![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 weeks ago
Last modified 2 weeks ago
#20504 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-26.2-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x000000020100ec40 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, PIL._imaging, chimerax.pdb_lib._load_libs, psutil._psutil_osx, psutil._psutil_posix, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, 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, PIL._imagingmath, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, pyKVFinder._pyKVFinder, chimerax.mlp._mlp, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, kiwisolver._cext, chimerax.atom_search.ast, chimerax.chem_group._chem_group, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 128)
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
__TEXT 1003e4000-1003e8000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
UNUSED SPACE AT START
--->
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__FONT_DATA 2352 1
__GLSLBUILTINS 5176K 1
__INFO_FILTER 8 1
__LINKEDIT 634.5M 248
__OBJC_RO 78.4M 1
__OBJC_RW 2570K 1
__TEXT 1.5G 1315
__TEXT (graphics) 4560K 5
__TPRO_CONST 128K 2
dyld private memory 14.4M 114
mapped file 836.5M 119
page table in kernel 4727K 1
shared memory 3248K 29
=========== ======= =======
TOTAL 9.8G 8645
TOTAL, minus reserved VM space 9.4G 8645
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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/eruboldi/Downloads/cryosparc_P2_J117_005_volume_map_sharp.mrc
Opened cryosparc_P2_J117_005_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 0.573, shown at level 0.0195, step 2, values float32
> volume #1 level 0.09875
> surface dust #1 size 5.73
> open /Users/eruboldi/Downloads/cryosparc_P2_J118_004_volume_map_sharp(2).mrc
Opened cryosparc_P2_J118_004_volume_map_sharp(2).mrc as #2, grid size
512,512,512, pixel 0.573, shown at level 0.0181, step 2, values float32
> volume #2 step 1
> volume #1 step 1
> volume #2 level 0.06514
> hide #!1 models
> open /Users/eruboldi/Downloads/cryosparc_P2_J119_012_volume_map_sharp(1).mrc
Opened cryosparc_P2_J119_012_volume_map_sharp(1).mrc as #3, grid size
512,512,512, pixel 0.573, shown at level 0.0218, step 2, values float32
> volume #3 level 0.05708
> volume #3 step 1
> hide #!2 models
> open /Users/eruboldi/Downloads/cryosparc_P2_J112_mask.mrc
Opened cryosparc_P2_J112_mask.mrc as #4, grid size 256,256,256, pixel 1.15,
shown at level 5e-05, step 1, values float32
> open /Users/eruboldi/Downloads/cryosparc_P2_pocket_zone.mrc
Opened cryosparc_P2_pocket_zone.mrc as #5, grid size 256,256,256, pixel 1.15,
shown at level 0.000153, step 1, values float32
> open /Users/eruboldi/Downloads/cryosparc_P2_pocket_zone.mrc
Opened cryosparc_P2_pocket_zone.mrc as #6, grid size 256,256,256, pixel 1.15,
shown at level 0.000153, step 1, values float32
> close #6
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!4 models
> hide #!5 models
> ui tool show "Map Coordinates"
> show #!2 models
> hide #!2 models
> hide #!3 models
> ui mousemode right pivot
> show #!1 models
> ui mousemode right "map eraser"
> select add #6
1 model selected
> measure center #6
Center of area of surface eraser sphere #6 = (166.08, 151.77, 139.14)
> measure center #6
Center of area of surface eraser sphere #6 = (166.92, 149.37, 144.61)
> show #!5 models
> hide #!5 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> open /Users/eruboldi/Downloads/cryosparc_P2_J41_mask.mrc
Opened cryosparc_P2_J41_mask.mrc as #7, grid size 256,256,256, pixel 1.15,
shown at level 5e-05, step 1, values float32
> hide #!7 models
> show #!7 models
> volume #7 level 0.005545
> hide #!7 models
> open /Users/eruboldi/Downloads/cryosparc_P2_J49_005_volume_map_sharp.mrc
Opened cryosparc_P2_J49_005_volume_map_sharp.mrc as #8, grid size 512,512,512,
pixel 0.573, shown at level 0.0183, step 2, values float32
> volume #8 level 0.1004
> close #8
> open "/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/scGPI8_model.cif"
Chain information for scGPI8_model.cif #8
---
Chain | Description
A | .
Computing secondary structure
> ui mousemode right select
> select /A:264
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,157.49,0,1,0,26.968,0,0,1,87.466
> view matrix models #8,1,0,0,134.81,0,1,0,21.411,0,0,1,93.877
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.39917,0.092616,0.91219,110.56,-0.8717,-0.34679,-0.34624,15.889,0.28427,-0.93336,0.21916,105.05
> view matrix models
> #8,0.66844,0.029165,-0.74319,137.79,-0.41707,-0.81265,-0.40701,22.019,-0.61582,0.58203,-0.53104,100.3
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.66844,0.029165,-0.74319,81.031,-0.41707,-0.81265,-0.40701,74.021,-0.61582,0.58203,-0.53104,142.08
> view matrix models
> #8,0.66844,0.029165,-0.74319,176.2,-0.41707,-0.81265,-0.40701,109.79,-0.61582,0.58203,-0.53104,145.03
> view matrix models
> #8,0.66844,0.029165,-0.74319,170.13,-0.41707,-0.81265,-0.40701,145.1,-0.61582,0.58203,-0.53104,154.12
> view matrix models
> #8,0.66844,0.029165,-0.74319,169.08,-0.41707,-0.81265,-0.40701,143.32,-0.61582,0.58203,-0.53104,156.84
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.71668,0.083033,-0.69244,169.12,-0.3634,-0.80298,-0.47241,144.52,-0.59524,0.5902,-0.5453,157.2
> view matrix models
> #8,0.69884,0.12238,-0.70473,169,-0.31357,-0.83312,-0.45563,144.96,-0.64288,0.53939,-0.54384,156.69
> view matrix models
> #8,0.72161,0.10655,-0.68405,169.08,-0.33667,-0.80937,-0.48123,144.91,-0.60492,0.57756,-0.54818,157.12
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.72161,0.10655,-0.68405,168.56,-0.33667,-0.80937,-0.48123,145.76,-0.60492,0.57756,-0.54818,159.03
> fitmap #8 inMap #1
Fit molecule scGPI8_model.cif (#8) to map
cryosparc_P2_J117_005_volume_map_sharp.mrc (#1) using 5770 atoms
average map value = 0.02028, steps = 296
shifted from previous position = 5.64
rotated from previous position = 7.13 degrees
atoms outside contour = 5147, contour level = 0.098752
Position of scGPI8_model.cif (#8) relative to
cryosparc_P2_J117_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.71779636 0.21765195 -0.66135923 165.63719187
-0.23155425 -0.82118933 -0.52156565 149.74454187
-0.65662092 0.52751846 -0.53904847 161.93839117
Axis 0.91926437 -0.00415196 -0.39361883
Axis point 0.00000000 41.75342475 142.01205706
Rotation angle (degrees) 145.20717960
Shift along axis 87.90063538
> view matrix models
> #8,0.7178,0.21765,-0.66136,165.66,-0.23155,-0.82119,-0.52157,155.98,-0.65662,0.52752,-0.53905,155.99
> fitmap #8 inMap #1
Fit molecule scGPI8_model.cif (#8) to map
cryosparc_P2_J117_005_volume_map_sharp.mrc (#1) using 5770 atoms
average map value = 0.02302, steps = 152
shifted from previous position = 3.76
rotated from previous position = 5.69 degrees
atoms outside contour = 5134, contour level = 0.098752
Position of scGPI8_model.cif (#8) relative to
cryosparc_P2_J117_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.74196785 0.23510976 -0.62785916 163.47744822
-0.26000535 -0.76229400 -0.59270995 156.35121066
-0.61796516 0.60301847 -0.50446784 152.71826487
Axis 0.92389946 -0.00764476 -0.38255894
Axis point 0.00000000 41.55591256 141.41207239
Rotation angle (degrees) 139.67596948
Shift along axis 91.41772192
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.46974,0.36786,-0.80251,161.86,-0.61097,-0.52071,-0.59631,152.19,-0.63723,0.77042,-0.01985,147.94
> ui tool show "Side View"
> view matrix models
> #8,0.71071,0.2295,-0.665,163.47,-0.50958,-0.48375,-0.71156,154.35,-0.485,0.84458,-0.22686,151.48
> fitmap #8 inMap #1
