291,0.92436,0.31658,-33.133,0.90182,0.061224,0.42775,-28.911,#2,0.37601,0.37658,-0.84665,208.95,-0.21291,0.92436,0.31658,-33.133,0.90182,0.061224,0.42775,-28.911,#4,0.37601,0.37658,-0.84665,208.95,-0.21291,0.92436,0.31658,-33.133,0.90182,0.061224,0.42775,-28.911
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.38108,0.48007,-0.79014,180.25,-0.35375,0.8653,0.35513,-5.1499,0.85419,0.14418,0.49957,-47.568,#2,0.38108,0.48007,-0.79014,180.25,-0.35375,0.8653,0.35513,-5.1499,0.85419,0.14418,0.49957,-47.568,#4,0.38108,0.48007,-0.79014,180.25,-0.35375,0.8653,0.35513,-5.1499,0.85419,0.14418,0.49957,-47.568
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.38108,0.48007,-0.79014,183.44,-0.35375,0.8653,0.35513,-9.5357,0.85419,0.14418,0.49957,-48.134,#2,0.38108,0.48007,-0.79014,183.44,-0.35375,0.8653,0.35513,-9.5357,0.85419,0.14418,0.49957,-48.134,#4,0.38108,0.48007,-0.79014,183.44,-0.35375,0.8653,0.35513,-9.5357,0.85419,0.14418,0.49957,-48.134
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.38776,0.44456,-0.80747,191.47,-0.28052,0.89137,0.35604,-26.942,0.87804,0.088449,0.47035,-37.508,#2,0.38776,0.44456,-0.80747,191.47,-0.28052,0.89137,0.35604,-26.942,0.87804,0.088449,0.47035,-37.508,#4,0.38776,0.44456,-0.80747,191.47,-0.28052,0.89137,0.35604,-26.942,0.87804,0.088449,0.47035,-37.508
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.92544,0.058135,-0.3744,89.441,-0.27634,0.7796,-0.56202,152.05,0.2592,0.62358,0.73754,-69.468,#2,0.92544,0.058135,-0.3744,89.441,-0.27634,0.7796,-0.56202,152.05,0.2592,0.62358,0.73754,-69.468,#4,0.92544,0.058135,-0.3744,89.441,-0.27634,0.7796,-0.56202,152.05,0.2592,0.62358,0.73754,-69.468
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.92544,0.058135,-0.3744,82.868,-0.27634,0.7796,-0.56202,161.75,0.2592,0.62358,0.73754,-67.862,#2,0.92544,0.058135,-0.3744,82.868,-0.27634,0.7796,-0.56202,161.75,0.2592,0.62358,0.73754,-67.862,#4,0.92544,0.058135,-0.3744,82.868,-0.27634,0.7796,-0.56202,161.75,0.2592,0.62358,0.73754,-67.862
> view matrix models
> #1,0.92544,0.058135,-0.3744,78.773,-0.27634,0.7796,-0.56202,159.49,0.2592,0.62358,0.73754,-63.308,#2,0.92544,0.058135,-0.3744,78.773,-0.27634,0.7796,-0.56202,159.49,0.2592,0.62358,0.73754,-63.308,#4,0.92544,0.058135,-0.3744,78.773,-0.27634,0.7796,-0.56202,159.49,0.2592,0.62358,0.73754,-63.308
> view matrix models
> #1,0.92544,0.058135,-0.3744,79.296,-0.27634,0.7796,-0.56202,159.12,0.2592,0.62358,0.73754,-63.465,#2,0.92544,0.058135,-0.3744,79.296,-0.27634,0.7796,-0.56202,159.12,0.2592,0.62358,0.73754,-63.465,#4,0.92544,0.058135,-0.3744,79.296,-0.27634,0.7796,-0.56202,159.12,0.2592,0.62358,0.73754,-63.465
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.92181,0.0056881,-0.3876,91.331,-0.23883,0.7959,-0.55633,148.78,0.30533,0.6054,0.73503,-67.887,#2,0.92181,0.0056881,-0.3876,91.331,-0.23883,0.7959,-0.55633,148.78,0.30533,0.6054,0.73503,-67.887,#4,0.92181,0.0056881,-0.3876,91.331,-0.23883,0.7959,-0.55633,148.78,0.30533,0.6054,0.73503,-67.887
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.92181,0.0056881,-0.3876,89.025,-0.23883,0.7959,-0.55633,150.6,0.30533,0.6054,0.73503,-67.625,#2,0.92181,0.0056881,-0.3876,89.025,-0.23883,0.7959,-0.55633,150.6,0.30533,0.6054,0.73503,-67.625,#4,0.92181,0.0056881,-0.3876,89.025,-0.23883,0.7959,-0.55633,150.6,0.30533,0.6054,0.73503,-67.625
> view matrix models
> #1,0.92181,0.0056881,-0.3876,88.21,-0.23883,0.7959,-0.55633,150.43,0.30533,0.6054,0.73503,-67.116,#2,0.92181,0.0056881,-0.3876,88.21,-0.23883,0.7959,-0.55633,150.43,0.30533,0.6054,0.73503,-67.116,#4,0.92181,0.0056881,-0.3876,88.21,-0.23883,0.7959,-0.55633,150.43,0.30533,0.6054,0.73503,-67.116
> view matrix models
> #1,0.92181,0.0056881,-0.3876,88.666,-0.23883,0.7959,-0.55633,150.28,0.30533,0.6054,0.73503,-67.117,#2,0.92181,0.0056881,-0.3876,88.666,-0.23883,0.7959,-0.55633,150.28,0.30533,0.6054,0.73503,-67.117,#4,0.92181,0.0056881,-0.3876,88.666,-0.23883,0.7959,-0.55633,150.28,0.30533,0.6054,0.73503,-67.117
> view matrix models
> #1,0.92181,0.0056881,-0.3876,88.196,-0.23883,0.7959,-0.55633,150.08,0.30533,0.6054,0.73503,-66.71,#2,0.92181,0.0056881,-0.3876,88.196,-0.23883,0.7959,-0.55633,150.08,0.30533,0.6054,0.73503,-66.71,#4,0.92181,0.0056881,-0.3876,88.196,-0.23883,0.7959,-0.55633,150.08,0.30533,0.6054,0.73503,-66.71
> hide #7 models
> show #!2 models
> color #4 #bbbbbbff models
> color #6 #bbbbbbff models
> color #5 #bbbbbbff models
> color #6 #bbbbbb0d models
> color #4 #bbbbbb0d models
> select subtract #1
4 models selected
> select subtract #2
2 models selected
> select subtract #4
Nothing selected
> ui tool show Distances
> hide #!5 models
> hide #!2 models
> ui mousemode right "rotate selected models"
> show #7 models
> hide #7 models
> hide #!4 models
> hide #!6 models
> select clear
> select #3/A:642
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:624
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> color sel #d3be99ff
> view matrix models
> #1,0.92032,0.0079164,-0.39108,88.692,-0.24283,0.79538,-0.55535,150.68,0.30666,0.60607,0.73392,-66.855
> view matrix models
> #1,0.92759,0.013038,-0.37338,83.431,-0.24139,0.7837,-0.57231,155.43,0.28516,0.621,0.7301,-65.024
> view matrix models
> #1,0.92437,0.006702,-0.38145,86.492,-0.23591,0.79581,-0.5577,149.84,0.29982,0.60551,0.7372,-66.171
> select #3/A:642
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> color sel #daabe0ff
> view matrix models
> #3,0.5519,-0.55109,-0.62587,232.16,-0.83336,-0.33728,-0.43789,387.96,0.030225,0.76325,-0.6454,183.65
> select #3/A:643
11 atoms, 10 bonds, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select #3/A:642@N
1 atom, 1 residue, 1 model selected
> select #1/A:624@O
1 atom, 1 residue, 1 model selected
> select add #3/A:642@N
2 atoms, 2 residues, 2 models selected
> distance #1/A:624@O #3/A:642@N
Distance between head_fit_real_space_refined_002.pdb #1/A ASP 624 O and
body_refined_update_real_space_refined_012_01.pdb #3/A GLU 642 N: 30.894Å
> close #8.1
> view matrix models
> #1,0.97854,-0.040619,-0.20203,50.147,-0.12705,0.653,-0.74663,194.45,0.16225,0.75627,0.63382,-49.149,#3,0.67063,-0.39856,-0.62562,187.2,-0.71611,-0.56786,-0.40587,401.25,-0.1935,0.7202,-0.66623,231.53
> close #8.1
> hide #8 models
> show #8 models
> select add #3
5751 atoms, 5857 bonds, 3 pseudobonds, 717 residues, 3 models selected
> show sel cartoons
> select add #1
10281 atoms, 10491 bonds, 4 pseudobonds, 1287 residues, 4 models selected
> show sel atoms
> hide sel atoms
> select subtract #1
5750 atoms, 5857 bonds, 3 pseudobonds, 716 residues, 2 models selected
> select subtract #3
Nothing selected
> split chains
Did not split head_fit_real_space_refined_002.pdb, has only one piece
Split body_refined_update_real_space_refined_012_01.pdb (#3) into 2 models
Split fold_vps33a_vps16_model_0.cif (#7) into 2 models
Chain information for body_refined_update_real_space_refined_012_01.pdb A #3.1
---
Chain | Description
A | No description available
Chain information for body_refined_update_real_space_refined_012_01.pdb B #3.2
---
Chain | Description
B | No description available
Chain information for fold_vps33a_vps16_model_0.cif A #7.1
---
Chain | Description
A | No description available
Chain information for fold_vps33a_vps16_model_0.cif B #7.2
---
Chain | Description
B | No description available
> color #1 #edbd7bff
> color #3.1 #72411cff
> color #3.1 #edbd7bff
> color #3.2 #72411cff
> color #7.1 #72411cff
> color #7.1 #c3c3c3ff
> color #7.2 #c3c3c3ff
> color #8 #e9c78aff models
> select subtract #8
Nothing selected
> hide #8 models
> show #8 models
Exactly two atoms must be selected!
