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Opened 9 hours ago
#19882 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.3-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",
"codeSigningFlags" : 570491649,
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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
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