Fit molecule scGPI8_model.cif (#8) to map
cryosparc_P2_J117_005_volume_map_sharp.mrc (#1) using 5770 atoms
average map value = 0.06134, steps = 112
shifted from previous position = 2.45
rotated from previous position = 5.83 degrees
atoms outside contour = 4111, contour level = 0.098752
Position of scGPI8_model.cif (#8) relative to
cryosparc_P2_J117_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.77375979 0.22909923 -0.59060083 163.73360311
-0.45927231 -0.43925139 -0.77209272 156.75909933
-0.43630808 0.86866091 -0.23465612 151.75385877
Axis 0.91868396 -0.08639096 -0.38543014
Axis point -0.00000000 25.08904811 165.03396707
Rotation angle (degrees) 116.74842283
Shift along axis 78.38635533
> select add #8
5770 atoms, 5908 bonds, 743 residues, 1 model selected
> select subtract #8
Nothing selected
> select add #8
5770 atoms, 5908 bonds, 743 residues, 1 model selected
> volume zone #1 nearAtoms sel newMap true
Opened cryosparc_P2_J117_005_volume_map_sharp.mrc zone as #9, grid size
512,512,512, pixel 0.573, shown at step 1, values float32
> view matrix models
> #8,0.22212,-0.67397,-0.70457,159.33,-0.97502,-0.15487,-0.15923,145.08,-0.0018018,0.72234,-0.69153,160.97
> ui mousemode right translate
> select subtract #8
Nothing selected
> ui mousemode right select
> select clear
> ui mousemode right translate
> volume #9 level 0.1271
> volume #9 level 0.1172
> molmap #9 4.5
No atoms specified
> ui mousemode right select
Drag select of eraser sphere, 68 of 1000 triangles, 403 residues, 9
cryosparc_P2_J117_005_volume_map_sharp.mrc zone
> select subtract #9
3104 atoms, 403 residues, 2 models selected
Drag select of eraser sphere, 455 residues, 9
cryosparc_P2_J117_005_volume_map_sharp.mrc zone
> molmap sel 4.5
Opened scGPI8_model.cif map 4.5 as #10, grid size 57,59,59, pixel 1.5, shown
at level 0.1, step 1, values float32
> molmap sel 10
Opened scGPI8_model.cif map 10 as #10, grid size 36,37,37, pixel 3.33, shown
at level 0.0644, step 1, values float32
> select subtract #9
3520 atoms, 455 residues, 2 models selected
> molmap sel 15
Opened scGPI8_model.cif map 15 as #10, grid size 30,31,31, pixel 5, shown at
level 0.0465, step 1, values float32
> molmap sel 2-
Missing or invalid "resolution" argument: Expected a number
> molmap sel 20
Opened scGPI8_model.cif map 20 as #10, grid size 27,28,28, pixel 6.67, shown
at level 0.0343, step 1, values float32
> rename #10 mask_TMDs
> volume #10 level 0.06766
> hide #!9 models
> select add #8
5770 atoms, 5908 bonds, 743 residues, 2 models selected
> select subtract #8
1 model selected
> volume #10 color #b2ffff9d
> volume #10 level 0.04401
> volume #10 level 0.045
> save "/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/mask_TMDs.mrc"
> models #10
> close #6
> resample #10 512
Unknown command: resample #10 512
> volume resample #10 512
Expected a keyword
> volume resample #10 onGrid #1
Opened mask_TMDs.mrc resampled as #6, grid size 512,512,512, pixel 0.573,
shown at step 1, values float32
> save "/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/mask_TMDs.mrc"
> models #10
> save "/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/mask_TMDs.mrc"
> models #6
> close #11
> volume #6 color #b2b2ff89
> open /Users/eruboldi/Downloads/cryosparc_P2_J126_mask.mrc
Opened cryosparc_P2_J126_mask.mrc as #11, grid size 512,512,512, pixel 0.573,
shown at level 0.39, step 2, values float32
> hide #!11 models
> open /Users/eruboldi/Downloads/cryosparc_P2_J126_mask(1).mrc
Opened cryosparc_P2_J126_mask(1).mrc as #12, grid size 512,512,512, pixel
0.573, shown at level 5e-05, step 2, values float32
> show #!11 models
> hide #!11 models
> volume #12 step 1
> volume #11 step 1
> volume #12 color #ffb2b285
> volume #11 color #ffb2ff83
> hide #!12 models
> show #!12 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> open /Users/eruboldi/Downloads/cryosparc_P2_J126_mask(2).mrc
Opened cryosparc_P2_J126_mask(2).mrc as #13, grid size 512,512,512, pixel
0.573, shown at level 5e-05, step 2, values float32
> close #13
> show #!11 models
> hide #!11 models
> close #11
> open /Users/eruboldi/Downloads/cryosparc_P2_J130_map_sharp.mrc
> /Users/eruboldi/Downloads/cryosparc_P2_J134_map_sharp.mrc
> /Users/eruboldi/Downloads/cryosparc_P2_J133_map_sharp.mrc
> /Users/eruboldi/Downloads/cryosparc_P2_J132_map_sharp.mrc
> /Users/eruboldi/Downloads/cryosparc_P2_J131_map_sharp.mrc
> /Users/eruboldi/Downloads/cryosparc_P2_J135_map_sharp.mrc
Opened cryosparc_P2_J130_map_sharp.mrc as #11.1, grid size 512,512,512, pixel
0.573, shown at level 0.0158, step 2, values float32
Opened cryosparc_P2_J134_map_sharp.mrc as #11.2, grid size 512,512,512, pixel
0.573, shown at level 0.0156, step 2, values float32
Opened cryosparc_P2_J133_map_sharp.mrc as #11.3, grid size 512,512,512, pixel
0.573, shown at level 0.0164, step 2, values float32
Opened cryosparc_P2_J132_map_sharp.mrc as #11.4, grid size 512,512,512, pixel
0.573, shown at level 0.0157, step 2, values float32
Opened cryosparc_P2_J131_map_sharp.mrc as #11.5, grid size 512,512,512, pixel
0.573, shown at level 0.0192, step 2, values float32
Opened cryosparc_P2_J135_map_sharp.mrc as #11.6, grid size 512,512,512, pixel
0.573, shown at level 0.015, step 2, values float32
> volume #11.5 step 1
> volume #11.4 step 1
> volume #11.2 step 1
> volume #11.1 step 1
> close #12
> hide #!11.6 models
> hide #!11.5 models
> hide #!11.4 models
> hide #!11.3 models
> hide #!11.2 models
> volume #11.1 level 0.02752
> hide #!6 models
> volume #11.2 level 0.03347
> volume #11.3 level 0.05914
> hide #8 models
> volume #11.4 level 0.03018
> volume #11.5 level 0.1208
> volume #11.3 level 0.07859
> volume #11.5 level 0.1111
> close #11
> open /Users/eruboldi/Downloads/cryosparc_P2_J134_map_sharp(1).mrc
Opened cryosparc_P2_J134_map_sharp(1).mrc as #11, grid size 512,512,512, pixel
0.573, shown at level 0.0169, step 2, values float32
> open /Users/eruboldi/Downloads/cryosparc_P2_J135_map_sharp(1).mrc
Opened cryosparc_P2_J135_map_sharp(1).mrc as #12, grid size 512,512,512, pixel
0.573, shown at level 0.0175, step 2, values float32
> open /Users/eruboldi/Downloads/cryosparc_P2_J132_map_sharp(1).mrc
Opened cryosparc_P2_J132_map_sharp(1).mrc as #13, grid size 512,512,512, pixel
0.573, shown at level 0.0159, step 2, values float32
> open /Users/eruboldi/Downloads/cryosparc_P2_J131_map_sharp(1).mrc
Opened cryosparc_P2_J131_map_sharp(1).mrc as #14, grid size 512,512,512, pixel
0.573, shown at level 0.0156, step 2, values float32
> open /Users/eruboldi/Downloads/cryosparc_P2_J130_map_sharp(1).mrc
Opened cryosparc_P2_J130_map_sharp(1).mrc as #15, grid size 512,512,512, pixel
0.573, shown at level 0.0152, step 2, values float32
> volume #15 step 1
> volume #14 step 1
> volume #13 step 1
> volume #11 step 1
> hide #!15 models
> hide #!14 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> open /Users/eruboldi/Downloads/cryosparc_P2_J133_map_sharp.mrc
Opened cryosparc_P2_J133_map_sharp.mrc as #16, grid size 512,512,512, pixel
0.573, shown at level 0.0164, step 2, values float32
> volume #16 step 1
> volume #16 level 0.05701
> volume #15 level 0.04022
> volume #12 level 0.04298
> select clear
> ui mousemode right translate
> volume #11 level 0.05933
> volume #13 level 0.05099
> volume #11 level 0.08054
> volume #11 level 0.06781
> volume #12 level 0.04722
> surface dust #12 size 5.73
> volume #14 level 0.0492
> volume #15 level 0.04738
> volume #16 level 0.07733
> show #!11 models
> show #!13 models
> close #11-16
> open /Users/eruboldi/Downloads/cryosparc_P2_J130_map_sharp(1).mrc