> show #7.1 models
> show #7.2 models
> select subtract #8
Nothing selected
> select add #7.1
6663 atoms, 6804 bonds, 839 residues, 1 model selected
> select add #7.2
11424 atoms, 11657 bonds, 1435 residues, 2 models selected
> view matrix models
> #7.1,-0.39814,0.85895,-0.32202,144.42,-0.80417,-0.49571,-0.328,121.65,-0.44137,0.12836,0.8881,226.16,#7.2,-0.39814,0.85895,-0.32202,144.42,-0.80417,-0.49571,-0.328,121.65,-0.44137,0.12836,0.8881,226.16
> ui mousemode right "translate selected models"
> view matrix models
> #7.1,-0.39814,0.85895,-0.32202,145.12,-0.80417,-0.49571,-0.328,121.46,-0.44137,0.12836,0.8881,222.35,#7.2,-0.39814,0.85895,-0.32202,145.12,-0.80417,-0.49571,-0.328,121.46,-0.44137,0.12836,0.8881,222.35
> view matrix models
> #7.1,-0.39814,0.85895,-0.32202,145.38,-0.80417,-0.49571,-0.328,119.99,-0.44137,0.12836,0.8881,221.56,#7.2,-0.39814,0.85895,-0.32202,145.38,-0.80417,-0.49571,-0.328,119.99,-0.44137,0.12836,0.8881,221.56
> hide #7.1 models
> show #7.1 models
> matchmaker #7.1 to #3.1
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 body_refined_update_real_space_refined_012_01.pdb A, chain A (#3.1)
with fold_vps33a_vps16_model_0.cif A, chain A (#7.1), sequence alignment score
= 775.8
RMSD between 138 pruned atom pairs is 0.940 angstroms; (across all 150 pairs:
1.104)
> matchmaker #7.2 to #3.2
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 body_refined_update_real_space_refined_012_01.pdb B, chain B (#3.2)
with fold_vps33a_vps16_model_0.cif B, chain B (#7.2), sequence alignment score
= 2750
RMSD between 462 pruned atom pairs is 1.114 angstroms; (across all 566 pairs:
1.625)
> select subtract #7.1
4761 atoms, 4853 bonds, 596 residues, 1 model selected
> select add #7
11424 atoms, 11657 bonds, 1435 residues, 3 models selected
> select subtract #7
Nothing selected
> select add #1
4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 2 models selected
> select add #2
4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 4 models selected
> select add #3.2
9057 atoms, 9245 bonds, 4 pseudobonds, 1137 residues, 6 models selected
> select subtract #3.2
4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 4 models selected
> select add #4
4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 6 models selected
> view matrix models
> #1,0.97854,-0.040619,-0.20203,49.793,-0.12705,0.653,-0.74663,194.52,0.16225,0.75627,0.63382,-50.066,#2,0.92181,0.0056881,-0.3876,87.843,-0.23883,0.7959,-0.55633,150.16,0.30533,0.6054,0.73503,-67.627,#4,0.92181,0.0056881,-0.3876,87.843,-0.23883,0.7959,-0.55633,150.16,0.30533,0.6054,0.73503,-67.627
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.98676,-0.046354,-0.1554,41.059,-0.094565,0.61401,-0.78361,202.1,0.13174,0.78793,0.6015,-44.425,#2,0.93833,-0.0097655,-0.34561,80.356,-0.21527,0.76571,-0.60609,160.21,0.27055,0.64311,0.71639,-65.056,#4,0.93833,-0.0097655,-0.34561,80.356,-0.21527,0.76571,-0.60609,160.21,0.27055,0.64311,0.71639,-65.056
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.98676,-0.046354,-0.1554,40.712,-0.094565,0.61401,-0.78361,201.87,0.13174,0.78793,0.6015,-44.454,#2,0.93833,-0.0097655,-0.34561,80.009,-0.21527,0.76571,-0.60609,159.98,0.27055,0.64311,0.71639,-65.085,#4,0.93833,-0.0097655,-0.34561,80.009,-0.21527,0.76571,-0.60609,159.98,0.27055,0.64311,0.71639,-65.085
> view matrix models
> #1,0.98676,-0.046354,-0.1554,40.612,-0.094565,0.61401,-0.78361,201.95,0.13174,0.78793,0.6015,-44.386,#2,0.93833,-0.0097655,-0.34561,79.909,-0.21527,0.76571,-0.60609,160.07,0.27055,0.64311,0.71639,-65.017,#4,0.93833,-0.0097655,-0.34561,79.909,-0.21527,0.76571,-0.60609,160.07,0.27055,0.64311,0.71639,-65.017
> view matrix models
> #1,0.98676,-0.046354,-0.1554,40.168,-0.094565,0.61401,-0.78361,201.81,0.13174,0.78793,0.6015,-44.712,#2,0.93833,-0.0097655,-0.34561,79.465,-0.21527,0.76571,-0.60609,159.92,0.27055,0.64311,0.71639,-65.343,#4,0.93833,-0.0097655,-0.34561,79.465,-0.21527,0.76571,-0.60609,159.92,0.27055,0.64311,0.71639,-65.343
> view matrix models
> #1,0.98676,-0.046354,-0.1554,39.683,-0.094565,0.61401,-0.78361,201.86,0.13174,0.78793,0.6015,-44.664,#2,0.93833,-0.0097655,-0.34561,78.98,-0.21527,0.76571,-0.60609,159.97,0.27055,0.64311,0.71639,-65.294,#4,0.93833,-0.0097655,-0.34561,78.98,-0.21527,0.76571,-0.60609,159.97,0.27055,0.64311,0.71639,-65.294
> view matrix models
> #1,0.98676,-0.046354,-0.1554,39.558,-0.094565,0.61401,-0.78361,201.77,0.13174,0.78793,0.6015,-44.689,#2,0.93833,-0.0097655,-0.34561,78.855,-0.21527,0.76571,-0.60609,159.89,0.27055,0.64311,0.71639,-65.32,#4,0.93833,-0.0097655,-0.34561,78.855,-0.21527,0.76571,-0.60609,159.89,0.27055,0.64311,0.71639,-65.32
> select subtract #1
4 models selected
> select subtract #2
2 models selected
> select subtract #4
Nothing selected
> select subtract #8
Nothing selected
> color #7.1 #c3c3c357
> color #7.2 #c3c3c34e
> color #7.2 #c3c3c366
> color #7.1 #c3c3c366
> show #!2 models
> hide #!2 models
> show #!4 models
> show #!6 models
> volume #6 level 0.8145
> hide #!6 models
> show #!6 models
> show #!5 models
> ui tool show "Fit in Map"
> select add #7.1
6663 atoms, 6804 bonds, 839 residues, 1 model selected
> select add #7.2
11424 atoms, 11657 bonds, 1435 residues, 2 models selected
> select add #3.1
12648 atoms, 12903 bonds, 1585 residues, 3 models selected
> select add #3.2
17174 atoms, 17514 bonds, 3 pseudobonds, 2151 residues, 5 models selected
> select subtract #8
17174 atoms, 17514 bonds, 3 pseudobonds, 2151 residues, 5 models selected
> fitmap sel inMap #2
Fit molecules body_refined_update_real_space_refined_012_01.pdb A (#3.1),
body_refined_update_real_space_refined_012_01.pdb B (#3.2),
fold_vps33a_vps16_model_0.cif A (#7.1), fold_vps33a_vps16_model_0.cif B (#7.2)
to map head_sharpened.ccp4 (#2) using 17174 atoms
average map value = 0.004934, steps = 292
shifted from previous position = 20.9
rotated from previous position = 14.7 degrees
atoms outside contour = 13987, contour level = 0.013253
Position of body_refined_update_real_space_refined_012_01.pdb A (#3.1)
relative to head_sharpened.ccp4 (#2) coordinates:
Matrix rotation and translation
0.65438901 0.16115234 -0.73878612 118.71316057
-0.75599779 0.11931857 -0.64360734 360.65900877
-0.01556793 0.97969025 0.19991158 -7.33060995
Axis 0.81171942 -0.36164056 -0.45861496
Axis point 0.00000000 219.79103216 242.36652220
Rotation angle (degrees) 90.75577740
Shift along axis -30.70522149
Position of body_refined_update_real_space_refined_012_01.pdb B (#3.2)
relative to head_sharpened.ccp4 (#2) coordinates:
Matrix rotation and translation
0.65438901 0.16115234 -0.73878612 118.71316057
-0.75599779 0.11931857 -0.64360734 360.65900877
-0.01556793 0.97969025 0.19991158 -7.33060995
Axis 0.81171942 -0.36164056 -0.45861496
Axis point 0.00000000 219.79103216 242.36652220
Rotation angle (degrees) 90.75577740
Shift along axis -30.70522149
Position of fold_vps33a_vps16_model_0.cif A (#7.1) relative to
head_sharpened.ccp4 (#2) coordinates:
Matrix rotation and translation
-0.36346722 0.87256139 0.32638658 153.95428804
-0.86226239 -0.44772861 0.23673335 154.49065449
0.35269699 -0.19538606 0.91511154 185.69585179
Axis -0.24167416 -0.01471479 -0.97024588
Axis point 101.97504290 43.74390158 0.00000000
Rotation angle (degrees) 116.61813922
Shift along axis -219.65070602
Position of fold_vps33a_vps16_model_0.cif B (#7.2) relative to
head_sharpened.ccp4 (#2) coordinates:
Matrix rotation and translation
-0.34238012 0.88837568 0.30588318 154.54217613
-0.86630367 -0.42451693 0.26325528 155.83617513
0.36372218 -0.17485435 0.91494926 186.05433877
Axis -0.24212029 -0.03196459 -0.96971956
Axis point 102.69426755 41.94363569 0.00000000
Rotation angle (degrees) 115.21232322
Shift along axis -222.81956819
> view matrix models
> #3.1,0.62679,-0.18854,-0.75603,176.92,-0.71031,-0.53711,-0.45495,406.55,-0.32029,0.82217,-0.47058,198.71,#3.2,0.62679,-0.18854,-0.75603,176.92,-0.71031,-0.53711,-0.45495,406.55,-0.32029,0.82217,-0.47058,198.71,#7.1,-0.45453,0.89065,-0.012323,145.29,-0.79577,-0.41224,-0.44363,124.11,-0.4002,-0.19184,0.89612,213.94,#7.2,-0.43851,0.89816,-0.031765,145.7,-0.81008,-0.41032,-0.41881,124.79,-0.38919,-0.15792,0.90752,215.22
> ui mousemode right "rotate selected models"
> view matrix models
> #3.1,0.5808,-0.59687,-0.55355,226.56,-0.81398,-0.43399,-0.38611,397.4,-0.0097745,0.67483,-0.7379,208.83,#3.2,0.5808,-0.59687,-0.55355,226.56,-0.81398,-0.43399,-0.38611,397.4,-0.0097745,0.67483,-0.7379,208.83,#7.1,-0.36746,0.81115,-0.45498,146.76,-0.7576,-0.54482,-0.35945,124.26,-0.53945,0.21261,0.81473,214.78,#7.2,-0.35999,0.80407,-0.47316,146.7,-0.77298,-0.54104,-0.33133,124.99,-0.52241,0.24647,0.8163,216.1
> ui mousemode right "translate selected models"
> view matrix models
> #3.1,0.5808,-0.59687,-0.55355,224.48,-0.81398,-0.43399,-0.38611,395.87,-0.0097745,0.67483,-0.7379,219.21,#3.2,0.5808,-0.59687,-0.55355,224.48,-0.81398,-0.43399,-0.38611,395.87,-0.0097745,0.67483,-0.7379,219.21,#7.1,-0.36746,0.81115,-0.45498,144.67,-0.7576,-0.54482,-0.35945,122.74,-0.53945,0.21261,0.81473,225.16,#7.2,-0.35999,0.80407,-0.47316,144.62,-0.77298,-0.54104,-0.33133,123.47,-0.52241,0.24647,0.8163,226.48
> fitmap sel inMap #2
Fit molecules body_refined_update_real_space_refined_012_01.pdb A (#3.1),
body_refined_update_real_space_refined_012_01.pdb B (#3.2),
fold_vps33a_vps16_model_0.cif A (#7.1), fold_vps33a_vps16_model_0.cif B (#7.2)
to map head_sharpened.ccp4 (#2) using 17174 atoms
average map value = 0.005148, steps = 448
shifted from previous position = 29.6
rotated from previous position = 22.5 degrees
atoms outside contour = 13872, contour level = 0.013253
Position of body_refined_update_real_space_refined_012_01.pdb A (#3.1)
relative to head_sharpened.ccp4 (#2) coordinates:
Matrix rotation and translation
0.74954332 0.09587242 -0.65497579 105.66387981
-0.65968709 0.02634601 -0.75107844 374.15695982
-0.05475171 0.99504490 0.08299327 7.33549087
Axis 0.87524311 -0.30086190 -0.37872368
Axis point -0.00000000 205.94427166 222.02601512
Rotation angle (degrees) 94.04607789
Shift along axis -22.86611528
Position of body_refined_update_real_space_refined_012_01.pdb B (#3.2)
relative to head_sharpened.ccp4 (#2) coordinates:
Matrix rotation and translation
0.74954332 0.09587242 -0.65497579 105.66387981
-0.65968709 0.02634601 -0.75107844 374.15695982
-0.05475171 0.99504490 0.08299327 7.33549087
Axis 0.87524311 -0.30086190 -0.37872368
Axis point -0.00000000 205.94427166 222.02601512
Rotation angle (degrees) 94.04607789
Shift along axis -22.86611528
Position of fold_vps33a_vps16_model_0.cif A (#7.1) relative to
head_sharpened.ccp4 (#2) coordinates:
Matrix rotation and translation
-0.26168474 0.93304532 0.24687555 158.70772508
-0.93610895 -0.30764474 0.17045455 153.49937761
0.23499178 -0.18649706 0.95393801 179.10022594
Axis -0.18757609 0.00624486 -0.98223022
Axis point 119.57971818 32.75984254 0.00000000
Rotation angle (degrees) 107.92041958
Shift along axis -204.72884837
Position of fold_vps33a_vps16_model_0.cif B (#7.2) relative to
head_sharpened.ccp4 (#2) coordinates:
Matrix rotation and translation
-0.24080862 0.94459665 0.22304348 159.09233189
-0.93866097 -0.28510173 0.19399124 154.85910068
0.24683355 -0.16264744 0.95531095 179.63667900
Axis -0.18605197 -0.01241085 -0.98246152
Axis point 120.32662883 30.60585760 0.00000000
Rotation angle (degrees) 106.57676371
Shift along axis -208.00749947
> view matrix models
> #3.1,0.72868,-0.25419,-0.63593,143.77,-0.6333,-0.60355,-0.48442,409.25,-0.26068,0.75572,-0.60078,222.69,#3.2,0.72868,-0.25419,-0.63593,143.77,-0.6333,-0.60355,-0.48442,409.25,-0.26068,0.75572,-0.60078,222.69,#7.1,-0.31762,0.94296,-0.099702,136.33,-0.80288,-0.32339,-0.5008,124.77,-0.50448,-0.079014,0.8598,218.18,#7.2,-0.3021,0.94534,-0.12277,136.49,-0.81651,-0.32307,-0.47848,125.4,-0.49199,-0.044306,0.86948,219.54
> fitmap sel inMap #5
Fit molecules body_refined_update_real_space_refined_012_01.pdb A (#3.1),
body_refined_update_real_space_refined_012_01.pdb B (#3.2),
fold_vps33a_vps16_model_0.cif A (#7.1), fold_vps33a_vps16_model_0.cif B (#7.2)
to map full_map_sharpened.ccp4 (#5) using 17174 atoms
average map value = 0.01875, steps = 340
shifted from previous position = 10.9
rotated from previous position = 22.2 degrees
atoms outside contour = 7489, contour level = 0.011478
Position of body_refined_update_real_space_refined_012_01.pdb A (#3.1)
relative to full_map_sharpened.ccp4 (#5) coordinates:
Matrix rotation and translation
0.99999900 0.00070524 0.00122795 -0.33946076
-0.00070328 0.99999848 -0.00159662 0.43461266
-0.00122907 0.00159575 0.99999797 -0.06563660
Axis 0.74805382 0.57574274 -0.33005420
Axis point -0.00000000 37.75641627 265.69839846
Rotation angle (degrees) 0.12225680
Shift along axis 0.01795380
Position of body_refined_update_real_space_refined_012_01.pdb B (#3.2)
relative to full_map_sharpened.ccp4 (#5) coordinates:
Matrix rotation and translation
0.99999900 0.00070524 0.00122795 -0.33946076
-0.00070328 0.99999848 -0.00159662 0.43461266
-0.00122907 0.00159575 0.99999797 -0.06563660
Axis 0.74805382 0.57574274 -0.33005420
Axis point -0.00000000 37.75641627 265.69839846
Rotation angle (degrees) 0.12225680
Shift along axis 0.01795380
Position of fold_vps33a_vps16_model_0.cif A (#7.1) relative to
full_map_sharpened.ccp4 (#5) coordinates:
Matrix rotation and translation
0.40975593 0.91195808 0.02079824 175.87794379
0.18236134 -0.10423493 0.97769087 170.26435524
0.89378098 -0.39682183 -0.20901678 145.23346250