Opened cryosparc_P2_J130_map_sharp(1).mrc as #11, grid size 512,512,512, pixel
0.573, shown at level 0.0152, step 2, values float32
> open /Users/eruboldi/Downloads/cryosparc_P2_J132_map_sharp(1).mrc
Opened cryosparc_P2_J132_map_sharp(1).mrc as #12, grid size 512,512,512, pixel
0.573, shown at level 0.0159, step 2, values float32
> open /Users/eruboldi/Downloads/cryosparc_P2_J131_map_sharp(1).mrc
Opened cryosparc_P2_J131_map_sharp(1).mrc as #13, grid size 512,512,512, pixel
0.573, shown at level 0.0156, step 2, values float32
> open /Users/eruboldi/Downloads/cryosparc_P2_J133_map_sharp.mrc
Opened cryosparc_P2_J133_map_sharp.mrc as #14, grid size 512,512,512, pixel
0.573, shown at level 0.0164, step 2, values float32
> open /Users/eruboldi/Downloads/cryosparc_P2_J134_map_sharp(1).mrc
Opened cryosparc_P2_J134_map_sharp(1).mrc as #15, grid size 512,512,512, pixel
0.573, shown at level 0.0169, step 2, values float32
> open /Users/eruboldi/Downloads/cryosparc_P2_J135_map_sharp(1).mrc
Opened cryosparc_P2_J135_map_sharp(1).mrc as #16, grid size 512,512,512, pixel
0.573, shown at level 0.0175, step 2, values float32
> volume #16 level 0.0345
> volume #15 level 0.04532
> volume #14 level 0.0747
> volume #13 level 0.05845
> volume #12 level 0.06065
> volume #11 level 0.03571
> volume #11 step 1
> volume #12 step 1
> volume #13 step 1
> volume #14 step 1
> volume #15 step 1
> volume #16 step 1
> hide #!16 models
> hide #!15 models
> hide #!14 models
> show #!14 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> show #8 models
> hide #8 models
> open "/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/ctGWT1_noGPF.pdb"
Chain information for ctGWT1_noGPF.pdb #17
---
Chain | Description
A | No description available
> ui mousemode right select
Drag select of 161 residues
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models #17,1,0,0,142.14,0,1,0,84.67,0,0,1,142.07
> view matrix models #17,1,0,0,153.13,0,1,0,66.462,0,0,1,107.32
> view matrix models #17,1,0,0,150.69,0,1,0,73.896,0,0,1,123
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.7091,0.5895,-0.38688,159.02,-0.7044,0.61686,-0.35115,76.227,0.031644,0.52152,0.85265,127.87
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.7091,0.5895,-0.38688,155.41,-0.7044,0.61686,-0.35115,135.12,0.031644,0.52152,0.85265,158.08
> view matrix models
> #17,0.7091,0.5895,-0.38688,142.81,-0.7044,0.61686,-0.35115,146.19,0.031644,0.52152,0.85265,146.87
> view matrix models
> #17,0.7091,0.5895,-0.38688,162.26,-0.7044,0.61686,-0.35115,142.91,0.031644,0.52152,0.85265,142.3
> view matrix models
> #17,0.7091,0.5895,-0.38688,158.96,-0.7044,0.61686,-0.35115,148.45,0.031644,0.52152,0.85265,133.95
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.86721,0.076857,-0.49197,159.41,-0.40389,0.68644,-0.60471,154.42,0.29123,0.72311,0.62633,139.8
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.86721,0.076857,-0.49197,161.04,-0.40389,0.68644,-0.60471,150.26,0.29123,0.72311,0.62633,138.85
> view matrix models
> #17,0.86721,0.076857,-0.49197,164.61,-0.40389,0.68644,-0.60471,153.12,0.29123,0.72311,0.62633,137.47
> fitmap #17 inMap #14
Fit molecule ctGWT1_noGPF.pdb (#17) to map cryosparc_P2_J133_map_sharp.mrc
(#14) using 3443 atoms
average map value = 0.0322, steps = 104
shifted from previous position = 4.83
rotated from previous position = 9.24 degrees
atoms outside contour = 2764, contour level = 0.0747
Position of ctGWT1_noGPF.pdb (#17) relative to cryosparc_P2_J133_map_sharp.mrc
(#14) coordinates:
Matrix rotation and translation
0.87996734 -0.01021308 -0.47492438 161.34502821
-0.37959597 0.58595191 -0.71593803 152.81620256
0.28559478 0.81028147 0.51174170 143.32772345
Axis 0.87474587 -0.43588815 -0.21171015
Axis point 0.00000000 -32.33354734 259.04742590
Rotation angle (degrees) 60.73625898
Shift along axis 44.18119100
> view matrix models
> #17,0.87997,-0.010213,-0.47492,167.94,-0.3796,0.58595,-0.71594,195.35,0.28559,0.81028,0.51174,181.69
> view matrix models
> #17,0.87997,-0.010213,-0.47492,169.74,-0.3796,0.58595,-0.71594,108.14,0.28559,0.81028,0.51174,147.27
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.77614,-0.078854,-0.6256,171.83,-0.55134,0.39659,-0.73399,107.1,0.30599,0.9146,0.26434,152.26
> view matrix models
> #17,-0.37438,0.15839,0.91365,140.62,-0.40471,-0.91442,-0.0073125,89.199,0.8343,-0.3725,0.40644,146.47
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.37438,0.15839,0.91365,118.88,-0.40471,-0.91442,-0.0073125,119.3,0.8343,-0.3725,0.40644,160.22
> view matrix models
> #17,-0.37438,0.15839,0.91365,111.85,-0.40471,-0.91442,-0.0073125,132.58,0.8343,-0.3725,0.40644,149.17
> view matrix models
> #17,-0.37438,0.15839,0.91365,118.67,-0.40471,-0.91442,-0.0073125,130.28,0.8343,-0.3725,0.40644,145.26
> view matrix models
> #17,-0.37438,0.15839,0.91365,118.59,-0.40471,-0.91442,-0.0073125,132.96,0.8343,-0.3725,0.40644,148.08
> view matrix models
> #17,-0.37438,0.15839,0.91365,120.27,-0.40471,-0.91442,-0.0073125,133.02,0.8343,-0.3725,0.40644,148.35
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.31644,0.12299,0.9406,119.85,-0.34499,-0.93858,0.0066597,132.88,0.88366,-0.32239,0.33944,149.94
> view matrix models
> #17,-0.30831,0.21146,0.92749,120.47,-0.24454,-0.95983,0.13754,130.78,0.91932,-0.1844,0.34764,150.47
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.30831,0.21146,0.92749,118.41,-0.24454,-0.95983,0.13754,133.79,0.91932,-0.1844,0.34764,147.82
> fitmap #17 inMap #14
Fit molecule ctGWT1_noGPF.pdb (#17) to map cryosparc_P2_J133_map_sharp.mrc
(#14) using 3443 atoms
average map value = 0.02918, steps = 96
shifted from previous position = 2.3
rotated from previous position = 4.18 degrees
atoms outside contour = 2814, contour level = 0.0747
Position of ctGWT1_noGPF.pdb (#17) relative to cryosparc_P2_J133_map_sharp.mrc
(#14) coordinates:
Matrix rotation and translation
-0.30371940 0.28188313 0.91010792 119.70951532
-0.27198365 -0.94113421 0.20072690 130.55899966
0.91311522 -0.18656982 0.36250832 146.39703125
Axis -0.57304943 -0.00444965 -0.81950873
Axis point 22.44753544 63.68027872 0.00000000
Rotation angle (degrees) 160.24942846
Shift along axis -189.15405591
> view matrix models
> #17,-0.30372,0.28188,0.91011,121.6,-0.27198,-0.94113,0.20073,134.92,0.91312,-0.18657,0.36251,150.43
> fitmap #17 inMap #14
Fit molecule ctGWT1_noGPF.pdb (#17) to map cryosparc_P2_J133_map_sharp.mrc
(#14) using 3443 atoms
average map value = 0.03012, steps = 2000
shifted from previous position = 2.91
rotated from previous position = 6.92 degrees
atoms outside contour = 2795, contour level = 0.0747
Position of ctGWT1_noGPF.pdb (#17) relative to cryosparc_P2_J133_map_sharp.mrc
(#14) coordinates:
Matrix rotation and translation
-0.28587070 0.19495150 0.93822804 120.89123326
-0.17562846 -0.97316168 0.14869765 137.42462625
0.94203640 -0.12227125 0.31243744 149.09858833
Axis -0.59022410 -0.00829537 -0.80719681
Axis point 15.72201488 67.43678169 0.00000000
Rotation angle (degrees) 166.72956931
Shift along axis -192.84481348
> view matrix models
> #17,-0.28587,0.19495,0.93823,139.12,-0.17563,-0.97316,0.1487,118.41,0.94204,-0.12227,0.31244,147.12
> view matrix models
> #17,-0.28587,0.19495,0.93823,139.32,-0.17563,-0.97316,0.1487,86.847,0.94204,-0.12227,0.31244,137.46
> view matrix models
> #17,-0.28587,0.19495,0.93823,113,-0.17563,-0.97316,0.1487,93.591,0.94204,-0.12227,0.31244,147.1
> view matrix models
> #17,-0.28587,0.19495,0.93823,99.122,-0.17563,-0.97316,0.1487,122.11,0.94204,-0.12227,0.31244,146.82