Axis -0.77034098 -0.48926021 -0.40890001
Axis point 0.00000000 41.83965371 12.31132467
Rotation angle (degrees) 116.85588197
Shift along axis -278.17552684
Position of fold_vps33a_vps16_model_0.cif B (#7.2) relative to
full_map_sharpened.ccp4 (#5) coordinates:
Matrix rotation and translation
0.42643508 0.90442945 -0.01266954 175.23877942
0.19608409 -0.07876091 0.97741893 170.87325609
0.88300859 -0.41929002 -0.21093064 144.00657220
Axis -0.77418462 -0.49646724 -0.39263017
Axis point 0.00000000 43.58535411 14.00313805
Rotation angle (degrees) 115.57093635
Shift along axis -277.04146713
> hide #!5 models
> hide #!6 models
> hide #!4 models
> select add #7
17174 atoms, 17514 bonds, 3 pseudobonds, 2151 residues, 6 models selected
> select subtract #7.1
10511 atoms, 10710 bonds, 3 pseudobonds, 1312 residues, 5 models selected
> select add #7
17174 atoms, 17514 bonds, 3 pseudobonds, 2151 residues, 6 models selected
> select add #3
17174 atoms, 17514 bonds, 3 pseudobonds, 2151 residues, 7 models selected
> select subtract #3
11424 atoms, 11657 bonds, 1435 residues, 3 models selected
> select subtract #7
Nothing selected
> select subtract #8
Nothing selected
> select add #1
4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 2 models selected
> select add #2
4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 4 models selected
> select add #4
4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 6 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.96266,-0.051478,-0.26578,64.178,-0.15294,0.70665,-0.69083,179.67,0.22337,0.70568,0.67239,-59.143,#2,0.89398,0.008526,-0.44802,101.16,-0.25189,0.83646,-0.48671,132.72,0.3706,0.54796,0.74993,-71.49,#4,0.89398,0.008526,-0.44802,101.16,-0.25189,0.83646,-0.48671,132.72,0.3706,0.54796,0.74993,-71.49
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.96266,-0.051478,-0.26578,67.137,-0.15294,0.70665,-0.69083,177.49,0.22337,0.70568,0.67239,-60.425,#2,0.89398,0.008526,-0.44802,104.11,-0.25189,0.83646,-0.48671,130.53,0.3706,0.54796,0.74993,-72.772,#4,0.89398,0.008526,-0.44802,104.11,-0.25189,0.83646,-0.48671,130.53,0.3706,0.54796,0.74993,-72.772
> view matrix models
> #1,0.96266,-0.051478,-0.26578,65.253,-0.15294,0.70665,-0.69083,175.68,0.22337,0.70568,0.67239,-57.724,#2,0.89398,0.008526,-0.44802,102.23,-0.25189,0.83646,-0.48671,128.72,0.3706,0.54796,0.74993,-70.071,#4,0.89398,0.008526,-0.44802,102.23,-0.25189,0.83646,-0.48671,128.72,0.3706,0.54796,0.74993,-70.071
> view matrix models
> #1,0.96266,-0.051478,-0.26578,65.54,-0.15294,0.70665,-0.69083,175.85,0.22337,0.70568,0.67239,-57.636,#2,0.89398,0.008526,-0.44802,102.52,-0.25189,0.83646,-0.48671,128.9,0.3706,0.54796,0.74993,-69.983,#4,0.89398,0.008526,-0.44802,102.52,-0.25189,0.83646,-0.48671,128.9,0.3706,0.54796,0.74993,-69.983
> view matrix models
> #1,0.96266,-0.051478,-0.26578,66.114,-0.15294,0.70665,-0.69083,174.48,0.22337,0.70568,0.67239,-58.504,#2,0.89398,0.008526,-0.44802,103.09,-0.25189,0.83646,-0.48671,127.52,0.3706,0.54796,0.74993,-70.851,#4,0.89398,0.008526,-0.44802,103.09,-0.25189,0.83646,-0.48671,127.52,0.3706,0.54796,0.74993,-70.851
> view matrix models
> #1,0.96266,-0.051478,-0.26578,66.015,-0.15294,0.70665,-0.69083,174.43,0.22337,0.70568,0.67239,-58.213,#2,0.89398,0.008526,-0.44802,102.99,-0.25189,0.83646,-0.48671,127.47,0.3706,0.54796,0.74993,-70.56,#4,0.89398,0.008526,-0.44802,102.99,-0.25189,0.83646,-0.48671,127.47,0.3706,0.54796,0.74993,-70.56
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.95395,-0.052695,-0.29531,72.963,-0.16243,0.73689,-0.6562,164.8,0.25219,0.67395,0.6944,-61.718,#2,0.8799,0.013564,-0.47496,109.22,-0.25365,0.85866,-0.44539,116.64,0.40179,0.51237,0.75898,-71.207,#4,0.8799,0.013564,-0.47496,109.22,-0.25365,0.85866,-0.44539,116.64,0.40179,0.51237,0.75898,-71.207
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.95395,-0.052695,-0.29531,72.682,-0.16243,0.73689,-0.6562,164.74,0.25219,0.67395,0.6944,-61.918,#2,0.8799,0.013564,-0.47496,108.94,-0.25365,0.85866,-0.44539,116.58,0.40179,0.51237,0.75898,-71.407,#4,0.8799,0.013564,-0.47496,108.94,-0.25365,0.85866,-0.44539,116.58,0.40179,0.51237,0.75898,-71.407
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.94692,-0.066282,-0.31456,79.6,-0.15582,0.76124,-0.62947,154.75,0.28118,0.64508,0.7105,-64.885,#2,0.86892,0.0043422,-0.49494,115.9,-0.24129,0.87681,-0.41591,106.17,0.43216,0.48082,0.76292,-71.719,#4,0.86892,0.0043422,-0.49494,115.9,-0.24129,0.87681,-0.41591,106.17,0.43216,0.48082,0.76292,-71.719
> view matrix models
> #1,0.95774,-0.078122,-0.27683,73.032,-0.12247,0.76006,-0.6382,150.78,0.26027,0.64514,0.71837,-62.709,#2,0.8861,-0.015188,-0.46325,110.82,-0.2102,0.8776,-0.43085,103.46,0.41309,0.47915,0.77445,-70.271,#4,0.8861,-0.015188,-0.46325,110.82,-0.2102,0.8776,-0.43085,103.46,0.41309,0.47915,0.77445,-70.271
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.95774,-0.078122,-0.27683,71.867,-0.12247,0.76006,-0.6382,152.07,0.26027,0.64514,0.71837,-62.89,#2,0.8861,-0.015188,-0.46325,109.66,-0.2102,0.8776,-0.43085,104.75,0.41309,0.47915,0.77445,-70.451,#4,0.8861,-0.015188,-0.46325,109.66,-0.2102,0.8776,-0.43085,104.75,0.41309,0.47915,0.77445,-70.451
> view matrix models
> #1,0.95774,-0.078122,-0.27683,72.415,-0.12247,0.76006,-0.6382,152.45,0.26027,0.64514,0.71837,-63.615,#2,0.8861,-0.015188,-0.46325,110.2,-0.2102,0.8776,-0.43085,105.13,0.41309,0.47915,0.77445,-71.176,#4,0.8861,-0.015188,-0.46325,110.2,-0.2102,0.8776,-0.43085,105.13,0.41309,0.47915,0.77445,-71.176
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.92245,-0.1597,-0.35154,105.49,-0.14221,0.70593,-0.69386,174.85,0.35897,0.69004,0.62848,-72.118,#2,0.83453,-0.079195,-0.54525,144.37,-0.24194,0.83642,-0.4918,128.31,0.495,0.54234,0.67885,-78.983,#4,0.83453,-0.079195,-0.54525,144.37,-0.24194,0.83642,-0.4918,128.31,0.495,0.54234,0.67885,-78.983
> view matrix models
> #1,0.90637,-0.14066,-0.39837,113.37,-0.18263,0.71984,-0.66968,175.14,0.38097,0.67974,0.62676,-73.847,#2,0.81076,-0.050723,-0.58318,150.1,-0.27662,0.84479,-0.45805,126.72,0.5159,0.53268,0.67089,-79.404,#4,0.81076,-0.050723,-0.58318,150.1,-0.27662,0.84479,-0.45805,126.72,0.5159,0.53268,0.67089,-79.404
> view matrix models
> #1,0.91164,-0.11051,-0.39586,106.94,-0.20392,0.71465,-0.6691,179.56,0.35685,0.6907,0.62896,-71.952,#2,0.81752,-0.021769,-0.57548,142.6,-0.29761,0.83954,-0.45454,130.52,0.49303,0.54287,0.67986,-78.923,#4,0.81752,-0.021769,-0.57548,142.6,-0.29761,0.83954,-0.45454,130.52,0.49303,0.54287,0.67986,-78.923
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.91164,-0.11051,-0.39586,104.4,-0.20392,0.71465,-0.6691,176.78,0.35685,0.6907,0.62896,-68.683,#2,0.81752,-0.021769,-0.57548,140.06,-0.29761,0.83954,-0.45454,127.75,0.49303,0.54287,0.67986,-75.654,#4,0.81752,-0.021769,-0.57548,140.06,-0.29761,0.83954,-0.45454,127.75,0.49303,0.54287,0.67986,-75.654
> view matrix models
> #1,0.91164,-0.11051,-0.39586,104.75,-0.20392,0.71465,-0.6691,176.36,0.35685,0.6907,0.62896,-68.737,#2,0.81752,-0.021769,-0.57548,140.41,-0.29761,0.83954,-0.45454,127.32,0.49303,0.54287,0.67986,-75.708,#4,0.81752,-0.021769,-0.57548,140.41,-0.29761,0.83954,-0.45454,127.32,0.49303,0.54287,0.67986,-75.708
> view matrix models
> #1,0.91164,-0.11051,-0.39586,105.67,-0.20392,0.71465,-0.6691,177.18,0.35685,0.6907,0.62896,-67.128,#2,0.81752,-0.021769,-0.57548,141.33,-0.29761,0.83954,-0.45454,128.15,0.49303,0.54287,0.67986,-74.099,#4,0.81752,-0.021769,-0.57548,141.33,-0.29761,0.83954,-0.45454,128.15,0.49303,0.54287,0.67986,-74.099
> color #7.1 #c3c3c393
> color #7.1 #c3c3c394
> view matrix models
> #1,0.91164,-0.11051,-0.39586,106.01,-0.20392,0.71465,-0.6691,176.32,0.35685,0.6907,0.62896,-67.326,#2,0.81752,-0.021769,-0.57548,141.67,-0.29761,0.83954,-0.45454,127.28,0.49303,0.54287,0.67986,-74.297,#4,0.81752,-0.021769,-0.57548,141.67,-0.29761,0.83954,-0.45454,127.28,0.49303,0.54287,0.67986,-74.297
> select subtract #1
4 models selected
> select subtract #2
2 models selected
> select subtract #4
Nothing selected
> select subtract #8
Nothing selected
> hide #8 models
> close #8
> show #!2 models
> show #!4 models
> show #!5 models
> show #!6 models
> hide #!1 models
> hide #3.1 models
> hide #!3.2 models
> hide #7.1 models
> hide #7.2 models
> volume #2 step 1
> volume #2 level 0.01971
> volume #2 level 0.021
> volume #2 level 0.018
> volume #5 step 1
> volume #5 level 0.014
> surface dust #2 size 5.9
> surface dust #4 size 5.9
> surface dust #5 size 5.9
> surface dust #6 size 5.9
> lighting soft
> show #!1 models
> show #7.1 models
> hide #!2 models
> hide #!4 models
> select add #1
4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 2 models selected
> select add #2
4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 4 models selected
> select add #3.2
9057 atoms, 9245 bonds, 4 pseudobonds, 1137 residues, 6 models selected
> select subtract #3.2
4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 4 models selected
> select add #4
4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 6 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.92192,-0.072166,-0.3806,95.072,-0.20676,0.73918,-0.64099,167.67,0.32759,0.66963,0.66654,-65.443,#2,0.83189,0.012503,-0.5548,129.68,-0.29427,0.85755,-0.42192,117.85,0.47049,0.51425,0.71707,-72.124,#4,0.83189,0.012503,-0.5548,129.68,-0.29427,0.85755,-0.42192,117.85,0.47049,0.51425,0.71707,-72.124
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.92192,-0.072166,-0.3806,96.404,-0.20676,0.73918,-0.64099,168.4,0.32759,0.66963,0.66654,-66.573,#2,0.83189,0.012503,-0.5548,131.01,-0.29427,0.85755,-0.42192,118.58,0.47049,0.51425,0.71707,-73.254,#4,0.83189,0.012503,-0.5548,131.01,-0.29427,0.85755,-0.42192,118.58,0.47049,0.51425,0.71707,-73.254
> view matrix models
> #1,0.92192,-0.072166,-0.3806,96.674,-0.20676,0.73918,-0.64099,168.55,0.32759,0.66963,0.66654,-67.253,#2,0.83189,0.012503,-0.5548,131.28,-0.29427,0.85755,-0.42192,118.73,0.47049,0.51425,0.71707,-73.934,#4,0.83189,0.012503,-0.5548,131.28,-0.29427,0.85755,-0.42192,118.73,0.47049,0.51425,0.71707,-73.934
> show #!2 models
> show #!4 models
> hide #!1 models
> hide #7.1 models
> select subtract #4
4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 4 models selected
> select subtract #1
2 models selected
> select subtract #2
Nothing selected
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> set bgColor white
> set bgColor #ffffff00
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> volume #2 level 0.019
> volume #2 level 0.02
> volume #2 level 0.019
> volume #5 step 4
> volume #5 step 2
> volume #5 step 1
> ui tool show "Surface Color"
> ui tool show "Surface Zone"
> select add #3.1
1224 atoms, 1246 bonds, 150 residues, 1 model selected
> select add #3.2
5750 atoms, 5857 bonds, 3 pseudobonds, 716 residues, 3 models selected
> surface zone #5 nearAtoms sel distance 196.86
> surface dust #2 size 5.9
> surface dust #4 size 5.9
> surface dust #5 size 5.9
> surface dust #6 size 5.9
> ui tool show "Color Zone"
> color zone #5 near sel distance 85.05
> color zone #2 near #1 distance 119.06
> lighting flat
> lighting soft
> select add #1
10281 atoms, 10491 bonds, 4 pseudobonds, 1287 residues, 5 models selected
> select add #3
10281 atoms, 10491 bonds, 4 pseudobonds, 1287 residues, 6 models selected
> select subtract #3
4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 2 models selected
> select add #2
4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 4 models selected
> select add #4
4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 6 models selected
> show #!1 models
> show #7.1 models
> view matrix models
> #1,0.92192,-0.072166,-0.3806,97.322,-0.20676,0.73918,-0.64099,169.13,0.32759,0.66963,0.66654,-67.618,#2,0.83189,0.012503,-0.5548,131.93,-0.29427,0.85755,-0.42192,119.31,0.47049,0.51425,0.71707,-74.299,#4,0.83189,0.012503,-0.5548,131.93,-0.29427,0.85755,-0.42192,119.31,0.47049,0.51425,0.71707,-74.299
> view matrix models
> #1,0.92192,-0.072166,-0.3806,96.289,-0.20676,0.73918,-0.64099,170.45,0.32759,0.66963,0.66654,-68.119,#2,0.83189,0.012503,-0.5548,130.9,-0.29427,0.85755,-0.42192,120.63,0.47049,0.51425,0.71707,-74.801,#4,0.83189,0.012503,-0.5548,130.9,-0.29427,0.85755,-0.42192,120.63,0.47049,0.51425,0.71707,-74.801
> view matrix models
> #1,0.92192,-0.072166,-0.3806,96.805,-0.20676,0.73918,-0.64099,169.81,0.32759,0.66963,0.66654,-68.029,#2,0.83189,0.012503,-0.5548,131.42,-0.29427,0.85755,-0.42192,119.99,0.47049,0.51425,0.71707,-74.711,#4,0.83189,0.012503,-0.5548,131.42,-0.29427,0.85755,-0.42192,119.99,0.47049,0.51425,0.71707,-74.711
> view matrix models
> #1,0.92192,-0.072166,-0.3806,95.941,-0.20676,0.73918,-0.64099,169.67,0.32759,0.66963,0.66654,-68.929,#2,0.83189,0.012503,-0.5548,130.55,-0.29427,0.85755,-0.42192,119.85,0.47049,0.51425,0.71707,-75.61,#4,0.83189,0.012503,-0.5548,130.55,-0.29427,0.85755,-0.42192,119.85,0.47049,0.51425,0.71707,-75.61
> fitmap #1 inMap #2
Fit molecule head_fit_real_space_refined_002.pdb (#1) to map
head_sharpened.ccp4 (#2) using 4531 atoms
average map value = 0.01843, steps = 160
shifted from previous position = 6.68
rotated from previous position = 16.4 degrees
atoms outside contour = 2427, contour level = 0.019
Position of head_fit_real_space_refined_002.pdb (#1) relative to
head_sharpened.ccp4 (#2) coordinates:
Matrix rotation and translation
0.99999251 -0.00227889 -0.00312948 1.09767996
0.00226897 0.99999241 -0.00316874 0.21223268
0.00313667 0.00316162 0.99999008 -1.11174684
Axis 0.63296916 -0.62654906 0.45473763