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.094315,-0.13063,0.98694,97.633,-0.72905,-0.66601,-0.15782,126.91,0.67793,-0.73441,-0.032419,149.72
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.094315,-0.13063,0.98694,120.11,-0.72905,-0.66601,-0.15782,128.35,0.67793,-0.73441,-0.032419,158.3
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.6247,0.067644,0.77793,122.79,-0.62188,-0.64559,-0.44326,134.01,0.47224,-0.76068,0.44537,148.76
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.6247,0.067644,0.77793,115.8,-0.62188,-0.64559,-0.44326,141.69,0.47224,-0.76068,0.44537,140.13
> view matrix models
> #17,-0.6247,0.067644,0.77793,124.23,-0.62188,-0.64559,-0.44326,142.06,0.47224,-0.76068,0.44537,138.23
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.68677,-0.16302,0.70836,124.35,-0.47837,-0.63236,-0.60933,145.65,0.54727,-0.75732,0.35631,140.13
> view matrix models
> #17,-0.66484,-0.1705,0.72727,124.06,-0.62419,-0.40803,-0.66626,147.06,0.41034,-0.89691,0.16485,142.57
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.66484,-0.1705,0.72727,123.75,-0.62419,-0.40803,-0.66626,147,0.41034,-0.89691,0.16485,146.7
> view matrix models
> #17,-0.66484,-0.1705,0.72727,125.88,-0.62419,-0.40803,-0.66626,147.64,0.41034,-0.89691,0.16485,148.06
> view matrix models
> #17,-0.66484,-0.1705,0.72727,122.2,-0.62419,-0.40803,-0.66626,142.31,0.41034,-0.89691,0.16485,139.22
> view matrix models
> #17,-0.66484,-0.1705,0.72727,120.22,-0.62419,-0.40803,-0.66626,144.44,0.41034,-0.89691,0.16485,134.78
> view matrix models
> #17,-0.66484,-0.1705,0.72727,131.28,-0.62419,-0.40803,-0.66626,126.22,0.41034,-0.89691,0.16485,93.657
> view matrix models
> #17,-0.66484,-0.1705,0.72727,127.89,-0.62419,-0.40803,-0.66626,155.18,0.41034,-0.89691,0.16485,135.02
> view matrix models
> #17,-0.66484,-0.1705,0.72727,131.96,-0.62419,-0.40803,-0.66626,153.58,0.41034,-0.89691,0.16485,142.61
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.52787,-0.12509,0.84007,130.58,-0.57146,-0.67941,-0.46025,148.94,0.62832,-0.72301,0.28716,141.86
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.52787,-0.12509,0.84007,129.09,-0.57146,-0.67941,-0.46025,150.21,0.62832,-0.72301,0.28716,138.84
> fitmap #17 inMap #14
Fit molecule ctGWT1_noGPF.pdb (#17) to map cryosparc_P2_J133_map_sharp.mrc
(#14) using 3443 atoms
average map value = 0.08104, steps = 160
shifted from previous position = 4.56
rotated from previous position = 16.8 degrees
atoms outside contour = 1744, contour level = 0.0747
Position of ctGWT1_noGPF.pdb (#17) relative to cryosparc_P2_J133_map_sharp.mrc
(#14) coordinates:
Matrix rotation and translation
-0.73804004 -0.17945467 0.65045592 128.55925345
-0.43846612 -0.60517067 -0.66446664 154.21643461
0.51287849 -0.77560587 0.36795540 139.89743742
Axis -0.35435943 0.43865571 -0.82583931
Axis point 43.58978446 109.70313086 0.00000000
Rotation angle (degrees) 170.97780258
Shift along axis -93.44106784
> surface dust #15 size 5.73
> ui mousemode right translate
> volume #15 level 0.007121
> volume #15 level 0.06654
> volume #16 level 0.06109
> surface dust #16 size 5.73
> select add #17
3443 atoms, 3524 bonds, 2 pseudobonds, 445 residues, 3 models selected
> select subtract #17
Nothing selected
> hide #!16 models
> show #!15 models
> hide #!15 models
> show #!14 models
> surface dust #14 size 5.73
> hide #!14 models
> show #!13 models
> surface dust #13 size 5.73
> volume #13 level 0.06591
> open /Users/eruboldi/Downloads/cryosparc_P2_J93_003_volume_map_sharp(2).mrc
Opened cryosparc_P2_J93_003_volume_map_sharp(2).mrc as #18, grid size
512,512,512, pixel 0.573, shown at level 0.0319, step 2, values float32
> volume #18 step 1
> volume #18 level 0.09101
> surface dust #13 size 5.73
> surface dust #18 size 5.73
> color #18 #ffb2b281 models
> color #18 #ffb2b29f models
> color #18 #ffb2b2c2 models
> color #17 #c4b92aff
> color #17 #fbed35ff
> color #18 #3649f7c2 models
> color #18 #3649f7b1 models
> color #18 #3649f7b3 models
> color #17 #fffb00ff
> color #17 #fffc79ff
> color #17 #fffb00ff
> color #17 #acab39ff
> color #17 #acab3aff
> color #18 #e6f0edb3 models
> color #18 #8c9290b3 models
> surface dust #11 size 5.73
> surface dust #18 size 5.73
> volume #11 level 0.03571
> volume #11 level 0.05717
> hide #!17 models
> select add #17
3443 atoms, 3524 bonds, 2 pseudobonds, 445 residues, 3 models selected
> show #!17 models
> volume zone #18 nearAtoms sel newMap true
Opened cryosparc_P2_J93_003_volume_map_sharp(2).mrc zone as #19, grid size
512,512,512, pixel 0.573, shown at step 1, values float32
> rename #19 new_mask_part_sub
> molmap #19 15
No atoms specified
> volume #19 level 0.1103
> volume #19 level 0.07817
> volume gaussian #19 sDev 3
Opened new_mask_part_sub gaussian as #20, grid size 512,512,512, pixel 0.573,
shown at step 1, values float32
> color #20 #e5bf99cc models
> color #20 #e5bf9995 models
> color #20 #e5bf9982 models
> volume gaussian #19 sDev 1
Opened new_mask_part_sub gaussian as #21, grid size 512,512,512, pixel 0.573,
shown at step 1, values float32
> close #20
> volume gaussian #19 sDev 2
Opened new_mask_part_sub gaussian as #20, grid size 512,512,512, pixel 0.573,
shown at step 1, values float32
> close #20
> close #21
> volume gaussian #19 sDev 2
Opened new_mask_part_sub gaussian as #20, grid size 512,512,512, pixel 0.573,
shown at step 1, values float32
> volume gaussian #19 sDev 1.5
Opened new_mask_part_sub gaussian as #21, grid size 512,512,512, pixel 0.573,
shown at step 1, values float32
> hide #!20 models
> show #!20 models
> hide #!20 models
> hide #!21 models
> show #!19 models
> hide #!19 models
> show #!19 models
> show #!20 models
> show #!21 models
> hide #!21 models
> hide #!20 models
> close #21
> close #20
No map chosen to save
> save "/Users/eruboldi/Desktop/GPI/chimeraX
> sessions/ctGWT1/mask_after_loc_ref_part_subtr.mrc" models #19
> volume #19 level 0.078
> volume #19 level 0.08
> open /Users/eruboldi/Downloads/cryosparc_P2_J138_mask.mrc
Opened cryosparc_P2_J138_mask.mrc as #20, grid size 512,512,512, pixel 0.573,
shown at level 5e-05, step 2, values float32
> volume #20 level 0.1091
> hide #!20 models
> show #!20 models
> hide #!19 models
> hide #!20 models
> show #!20 models
> hide #!20 models
> show #!20 models
> close #19
> open "/Users/eruboldi/Desktop/GPI/chimeraX
> sessions/ctGWT1/mask_after_loc_ref_part_subtr.mrc"
Opened mask_after_loc_ref_part_subtr.mrc as #19, grid size 512,512,512, pixel
0.573, shown at level 0.000229, step 2, values float32
> volume #15 level 0.07927
> volume #19 level 0.06016
> show #!18 models
> volume #19 level 0.06615
> volume #19 step 1
> volume #19 level 0.08541
> open /Users/eruboldi/Downloads/cryosparc_P2_J130_map_sharp.mrc
Opened cryosparc_P2_J130_map_sharp.mrc as #21, grid size 512,512,512, pixel
0.573, shown at level 0.0344, step 2, values float32
> volume #21 step 1
> volume #21 level 0.08033
> surface dust #18 size 5.73
> surface dust #20 size 5.73
> surface dust #19 size 5.73
> surface dust #21 size 5.73
> hide #!19 models
> hide #!20 models
> show #!20 models
> hide #!21 models
> hide #!20 models
> show #!20 models
> close #20
> show #!21 models
> close #21
> open /Users/eruboldi/Downloads/cryosparc_P2_J130_map_sharp.mrc
Opened cryosparc_P2_J130_map_sharp.mrc as #20, grid size 512,512,512, pixel
0.573, shown at level 0.0344, step 2, values float32
> volume #20 step 1
> volume #20 level 0.08033
> surface dust #18 size 5.73
> surface dust #20 size 5.73
> volume #20 level 0.08797
> hide #!18 models
> show #!18 models
> color #20 #ffb2b284 models
> ui tool show "Model Panel"
> ui tool show Log
> select subtract #17
Nothing selected
> color #18 #8c9290ff models
> color #20 #ffb2b2ff models
> hide #!20 models
> show #!20 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!20 models
> show #!20 models
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> rename #20 -200
> open /Users/eruboldi/Downloads/cryosparc_P2_J131_map_sharp.mrc
Opened cryosparc_P2_J131_map_sharp.mrc as #21, grid size 512,512,512, pixel
0.573, shown at level 0.0192, step 2, values float32
> open /Users/eruboldi/Downloads/cryosparc_P2_J132_map_sharp.mrc
Opened cryosparc_P2_J132_map_sharp.mrc as #22, grid size 512,512,512, pixel
0.573, shown at level 0.0147, step 2, values float32
> volume #21 step 1
> volume #21 level 0.03556
> volume #22 step 1
> volume #22 level 0.04319
> volume #21 level 0.05737
> rename #21 -150, rename #22 -100
Expected a keyword
> rename #21 -150 & rename #22 -100
Expected a keyword
> ui tool show Log
> rename #21 -150
> rename #22 -100
> hide #!18 models
> cofr #17
> volume #22 level 0.05385
> hide #!21 models
> volume #22 level 0.05385
> hide #!22 models
> show #!21 models
> volume #21 level 0.07919
> show #!20 models
> volume #21 level 0.088
> volume #21 level 0.06074
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> show #!21 models
> hide #!21 models
> close #21
> close #22
> close #16
> close #12-13
> close #15
> close #11
> show #!14 models
> volume #14 level 0.05179
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> close #14
> open /Users/eruboldi/Downloads/cryosparc_P2_J131_map_sharp(2).mrc
Opened cryosparc_P2_J131_map_sharp(2).mrc as #11, grid size 512,512,512, pixel
0.573, shown at level 0.0453, step 2, values float32
> volume #11 step 1
> open /Users/eruboldi/Downloads/cryosparc_P2_J132_map_sharp(2).mrc
Opened cryosparc_P2_J132_map_sharp(2).mrc as #12, grid size 512,512,512, pixel
0.573, shown at level 0.0266, step 2, values float32
> volume #11 level 0.1081
> rename #11 -220
> rename #12 -180
> volume #12 level 0.06078
> surface dust #20 size 5.73
> surface dust #11 size 5.73
> surface dust #12 size 5.73
> open /Users/eruboldi/Downloads/cryosparc_P2_J41_mask(1).mrc
Opened cryosparc_P2_J41_mask(1).mrc as #13, grid size 256,256,256, pixel 1.15,
shown at level 5e-05, step 1, values float32
> hide #!13 models
> show #!13 models
> color #13 #b2b2b288 models
> open "/Users/eruboldi/Downloads/cryosparc_P2_Mask HRHAIR recon.mrc"
Opened cryosparc_P2_Mask HRHAIR recon.mrc as #14, grid size 256,256,256, pixel
1.15, shown at level 3.23e-05, step 1, values float32
> hide #!14 models
> show #!14 models
> hide #!13 models
> hide #!11 models
> show #!11 models
> color #14 #ffffb297 models
> hide #!11 models
> close #14
> molmap #17 15
Opened ctGWT1_noGPF.pdb map 15 as #14, grid size 30,31,31, pixel 5, shown at
level 0.0451, step 1, values float32
> color #14 #b2ffff9d models
> open "/Users/eruboldi/Downloads/cryosparc_P2_Mask HRHAIR recon.mrc"
Opened cryosparc_P2_Mask HRHAIR recon.mrc as #15, grid size 256,256,256, pixel
1.15, shown at level 3.23e-05, step 1, values float32
> show #!20 models
> open "/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/mask_TMDs.mrc"
Opened mask_TMDs.mrc as #16, grid size 512,512,512, pixel 0.573, shown at
level 0.00261, step 2, values float32
> close #16
> close #15
> close #20
> resample #14 ongrid #18
Unknown command: resample #14 ongrid #18
> volume resample #14 onGrid #18
Opened ctGWT1_noGPF.pdb map 15 resampled as #15, grid size 512,512,512, pixel
0.573, shown at step 1, values float32
> color #15 #ffb2b295 models
> save "/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/mask_TMDs.mrc"
> models #15
> open "/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/mask_TMDs.mrc"
Opened mask_TMDs.mrc as #16, grid size 512,512,512, pixel 0.573, shown at
level 0.000331, step 2, values float32
> volume #16 level 0.04252
> volume #15 level 0.0425
> open /Volumes/mpb-1/eruboldi/cryosparc/CS-scgpi17-cu-10-mg-
> ml/uploads/resampled_helices_mask.mrc
Opened resampled_helices_mask.mrc as #20, grid size 256,256,256, pixel 1.15,
shown at level 1.08e-05, step 1, values float32
> open /Volumes/mpb-1/eruboldi/cryosparc/CS-scgpi17-cu-10-mg-
> ml/uploads/resampled_helices_mask.mrc
Opened resampled_helices_mask.mrc as #21, grid size 256,256,256, pixel 1.15,
shown at level 1.08e-05, step 1, values float32
> hide #!20 models
> show #!20 models
> close #21
> hide #!20 models
> show #!20 models
> hide #!17 models
> hide #!16 models
> show #!17 models
> hide #!20 models
> open /Users/eruboldi/Downloads/cryosparc_P2_mask_TMDs.mrc
Opened cryosparc_P2_mask_TMDs.mrc as #21, grid size 512,512,512, pixel 0.573,
shown at level 0.000331, step 2, values float32
> volume #21 level 0.04252
> close #20
> open /Users/eruboldi/Downloads/cryosparc_P2_J138_mask(1).mrc
Opened cryosparc_P2_J138_mask(1).mrc as #20, grid size 512,512,512, pixel
0.573, shown at level 5e-05, step 2, values float32
> hide #!21 models
> volume #20 color #b2b2b27c
> volume #20 step 1
> volume #21 level 0.08309
> volume #21 step 1
> volume #21 level 0.07821
> volume #21 color #cccc997f
> volume #21 level 0.1018
> volume #21 level 0.05623
> volume #21 level 0.136
> volume #21 level 0.13
> rename #20 0.0425
> open /Users/eruboldi/Downloads/cryosparc_P2_J138_mask(2).mrc
Opened cryosparc_P2_J138_mask(2).mrc as #22, grid size 512,512,512, pixel
0.573, shown at level 5e-05, step 2, values float32
> color #22 #ffffb2b7 models
> open /Users/eruboldi/Downloads/cryosparc_P2_J138_mask(4).mrc
Opened cryosparc_P2_J138_mask(4).mrc as #23, grid size 512,512,512, pixel
0.573, shown at level 5e-05, step 2, values float32
> color #23 #b2ffff92 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
Unsupported scale factor (0.000000) detected on Display1
> open /Users/eruboldi/Downloads/cryosparc_P2_J89_006_volume_map_sharp.mrc
Opened cryosparc_P2_J89_006_volume_map_sharp.mrc as #24, grid size
512,512,512, pixel 0.573, shown at level 0.0204, step 2, values float32
> volume #24 step 1
> volume #24 level 0.05188
> hide #!22 models
> hide #!21 models
> volume #24 level 0.1148
> open /Users/eruboldi/Downloads/cryosparc_P2_J49_005_volume_map_sharp(1).mrc
Opened cryosparc_P2_J49_005_volume_map_sharp(1).mrc as #25, grid size
512,512,512, pixel 0.573, shown at level 0.0183, step 2, values float32
> volume #25 step 1
> volume #25 level 0.09151
> surface dust #24 size 5.73
> surface dust #25 size 5.73
> hide #!25 models
> show #!25 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> open /Users/eruboldi/Downloads/cryosparc_P2_J112_mask(1).mrc
Opened cryosparc_P2_J112_mask(1).mrc as #26, grid size 256,256,256, pixel
1.15, shown at level 5e-05, step 1, values float32
> hide #!25 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> close #26
> open /Users/eruboldi/Downloads/cryosparc_P2_J139_003_volume_map_sharp.mrc
Opened cryosparc_P2_J139_003_volume_map_sharp.mrc as #26, grid size
512,512,512, pixel 0.573, shown at level 0.0261, step 2, values float32
> volume #26 step 1
> volume #26 level 0.02609
> volume #26 level 0.05532
> volume #26 level 0.1503
> surface dust #26 size 5.73
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
Errors may have occurred when running pip:
pip standard error:
\---
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.
nptyping 2.5.0 requires numpy=1.20.0; python_version >= "3.8", but you
have numpy 2.4.6 which is incompatible.
scipy 1.14.0 requires numpy=1.23.5, but you have numpy 2.4.6 which is
incompatible.
\---
pip standard output:
\---
\---
pyKVFinder module installed from PyPi repository.