Axis point 0.00000000 359.97435545 77.24041076
Rotation angle (degrees) 0.28651028
Shift along axis 0.05627026
> view matrix models
> #1,0.83017,0.0088531,-0.55744,132.04,-0.29364,0.85688,-0.42371,126.52,0.4739,0.51544,0.71396,-75.68,#2,0.83189,0.012503,-0.5548,130.51,-0.29427,0.85755,-0.42192,126.19,0.47049,0.51425,0.71707,-75.508,#4,0.83189,0.012503,-0.5548,130.51,-0.29427,0.85755,-0.42192,126.19,0.47049,0.51425,0.71707,-75.508
> view matrix models
> #1,0.83017,0.0088531,-0.55744,133.84,-0.29364,0.85688,-0.42371,124.06,0.4739,0.51544,0.71396,-75.85,#2,0.83189,0.012503,-0.5548,132.31,-0.29427,0.85755,-0.42192,123.73,0.47049,0.51425,0.71707,-75.678,#4,0.83189,0.012503,-0.5548,132.31,-0.29427,0.85755,-0.42192,123.73,0.47049,0.51425,0.71707,-75.678
> view matrix models
> #1,0.83017,0.0088531,-0.55744,133.83,-0.29364,0.85688,-0.42371,124.58,0.4739,0.51544,0.71396,-79.263,#2,0.83189,0.012503,-0.5548,132.3,-0.29427,0.85755,-0.42192,124.25,0.47049,0.51425,0.71707,-79.092,#4,0.83189,0.012503,-0.5548,132.3,-0.29427,0.85755,-0.42192,124.25,0.47049,0.51425,0.71707,-79.092
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.89976,-0.03417,-0.43505,107.83,-0.22288,0.82112,-0.52544,136.27,0.37518,0.56973,0.73119,-74.55,#2,0.90119,-0.030749,-0.43233,106.37,-0.2231,0.82227,-0.52354,135.75,0.37159,0.56826,0.73416,-74.262,#4,0.90119,-0.030749,-0.43233,106.37,-0.2231,0.82227,-0.52354,135.75,0.37159,0.56826,0.73416,-74.262
> view matrix models
> #1,0.90249,0.018977,-0.43028,97.309,-0.24361,0.84636,-0.47363,126.44,0.35519,0.53228,0.76846,-71.092,#2,0.90379,0.022388,-0.42739,95.838,-0.24406,0.8473,-0.47172,126,0.35156,0.53064,0.77125,-70.733,#4,0.90379,0.022388,-0.42739,95.838,-0.24406,0.8473,-0.47172,126,0.35156,0.53064,0.77125,-70.733
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.90249,0.018977,-0.43028,96.179,-0.24361,0.84636,-0.47363,127.61,0.35519,0.53228,0.76846,-71.153,#2,0.90379,0.022388,-0.42739,94.707,-0.24406,0.8473,-0.47172,127.17,0.35156,0.53064,0.77125,-70.794,#4,0.90379,0.022388,-0.42739,94.707,-0.24406,0.8473,-0.47172,127.17,0.35156,0.53064,0.77125,-70.794
> hide #!4 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> view matrix models
> #1,0.90249,0.018977,-0.43028,96.848,-0.24361,0.84636,-0.47363,128.08,0.35519,0.53228,0.76846,-70.908,#2,0.90379,0.022388,-0.42739,95.376,-0.24406,0.8473,-0.47172,127.65,0.35156,0.53064,0.77125,-70.549,#4,0.90379,0.022388,-0.42739,95.376,-0.24406,0.8473,-0.47172,127.65,0.35156,0.53064,0.77125,-70.549
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.94648,0.080547,-0.31254,57.997,-0.25881,0.76798,-0.58585,163.85,0.19283,0.63539,0.74773,-56.766,#2,0.94727,0.083684,-0.30931,56.596,-0.25872,0.76925,-0.58423,163.32,0.18904,0.63345,0.75034,-56.274,#4,0.94727,0.083684,-0.30931,56.596,-0.25872,0.76925,-0.58423,163.32,0.18904,0.63345,0.75034,-56.274
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.94648,0.080547,-0.31254,60.607,-0.25881,0.76798,-0.58585,162.41,0.19283,0.63539,0.74773,-57.485,#2,0.94727,0.083684,-0.30931,59.205,-0.25872,0.76925,-0.58423,161.88,0.18904,0.63345,0.75034,-56.993,#4,0.94727,0.083684,-0.30931,59.205,-0.25872,0.76925,-0.58423,161.88,0.18904,0.63345,0.75034,-56.993
> view matrix models
> #1,0.94648,0.080547,-0.31254,60.872,-0.25881,0.76798,-0.58585,162.3,0.19283,0.63539,0.74773,-57.439,#2,0.94727,0.083684,-0.30931,59.47,-0.25872,0.76925,-0.58423,161.77,0.18904,0.63345,0.75034,-56.946,#4,0.94727,0.083684,-0.30931,59.47,-0.25872,0.76925,-0.58423,161.77,0.18904,0.63345,0.75034,-56.946
> show #!2 models
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.90737,0.042199,-0.4182,92.867,-0.31902,0.71697,-0.61982,187.51,0.27368,0.69582,0.66402,-67.134,#2,0.90858,0.045582,-0.41522,91.399,-0.31871,0.71821,-0.61855,187.02,0.27002,0.69434,0.66708,-66.836,#4,0.90858,0.045582,-0.41522,91.399,-0.31871,0.71821,-0.61855,187.02,0.27002,0.69434,0.66708,-66.836
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.90737,0.042199,-0.4182,91.309,-0.31902,0.71697,-0.61982,184.17,0.27368,0.69582,0.66402,-62.062,#2,0.90858,0.045582,-0.41522,89.84,-0.31871,0.71821,-0.61855,183.68,0.27002,0.69434,0.66708,-61.764,#4,0.90858,0.045582,-0.41522,89.84,-0.31871,0.71821,-0.61855,183.68,0.27002,0.69434,0.66708,-61.764
> hide #!2 models
> show #!2 models
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.8837,-0.0094113,-0.46796,113.08,-0.33247,0.6911,-0.64175,194.83,0.32945,0.72269,0.6076,-66.432,#2,0.88518,-0.0059233,-0.46521,111.59,-0.33204,0.69238,-0.6406,194.34,0.3259,0.72151,0.61091,-66.264,#4,0.88518,-0.0059233,-0.46521,111.59,-0.33204,0.69238,-0.6406,194.34,0.3259,0.72151,0.61091,-66.264
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.8837,-0.0094113,-0.46796,111.09,-0.33247,0.6911,-0.64175,192.84,0.32945,0.72269,0.6076,-63.394,#2,0.88518,-0.0059233,-0.46521,109.6,-0.33204,0.69238,-0.6406,192.34,0.3259,0.72151,0.61091,-63.226,#4,0.88518,-0.0059233,-0.46521,109.6,-0.33204,0.69238,-0.6406,192.34,0.3259,0.72151,0.61091,-63.226
> view matrix models
> #1,0.8837,-0.0094113,-0.46796,110.8,-0.33247,0.6911,-0.64175,193.22,0.32945,0.72269,0.6076,-63.551,#2,0.88518,-0.0059233,-0.46521,109.31,-0.33204,0.69238,-0.6406,192.72,0.3259,0.72151,0.61091,-63.382,#4,0.88518,-0.0059233,-0.46521,109.31,-0.33204,0.69238,-0.6406,192.72,0.3259,0.72151,0.61091,-63.382
> hide #!2 models
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.89303,-0.032896,-0.44878,109.75,-0.29696,0.70624,-0.64269,184.75,0.33809,0.70721,0.62093,-64.792,#2,0.89451,-0.029448,-0.44608,108.28,-0.29655,0.70759,-0.64138,184.21,0.33453,0.706,0.62422,-64.615,#4,0.89451,-0.029448,-0.44608,108.28,-0.29655,0.70759,-0.64138,184.21,0.33453,0.706,0.62422,-64.615
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.89303,-0.032896,-0.44878,109.1,-0.29696,0.70624,-0.64269,184.64,0.33809,0.70721,0.62093,-64.785,#2,0.89451,-0.029448,-0.44608,107.63,-0.29655,0.70759,-0.64138,184.1,0.33453,0.706,0.62422,-64.609,#4,0.89451,-0.029448,-0.44608,107.63,-0.29655,0.70759,-0.64138,184.1,0.33453,0.706,0.62422,-64.609
> view matrix models
> #1,0.89303,-0.032896,-0.44878,108.79,-0.29696,0.70624,-0.64269,186.02,0.33809,0.70721,0.62093,-64.669,#2,0.89451,-0.029448,-0.44608,107.32,-0.29655,0.70759,-0.64138,185.49,0.33453,0.706,0.62422,-64.492,#4,0.89451,-0.029448,-0.44608,107.32,-0.29655,0.70759,-0.64138,185.49,0.33453,0.706,0.62422,-64.492
> show #!2 models
> hide #!2 models
> view matrix models
> #1,0.89303,-0.032896,-0.44878,108.52,-0.29696,0.70624,-0.64269,186.53,0.33809,0.70721,0.62093,-64.659,#2,0.89451,-0.029448,-0.44608,107.05,-0.29655,0.70759,-0.64138,185.99,0.33453,0.706,0.62422,-64.483,#4,0.89451,-0.029448,-0.44608,107.05,-0.29655,0.70759,-0.64138,185.99,0.33453,0.706,0.62422,-64.483