> kvfinder #8
31 cavities found for scGPI8_model.cif #8
scGPI8_model.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
8.1.2 | | 2901.31 | 2117.49 | 13432 | 18.09 | 5.38
8.1.14 | | 2148.98 | 1533.78 | 9949 | 8.16 | 2.56
8.1.3 | | 67.18 | 102.2 | 311 | 2.47 | 0.63
8.1.13 | | 65.66 | 76.82 | 304 | 3 | 1.02
8.1.11 | | 63.07 | 83.75 | 292 | 0 | 0
8.1.8 | | 47.95 | 62.18 | 222 | 2.55 | 1.16
8.1.17 | | 46.22 | 67.66 | 214 | 1.9 | 0.47
8.1.22 | | 45.58 | 74.53 | 211 | 0 | 0
8.1.5 | | 31.54 | 47.34 | 146 | 3.06 | 1.36
8.1.4 | | 31.32 | 52.92 | 145 | 0 | 0
8.1.28 | | 30.24 | 55.56 | 140 | 0 | 0
8.1.15 | | 29.81 | 34.16 | 138 | 1.8 | 0.6
8.1.9 | | 28.94 | 48.7 | 134 | 0 | 0
8.1.30 | | 21.17 | 39.07 | 98 | 0 | 0
8.1.10 | | 19.01 | 38.34 | 88 | 0 | 0
8.1.20 | | 17.06 | 17.03 | 79 | 0.85 | 0.25
8.1.21 | | 16.85 | 32.3 | 78 | 0 | 0
8.1.6 | | 12.31 | 29.54 | 57 | 0 | 0
8.1.7 | | 12.31 | 29.54 | 57 | 0 | 0
8.1.12 | | 12.31 | 29.54 | 57 | 0 | 0
8.1.19 | | 12.31 | 29.54 | 57 | 0 | 0
8.1.23 | | 12.31 | 29.54 | 57 | 0 | 0
8.1.24 | | 12.31 | 29.54 | 57 | 0 | 0
8.1.27 | | 12.31 | 29.54 | 57 | 0 | 0
8.1.25 | | 11.23 | 19.05 | 52 | 1.7 | 0.5
8.1.18 | | 10.15 | 17.89 | 47 | 1.2 | 0.32
8.1.1 | | 9.5 | 17.61 | 44 | 1.2 | 0.34
8.1.16 | | 9.29 | 15.01 | 43 | 0.85 | 0.29
8.1.26 | | 8.64 | 13.16 | 40 | 0.85 | 0.19
8.1.29 | | 8.42 | 16.15 | 39 | 1.34 | 0.48
8.1.31 | | 7.78 | 16.91 | 36 | 1.04 | 0.38
Populating font family aliases took 150 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> hide #!17 models
> show #!17 models
> ui tool show "Find Cavities"
> kvfinder #17
16 cavities found for ctGWT1_noGPF.pdb #17
ctGWT1_noGPF.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
17.2.3 | | 2935.44 | 2126.31 | 13590 | 18.09 | 5.36
17.2.13 | | 412.78 | 309.39 | 1911 | 5.2 | 1.44
17.2.14 | | 67.18 | 72.72 | 311 | 3 | 1.04
17.2.12 | | 61.34 | 82.94 | 284 | 0 | 0
17.2.2 | | 42.55 | 72.32 | 197 | 3.06 | 0.81
17.2.8 | | 33.48 | 45.86 | 155 | 2.16 | 0.96
17.2.9 | | 30.24 | 48.47 | 140 | 0 | 0
17.2.5 | | 29.59 | 43.28 | 137 | 3.06 | 1.25
17.2.4 | | 28.3 | 49.03 | 131 | 0 | 0
17.2.10 | | 17.28 | 36.68 | 80 | 0 | 0
17.2.6 | | 14.04 | 25.09 | 65 | 1.2 | 0.25
17.2.7 | | 12.31 | 29.54 | 57 | 0 | 0
17.2.11 | | 12.31 | 29.54 | 57 | 0 | 0
17.2.16 | | 12.31 | 29.54 | 57 | 0 | 0
17.2.1 | | 9.29 | 17.04 | 43 | 1.2 | 0.35
17.2.15 | | 7.56 | 14.57 | 35 | 0.85 | 0.2
> hide #!26 models
> mlp #17.2.1-16#!17
Map values for surface "ctGWT1_noGPF.pdb_A SES surface": minimum -26.61, mean
-0.3621, maximum 24.49
To also show corresponding color key, enter the above mlp command and add key
true
> ui tool show "Side View"
> hide #!17.2 models
> hide #!17.3 models
> show #17.3 models
> hide #17.3 models
> show #!26 models
> open /Users/eruboldi/Downloads/cryosparc_P2_J138_mask(4).mrc
Opened cryosparc_P2_J138_mask(4).mrc as #27, grid size 512,512,512, pixel
0.573, shown at level 5e-05, step 2, values float32
> color #27 #99bfe57b models
> hide #!27 models
> open /Users/eruboldi/Downloads/cryosparc_P2_J141_004_volume_map_sharp.mrc
Opened cryosparc_P2_J141_004_volume_map_sharp.mrc as #28, grid size
512,512,512, pixel 0.573, shown at level 0.0271, step 2, values float32
> volume #28 step 1
> volume #28 level 0.07878
> surface dust #26 size 5.73
> surface dust #28 size 5.73
> hide #!26 models
> show #!26 models
> hide #!28 models
> show #!28 models
> volume #28 level 0.1111
> hide #!26 models
> show #!26 models
> hide #!28 models
> show #!28 models
> hide #!28 models
> volume #26 level 0.1211
> show #!28 models
> hide #!28 models
> show #!28 models
> hide #!28 models
> hide #!26 models
> show #!28 models
> show #!26 models
> hide #!28 models
> show #!28 models
> hide #!26 models
> open /Users/eruboldi/Downloads/cryosparc_P2_J126_mask.mrc
Opened cryosparc_P2_J126_mask.mrc as #29, grid size 512,512,512, pixel 0.573,
shown at level 5e-05, step 2, values float32
> show #!1 models
> hide #!28 models
> hide #!29 target m
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!17 models
> surface dust #1 size 5.73
> volume #1 level 0.1195
> volume #1 level 0.1291
> hide #!8.1 models
> show #!29 target m
> color #29 #b2b2b28a models
> open /Users/eruboldi/Downloads/cryosparc_P2_J121_003_volume_map_sharp.mrc
Opened cryosparc_P2_J121_003_volume_map_sharp.mrc as #30, grid size
512,512,512, pixel 0.573, shown at level 0.017, step 2, values float32
> volume #30 step 1
> surface dust #1 size 5.73
> surface dust #29 size 5.73
> surface dust #30 size 5.73
> volume #30 level 0.04034
> hide #!29 models
> volume #30 level 0.05735
> volume #30 level 0.06798
> hide #!1 models
> volume #30 level 0.07435
> show #!29 models
> hide #!29 models
> open "/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/ctGWT1_noGPF.pdb"
Chain information for ctGWT1_noGPF.pdb #31
---
Chain | Description
A | No description available
> rename #31 TMDs_Julian
> mmaker #31 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker scGPI8_model.cif, chain A (#8) with TMDs_Julian, chain A (#31),
sequence alignment score = 3391.1
RMSD between 445 pruned atom pairs is 0.000 angstroms; (across all 445 pairs:
0.000)
> hide #!8 models
> select add #31
3443 atoms, 3524 bonds, 2 pseudobonds, 445 residues, 3 models selected
> hide #!30 models
> show #!30 models
> volume zone #30 nearAtoms sel newMap true
Opened cryosparc_P2_J121_003_volume_map_sharp.mrc zone as #32, grid size
512,512,512, pixel 0.573, shown at step 1, values float32
> volume #32 level 0.09221
> show #!30 models
> hide #!31 models
> show #!31 models
> hide #!31 models
> show #!31 models
> hide #!32 models
> hide #!30 models
> show #!32 models
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> show #!30 models
> hide #!30 models
> close #32
> show #!30 models
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 62 residues in model #31 to IUPAC-IUB
standards.
Chain information for TMDs_Julian #31.2
---
Chain | Description
A | No description available
> clipper associate #30 toModel #31
Opened cryosparc_P2_J121_003_volume_map_sharp.mrc as #31.1.1.1, grid size
512,512,512, pixel 0.573, shown at step 1, values float32
> isolde sim start #31.2/A
Sim termination reason: None
ISOLDE: stopped sim
> addh #31.2
Summary of feedback from adding hydrogens to TMDs_Julian #31.2
---
notes | Termini for TMDs_Julian (#31.2) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: TMDs_Julian #31.2/A TYR
18, TMDs_Julian #31.2/A PRO 146, TMDs_Julian #31.2/A SER 666
Chain-final residues that are actual C termini: TMDs_Julian #31.2/A LEU 743
Chain-final residues that are not actual C termini: TMDs_Julian #31.2/A ALA
107, TMDs_Julian #31.2/A PHE 422
466 hydrogen bonds
Adding 'H' to TMDs_Julian #31.2/A TYR 18
Adding 'H' to TMDs_Julian #31.2/A SER 666
3584 hydrogens added
> isolde sim start #31.2/A
ISOLDE: started sim
> ui mousemode right translate
> volume #31.1.1.1 level 0.09731
> hide #!31.1 models
> show #!31.1 models
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 11 residues in model #31.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select add #31.2
7027 atoms, 7108 bonds, 2 pseudobonds, 445 residues, 16 models selected
> select add #31.2
7027 atoms, 7108 bonds, 2 pseudobonds, 445 residues, 16 models selected
> select add #31
7027 atoms, 7108 bonds, 2 pseudobonds, 445 residues, 23 models selected
> select add #31
7027 atoms, 7108 bonds, 2 pseudobonds, 445 residues, 23 models selected
> select subtract #31.1
7027 atoms, 7108 bonds, 2 pseudobonds, 445 residues, 18 models selected
> select subtract #31.3
7027 atoms, 7108 bonds, 2 pseudobonds, 445 residues, 17 models selected
> hide #!31.1 models
> hide #!31.2 models
> show #!31.1 models
> show #!31.2 models
> save "/Users/eruboldi/Desktop/GPI/chimeraX
> sessions/ctGWT1/J121_after_Isolde.mrc" models #31.1.1.1
> close #31
> undo
> open "/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/ctGWT1_noGPF.pdb"
Chain information for ctGWT1_noGPF.pdb #30
---
Chain | Description
A | No description available
> open "/Users/eruboldi/Desktop/GPI/chimeraX
> sessions/ctGWT1/J121_after_Isolde.mrc"
Opened J121_after_Isolde.mrc as #31, grid size 42,42,42, pixel 0.573, shown at
level 0.203, step 1, values float32
> volume #31 level 0.05111
> close #31
> open /Users/eruboldi/Downloads/cryosparc_P2_J121_003_volume_map_sharp.mrc
Opened cryosparc_P2_J121_003_volume_map_sharp.mrc as #31, grid size
512,512,512, pixel 0.573, shown at level 0.017, step 2, values float32
> mmaker #30 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker scGPI8_model.cif, chain A (#8) with ctGWT1_noGPF.pdb, chain A
(#30), sequence alignment score = 3391.1
RMSD between 445 pruned atom pairs is 0.000 angstroms; (across all 445 pairs:
0.000)
> volume #31 level 0.08558
> hide #!31 models
> show #!31 target m
> color #31 #ffb2ff80 models
> color #30 #f39d37ff
> color #30 #f8a138ff
> surface dust #31 size 5.73
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 62 residues in model #30 to IUPAC-IUB
standards.
Chain information for ctGWT1_noGPF.pdb #30.2
---
Chain | Description
A | No description available
> clipper associate #31 toModel #30
Opened cryosparc_P2_J121_003_volume_map_sharp.mrc as #30.1.1.1, grid size
512,512,512, pixel 0.573, shown at step 1, values float32
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
> clipper associate #28 toModel #30
Opened cryosparc_P2_J141_004_volume_map_sharp.mrc as #30.1.1.2, grid size
512,512,512, pixel 0.573, shown at step 1, values float32
> close #30
> open "/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/ctGWT1_noGPF.pdb"
Chain information for ctGWT1_noGPF.pdb #28
---
Chain | Description
A | No description available
> open /Users/eruboldi/Downloads/cryosparc_P2_J121_003_volume_map_sharp.mrc
Opened cryosparc_P2_J121_003_volume_map_sharp.mrc as #30, grid size
512,512,512, pixel 0.573, shown at level 0.017, step 2, values float32
> mmaker #28 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker scGPI8_model.cif, chain A (#8) with ctGWT1_noGPF.pdb, chain A
(#28), sequence alignment score = 3391.1
RMSD between 445 pruned atom pairs is 0.000 angstroms; (across all 445 pairs:
0.000)
> color #28 #a27d15ff
> color #28 #eab51eff
> color #30 #ffb2b27d models
> volume #30 level 0.03916
> surface dust #30 size 5.73
> volume #30 level 0.07347
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 62 residues in model #28 to IUPAC-IUB
standards.
Chain information for ctGWT1_noGPF.pdb #28.2
---
Chain | Description
A | No description available
> clipper associate #30 toModel #28
Opened cryosparc_P2_J121_003_volume_map_sharp.mrc as #28.1.1.1, grid size
512,512,512, pixel 0.573, shown at step 1, values float32
> close #28
> open /Users/eruboldi/Downloads/cryosparc_P2_J121_003_volume_map_sharp.mrc
Opened cryosparc_P2_J121_003_volume_map_sharp.mrc as #28, grid size
512,512,512, pixel 0.573, shown at level 0.017, step 2, values float32
> open "/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/ctGWT1_noGPF.pdb"
Chain information for ctGWT1_noGPF.pdb #30
---
Chain | Description
A | No description available
> color #28 #b2ffb283 models
> mmaker #30 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker scGPI8_model.cif, chain A (#8) with ctGWT1_noGPF.pdb, chain A
(#30), sequence alignment score = 3391.1
RMSD between 445 pruned atom pairs is 0.000 angstroms; (across all 445 pairs:
0.000)
> color #30 #946b18ff
> color #30 #fcb62aff
> volume #28 step 1
> volume #28 level 0.05735
> surface dust #28 size 5.73
> color #28 #fa8be583 models
> color #28 #ffb1f683 models
> color #28 #ffc9f983 models
> volume #28 level 0.1041
> volume #28 level 0.06373
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 62 residues in model #30 to IUPAC-IUB
standards.
Chain information for ctGWT1_noGPF.pdb #30.2
---
Chain | Description
A | No description available
> clipper associate #28 toModel #30
Opened cryosparc_P2_J121_003_volume_map_sharp.mrc as #30.1.1.1, grid size
512,512,512, pixel 0.573, shown at step 1, values float32
> isolde sim start #30.2/A
Sim termination reason: None
ISOLDE: stopped sim
> addh #30.2
Summary of feedback from adding hydrogens to ctGWT1_noGPF.pdb #30.2
---
notes | Termini for ctGWT1_noGPF.pdb (#30.2) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: ctGWT1_noGPF.pdb #30.2/A
TYR 18, ctGWT1_noGPF.pdb #30.2/A PRO 146, ctGWT1_noGPF.pdb #30.2/A SER 666
Chain-final residues that are actual C termini: ctGWT1_noGPF.pdb #30.2/A LEU
743
Chain-final residues that are not actual C termini: ctGWT1_noGPF.pdb #30.2/A
ALA 107, ctGWT1_noGPF.pdb #30.2/A PHE 422
466 hydrogen bonds
Adding 'H' to ctGWT1_noGPF.pdb #30.2/A TYR 18
Adding 'H' to ctGWT1_noGPF.pdb #30.2/A SER 666
3584 hydrogens added
> isolde sim start #30.2/A
ISOLDE: started sim
> ui mousemode right translate
> volume #30.1.1.1 level 0.08194
> volume #30.1.1.1 level 0.06839
> cofr #30
> save "/Users/eruboldi/Desktop/GPI/chimeraX
> sessions/ctGWT1/ctGWT1-noGFP_after_ISOLDE_J121.pdb" models #30
> close #30
Sim termination reason: model deleted
ISOLDE: model deleted during running simulation.