> show #!2 models
> hide #7.1 models
> hide #!7 models
> hide #!1 models
> show #!4 models
> select subtract #1
4 models selected
> select subtract #2
2 models selected
> select subtract #4
Nothing selected
> color #6 #bbbbbb03 models
> volume #6 level 0.5714
> volume #6 level 0.6
> volume #6 level 0.55
> volume #6 level 0.65
> volume #6 level 0.7
> volume #4 level 0.7
> color #4 #bbbbbb03 models
> turn y 180
> volume #5 step 2
> surface dust #2 size 5.9
> surface dust #4 size 5.9
> surface dust #5 size 5.9
> surface dust #6 size 5.9
> surface dust #2 size 5.9
> surface dust #4 size 5.9
> surface dust #5 size 5.9
> surface dust #6 size 5.9
> surface dust #2 size 5.9
> surface dust #4 size 5.9
> surface dust #5 size 5.9
> surface dust #6 size 5.9
> turn y 180
> show #7.1 models
> hide #7.1 models
> show #7.1 models
> hide #7.1 models
> color #7.1 #c3c3c3ff
> show #7.1 models
> hide #!2 models
> show #!1 models
> hide #!5 models
> show #3.1 models
> show #!3.2 models
> color #7.1 #c3c3c3ff
> hide #7.1 models
> hide #!6 models
> hide #!4 models
> select #1/A:624
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Distances
> select add #3.1/A:642
17 atoms, 15 bonds, 2 residues, 2 models selected
Exactly two atoms must be selected!
> select subtract #3.1/A:642
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3.1/A:642
17 atoms, 15 bonds, 2 residues, 2 models selected
> select subtract #3.1/A:642
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3.1/A:642
17 atoms, 15 bonds, 2 residues, 2 models selected
> select subtract #3.1/A:642
8 atoms, 7 bonds, 1 residue, 1 model selected
> select subtract #1/A:624
Nothing selected
> select #3.1/A:642
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> select #1/A:624
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> select #1/A:624@O
1 atom, 1 residue, 1 model selected
> select add #3.1/A:642@N
2 atoms, 2 residues, 2 models selected
> distance #1/A:624@O #3.1/A:642@N
Distance between head_fit_real_space_refined_002.pdb #1/A ASP 624 O and
body_refined_update_real_space_refined_012_01.pdb A #3.1/A GLU 642 N: 29.694Å
> hide #8.1 models
> color #8 #f9de49ff models
> color #8 #e9c78aff models
> select add #1
4532 atoms, 4634 bonds, 1 pseudobond, 572 residues, 3 models selected
> select add #3
10281 atoms, 10491 bonds, 4 pseudobonds, 1287 residues, 6 models selected
> show sel cartoons
> show #8.1 models
> hide #8.1 models
> select subtract #1
5750 atoms, 5857 bonds, 3 pseudobonds, 716 residues, 4 models selected
> select subtract #3
Nothing selected
> show #!4 models
> show #!6 models
> show #7.1 models
> transparency #7.1 50
> hide #7.1 models
> show #!2 models
> show #!5 models
> hide #!1 models
> hide #3.1 models
> hide #!3.2 models
> turn y 180
> turn y 90
> turn y 180
> show #!1 models
> hide #!2 models
> hide #!3 models
> show #3.1 models
> show #!3.2 models
> hide #!3 models
> hide #3.1 models
> hide #!3.2 models
> show #3.1 models
> show #!3.2 models
> hide #!5 models
> turn y 180
> show #!5 models
> show #!2 models
> hide #!1 models
> hide #!3 models
> hide #3.1 models
> hide #!3.2 models
> turn y 180
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> turn y 180
> volume #2 level 0.01589
> turn y 180
> select add #3.1
1224 atoms, 1246 bonds, 150 residues, 1 model selected
> select add #3.2
5750 atoms, 5857 bonds, 3 pseudobonds, 716 residues, 3 models selected
> surface dust #2 size 5.9
> surface dust #4 size 5.9
> surface dust #5 size 5.9
> surface dust #6 size 5.9
> surface dust #2 size 5.9
> surface dust #4 size 5.9
> surface dust #5 size 5.9
> surface dust #6 size 5.9
> surface dust #2 size 5.9
> surface dust #4 size 5.9
> surface dust #5 size 5.9
> surface dust #6 size 5.9
> surface dust #2 size 5.9
> surface dust #4 size 5.9
> surface dust #5 size 5.9
> surface dust #6 size 5.9
> surface dust #2 size 5.9
> surface dust #4 size 5.9
> surface dust #5 size 5.9
> surface dust #6 size 5.9
> select add #3
5750 atoms, 5857 bonds, 3 pseudobonds, 716 residues, 4 models selected
> select subtract #3
Nothing selected
> volume #5 level 0.015
> turn y 180
> turn x 90
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> turn x 90
> show #!1 models
> hide #!2 models
> show #3.1 models
> show #!3.2 models
> hide #!5 models
> turn x 90
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> turn x 90
> show #!2 models
> hide #!1 models
> hide #!3 models
> hide #3.1 models
> hide #!3.2 models
> show #!5 models
> lighting soft
> hide #!6 models
> hide #!4 models
> hide #!2 models
> show #!1 models
> show #3.1 models
> show #!3.2 models
> hide #!5 models
> show #7.1 models
> color #7.1 #c3c3c365
> color #7.1 #c3c3c366
> hide #7.1 models
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> graphics silhouettes width0.5
Expected true or false or a keyword
> graphics silhouettes width 0.5
> graphics silhouettes width 0.75
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting shadows false
> lighting shadows true
> graphics silhouettes true
> lighting full
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes width 1
> graphics silhouettes true
> show #!6 models
> show #7.1 models
> hide #7.1 models
> show #!4 models
> lighting soft
> lighting full
> lighting flat
> graphics silhouettes width 0.8
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> graphics silhouettes true
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting shadows false
> graphics silhouettes width 1
> graphics silhouettes true
> lighting soft
> turn Y 1801
> turn Y 180
> hide #!1 models
> show #!2 models
> hide #!3 models
> hide #3.1 models
> hide #!3.2 models
> show #!5 models
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> turn Y 180
> hide #!2 models
> show #!1 models
> turn Y 180
> hide #!1 models
> show #!2 models
> turn Y 180
> volume #5 level 0.016
> turn Y 180
> lighting soft
> lighting flat
> lighting soft
> volume #5 step 1
> volume #5 step 2
> volume #2 step 2
> volume #2 step 4
> volume #2 step 2
> turn Y 180
> show #!1 models
> hide #!2 models
> show #3.1 models
> show #!3.2 models
> hide #!5 models
> show #!2 models
> hide #!1 models
> hide #!3 models
> hide #3.1 models
> hide #!3.2 models
> show #!5 models
> turn Y 180
> save "/Users/whole.grains/Documents/HOPS-SNARE paper/fourth draft/cryoEM
> figure images/map1.tif" width 2000 height 1342 supersample 3
> transparentBackground true
> turn Y 180
> save "/Users/whole.grains/Documents/HOPS-SNARE paper/fourth draft/cryoEM
> figure images/map2.tif" width 2000 height 1342 supersample 3
> transparentBackground true
> undo
> turn Y 180
> show #!1 models
> hide #!2 models
> undo
> show #!1 models
> hide #!2 models
> hide #!4 models
> show #7.1 models
> hide #7.1 models
> show #3.1 models
> show #!3.2 models
> hide #!5 models
> hide #!6 models
> turn Y 180
> show #7.1 models
> hide #7.1 models
> show #!6 models
> show #7.1 models
> hide #7.1 models
> show #!2 models
> hide #!1 models
> show #!4 models
> show #!5 models
> hide #3.1 models
> hide #!3.2 models
> turn Y 180
> save "/Users/whole.grains/Documents/HOPS-SNARE paper/fourth draft/cryoEM
> figure images/map1.tif" width 2000 height 1342 supersample 3
> transparentBackground true
> turn Y 180
> save "/Users/whole.grains/Documents/HOPS-SNARE paper/fourth draft/cryoEM
> figure images/map2.tif" width 2000 height 1342 supersample 3
> transparentBackground true
> turn Y 180
> show #7.1 models
> hide #!4 models
> show #!1 models
> hide #!2 models
> turn Y 180
> color #7.1 #c3c3c34d
> show #3.1 models
> show #!3.2 models
> hide #!5 models
> hide #!6 models
> show #7.2 models
> color #7.2 #c3c3c34d
> color #7.2 #c3c3c340
> color #7.1 #c3c3c340
> turn Y 180
> save "/Users/whole.grains/Documents/HOPS-SNARE paper/fourth draft/cryoEM
> figure images/model1.tif" width 2000 height 1342 supersample 3
> transparentBackground true
> turn Y 180
> hide #!7 models
> hide #7.1 models
> hide #7.2 models
> hide #!1 models
> show #!6 models
> show #!4 models
> open /Users/whole.grains/Desktop/16-33a_modelling/body/4bx9.pdb
4bx9.pdb title:
Human VPS33A In complex with A fragment of human VPS16 [more info...]
Chain information for 4bx9.pdb #9
---
Chain | Description
A | No description available
C | No description available
Non-standard residues in 4bx9.pdb #9
---
FMT — formic acid
LMR — (2S)-2-hydroxybutanedioic acid (L-malate)
MLA — malonic acid (dicarboxylic acid C3; propanediolic
acid;methanedicarboxylic acid)
5336 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> hide #3.1#!9#!3.2 atoms
> select add #9
5466 atoms, 5450 bonds, 2 pseudobonds, 783 residues, 3 models selected
> view matrix models #9,1,0,0,-44.008,0,1,0,-63.605,0,0,1,31.229
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.38169,-0.21859,-0.89807,254.4,-0.75115,-0.63954,-0.16359,390.97,-0.53859,0.73703,-0.4083,229.02
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.38169,-0.21859,-0.89807,248.3,-0.75115,-0.63954,-0.16359,381.93,-0.53859,0.73703,-0.4083,239.03
> matchmaker #9 to #3.2
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 body_refined_update_real_space_refined_012_01.pdb B, chain B (#3.2)
with 4bx9.pdb, chain A (#9), sequence alignment score = 2748.2
RMSD between 473 pruned atom pairs is 1.021 angstroms; (across all 563 pairs:
1.608)
> select subtract #9
Nothing selected
> split chains
Did not split head_fit_real_space_refined_002.pdb, has only one piece
Did not split body_refined_update_real_space_refined_012_01.pdb A, has only
one piece
Did not split body_refined_update_real_space_refined_012_01.pdb B, has only
one piece
Did not split fold_vps33a_vps16_model_0.cif A, has only one piece
Did not split fold_vps33a_vps16_model_0.cif B, has only one piece
Split 4bx9.pdb (#9) into 2 models
Chain information for 4bx9.pdb A #9.1
---
Chain | Description
A | No description available
Chain information for 4bx9.pdb C #9.2
---
Chain | Description
C | No description available
> color #9.2 dodgerblue
> hide #!6 models
> show #!6 models
> color #9.2 #1e90fffc
> color #9.2 dodgerblue
> hide #!6 models
> show #!6 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
> hide #!6 models
> show #!6 models
> hide #!9.1 models
> show #!9.1 models
> hide #9.2 models
> show #9.2 models
> color #9.2 #0081fffc
> color #9.2 #0081ffff
> color #9.2 #5dafffff
> color #9.2 #5dff8bff
> color #9.2 #5dff79ff
> color #9.2 #5dfffeff
> color #9.2 #6dff5dff
> color #9.2 #5dff9cff
> matchmaker #9.2 to #3.1
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 body_refined_update_real_space_refined_012_01.pdb A, chain A (#3.1)
with 4bx9.pdb C, chain C (#9.2), sequence alignment score = 478.3
RMSD between 85 pruned atom pairs is 0.907 angstroms; (across all 95 pairs:
1.580)
> matchmaker #9.1 to #3.2
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 body_refined_update_real_space_refined_012_01.pdb B, chain B (#3.2)
with 4bx9.pdb A, chain A (#9.1), sequence alignment score = 2751.7
RMSD between 473 pruned atom pairs is 1.021 angstroms; (across all 563 pairs:
1.608)
> show #!1 models
> cartoon style #1,3-4,6,9#!8 modeHelix tube sides 20
> cartoon style #1,3-4,6,9#!8 xsection oval modeHelix default
> show #!2 models
> hide #!1 models
> show #7.1 models
> hide #7.1 models
> show #7.2 models
> hide #7.2 models
> show #7.2 models
> hide #7.2 models
> save "/Users/whole.grains/Documents/HOPS-SNARE paper/fourth draft/cryoEM
> figure images/model2_4bx9_overlay.tif" width 2000 height 1342 supersample 3
> transparentBackground true
> hide #!9.1 models
> hide #9.2 models
> save "/Users/whole.grains/Documents/HOPS-SNARE paper/fourth draft/cryoEM
> figure images/model2.tif" width 1346 height 903 supersample 3
> save "/Users/whole.grains/Documents/HOPS-SNARE paper/fourth draft/cryoEM
> figure images/model2.tif" width 2000 height 1342 supersample 3
> transparentBackground true
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!1 models
> hide #!6 models
> show #!6 models
===== 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
> ui tool show Registration
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2
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 Air
Model Identifier: Mac14,2
Model Number: Z16000944LL/A
Chip: Apple M2
Total Number of Cores: 8 (4 Performance and 4 Efficiency)
Memory: 16 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3 (25D125)
Kernel Version: Darwin 25.3.0
Time since boot: 3 days, 9 hours, 32 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
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-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-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
Change History (2)
comment:1 by , 3 days ago
| Component: | Unassigned → Graphics |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in swap_buffers exposing status line during Mac wakeup, macOS 26 |
comment:2 by , 3 days ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Note:
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This ChimeraX crash is caused by a bug in the Qt window toolkit version 6.9.2 when redrawing the status line. It has only been observed with macOS 26. We have no way to fix this and are hoping a new Qt window toolkit version will fix it. The ChimeraX daily build is using Qt 6.10.2 and this crash has not been reported in that Qt version, although it was reported once a month ago in Qt 6.10.1 (#19773). You may want to try the daily build of ChimeraX is crashing more than this one time.