> open "/Users/eruboldi/Desktop/GPI/chimeraX
> sessions/ctGWT1/ctGWT1-noGFP_after_ISOLDE_J121.pdb"
Chain information for ctGWT1-noGFP_after_ISOLDE_J121.pdb #28
---
Chain | Description
A | No description available
> open /Users/eruboldi/Downloads/cryosparc_P2_J121_003_volume_map_sharp.mrc
Opened cryosparc_P2_J121_003_volume_map_sharp.mrc as #30, grid size
512,512,512, pixel 0.573, shown at level 0.017, step 2, values float32
> view
> ui tool show "Side View"
> color #30 #e5bf9989 models
> volume #30 level 0.0654
> hide #!30 models
> show #!30 models
> hide #!30 models
> open "/Users/eruboldi/Desktop/GPI/chimeraX sessions/ctGWT1/ctGWT1_noGPF.pdb"
Chain information for ctGWT1_noGPF.pdb #31
---
Chain | Description
A | No description available
> mmaker #31 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker scGPI8_model.cif, chain A (#8) with ctGWT1_noGPF.pdb, chain A
(#31), sequence alignment score = 3391.1
RMSD between 445 pruned atom pairs is 0.000 angstroms; (across all 445 pairs:
0.000)
> show #!30 models
> hide #!30 models
> swapaa ALA #31:177
Missing or invalid "residues" argument: invalid residues specifier
> swapaa ALA #31:177.A
Missing or invalid "residues" argument: invalid residues specifier
> swapaa A #31:177
Missing or invalid "residues" argument: invalid residues specifier
> swapaa #31:177 ALA
Using Dunbrack library
Swapping ctGWT1_noGPF.pdb #31/A LYS 177 to ALA
> swapaa #28:177 ALA
Using Dunbrack library
Swapping ctGWT1-noGFP_after_ISOLDE_J121.pdb #28/A LYS 177 to ALA
> show #28:177, #31:177
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #28:177
> select #28:177
5 atoms, 4 bonds, 1 residue, 1 model selected
> rmsd #28 #31
Missing required "to" argument
> rmsd #28 to #31
Number of atoms from first atom spec (7010) differs from number in second
(3439)
> show H
> delete H
> rmsd #28 to #31
RMSD between 3439 atom pairs is 1.077
> rmsd #28:218-244 to #31:218-244
RMSD between 199 atom pairs is 1.221
> rmsd #28:690-708 to #31:690-708
RMSD between 139 atom pairs is 1.241
> save "/Users/eruboldi/Desktop/GPI/chimeraX
> sessions/ctGWT1/ctGWT1_K177A-noGFP_after_ISOLDE_J121.pdb" models #28
> relModel #30
> save "/Users/eruboldi/Desktop/GPI/chimeraX
> sessions/ctGWT1/ctGWT1_K177A_noGPF.pdb" models #31 relModel #30
> hide #!31 models
> show #!30 models
> show #!29 models
> volume #30 level 0.06338
> open /Users/eruboldi/Downloads/cryosparc_P2_mask_TMDs(1).mrc
Opened cryosparc_P2_mask_TMDs(1).mrc as #32, grid size 512,512,512, pixel
0.573, shown at level 0.00261, step 2, values float32
> volume #32 level 0.009252
> hide #!29 models
> volume #32 level 0.009991
> volume #32 level 0.045
> color #32 #99bfe587 models
> volume #32 level 0.07085
> show #!29 models
> hide #!29 models
> volume #32 level 0.07
> select add #28
3439 atoms, 3520 bonds, 2 pseudobonds, 445 residues, 3 models selected
> select subtract #28
Nothing selected
> open /Users/eruboldi/Downloads/cryosparc_P2_J146_003_volume_map_sharp.mrc
Opened cryosparc_P2_J146_003_volume_map_sharp.mrc as #33, grid size
512,512,512, pixel 0.573, shown at level 0.0155, step 2, values float32
> volume #33 level 0.04583
> hide #!32 models
> volume #33 level 0.07402
> surface dust #33 size 5.73
> cofr #28
> open /Users/eruboldi/Downloads/cryosparc_P2_J148_mask.mrc
Opened cryosparc_P2_J148_mask.mrc as #34, grid size 512,512,512, pixel 0.573,
shown at level 5e-05, step 2, values float32
> volume #33 step 1
> volume #34 step 1
> color #34 #b2b2b27e models
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!28 models
> show #!28 models
> hide #!29 models
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!29 models
> show #!26 models
> hide #!26 models
> hide #!34 models
> show #!34 models
> show #!29 models
> hide #!29 models
> show #!29 models
> show #!27 models
> hide #!27 models
> show #!27 models
> hide #!27 models
> save "/Users/eruboldi/Desktop/GPI/chimeraX
> sessions/ctGWT1/scGPI17_Cu_Ermanno.cxs"
> save "/Users/eruboldi/Desktop/GPI/chimeraX
> sessions/ctGWT1/scGPI17_Cu_Julian.cxs" includeMaps true
> close #25
> close #1
> close #2-13
> show #!14 models
> hide #!14 models
> close #14
> show #!15 models
> show #!16 models
> close #15
> close #16
> show #!17 models
> show #!19 models
> show #!21 models
> hide #!34 models
> hide #!29 models
> hide #!28 models
> hide #!21 models
> show #!21 models
> hide #!19 models
> show #!19 models
> show #!18 models
> close #18
> show #!20 models
> hide #!21 models
> show #!21 models
> hide #!20 models
> hide #!21 models
> show #!21 models
> show #!22 models
> show #!23 models
> close #22
> close #23
> close #20
> show #!24 models
> show #!26 models
> hide #!21 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> hide #!19 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!26 models
> show #!26 models
> hide #!24 models
> show #!28 models
> hide #!28 models
> close #28
> close #29
> close #30
> close #31
> close #32
> open "/Users/eruboldi/Downloads/GlcNPI (1).pdb"
> select add #1
36 atoms, 37 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,151.44,0,1,0,137.32,0,0,1,130.62
> view matrix models #1,1,0,0,172.48,0,1,0,145,0,0,1,133.52
> view matrix models #1,1,0,0,177.42,0,1,0,151.39,0,0,1,138.14
> view matrix models #1,1,0,0,177.43,0,1,0,152.25,0,0,1,119.35
> view matrix models #1,1,0,0,163.6,0,1,0,147.61,0,0,1,110.31
> ui mousemode right translate
> ui tool show "Side View"
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,184.54,0,1,0,167.98,0,0,1,184.43
> open /Users/eruboldi/Downloads/cryosparc_P2_J146_003_volume_map_sharp(1).mrc
Opened cryosparc_P2_J146_003_volume_map_sharp(1).mrc as #2, grid size
512,512,512, pixel 0.573, shown at level 0.0155, step 2, values float32
> hide #!2 models
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.79262,-0.18585,0.5807,182.51,0.39175,0.57457,0.71861,168.98,-0.46721,0.79707,-0.38261,182.89
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.79262,-0.18585,0.5807,176.13,0.39175,0.57457,0.71861,164.42,-0.46721,0.79707,-0.38261,143.88
> view matrix models
> #1,-0.79262,-0.18585,0.5807,166.7,0.39175,0.57457,0.71861,165.62,-0.46721,0.79707,-0.38261,152.79
> open /Users/eruboldi/Downloads/cryosparc_P2_J150_003_volume_map_sharp.mrc
Opened cryosparc_P2_J150_003_volume_map_sharp.mrc as #3, grid size
512,512,512, pixel 0.573, shown at level 0.0158, step 2, values float32
> view matrix models
> #1,-0.79262,-0.18585,0.5807,170.6,0.39175,0.57457,0.71861,158.65,-0.46721,0.79707,-0.38261,146.97
> hide #!3 models
> view matrix models
> #1,-0.79262,-0.18585,0.5807,182.73,0.39175,0.57457,0.71861,146.2,-0.46721,0.79707,-0.38261,148.33
> view matrix models
> #1,-0.79262,-0.18585,0.5807,149.49,0.39175,0.57457,0.71861,125.15,-0.46721,0.79707,-0.38261,163.93
> view matrix models
> #1,-0.79262,-0.18585,0.5807,149.02,0.39175,0.57457,0.71861,120.9,-0.46721,0.79707,-0.38261,154.97
> view matrix models
> #1,-0.79262,-0.18585,0.5807,155.24,0.39175,0.57457,0.71861,124.67,-0.46721,0.79707,-0.38261,149.6
> view matrix models
> #1,-0.79262,-0.18585,0.5807,152.17,0.39175,0.57457,0.71861,128.28,-0.46721,0.79707,-0.38261,152.54
> view matrix models
> #1,-0.79262,-0.18585,0.5807,154.12,0.39175,0.57457,0.71861,129.04,-0.46721,0.79707,-0.38261,150.74
> view matrix models
> #1,-0.79262,-0.18585,0.5807,153.57,0.39175,0.57457,0.71861,130.11,-0.46721,0.79707,-0.38261,151.56
> fitmap #1 inMap #26
Fit molecule GlcNPI (1).pdb (#1) to map
cryosparc_P2_J139_003_volume_map_sharp.mrc (#26) using 36 atoms
average map value = 0.1262, steps = 356
shifted from previous position = 3.66
rotated from previous position = 55.4 degrees
atoms outside contour = 17, contour level = 0.12107
Position of GlcNPI (1).pdb (#1) relative to
cryosparc_P2_J139_003_volume_map_sharp.mrc (#26) coordinates:
Matrix rotation and translation
-0.40645676 -0.89682846 0.17461850 155.66551378
0.19401174 0.10204180 0.97567767 132.96273726
-0.89283389 0.43044882 0.13251967 150.37079508
Axis -0.33641610 0.65863751 0.67306822
Axis point 99.04730815 69.41370304 0.00000000
Rotation angle (degrees) 125.86996479
Shift along axis 136.41566484
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Computing secondary structure
> clipper associate #26 toModel #1
Opened cryosparc_P2_J139_003_volume_map_sharp.mrc as #1.1.1.1, grid size
512,512,512, pixel 0.573, shown at step 1, values float32
> isolde sim start #1.2/A
Loading residue template for GPI from internal database
Sim termination reason: None
ISOLDE: stopped sim
> addh #1.2
Summary of feedback from adding hydrogens to GlcNPI (1).pdb #1.2
---
notes | Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
9 hydrogen bonds
30 hydrogens added
> isolde sim start #1.2/A
Sim termination reason: None
ISOLDE: stopped sim
> isolde sim start #1.2/A
Sim termination reason: None
ISOLDE: stopped sim
Fetching CCD GPI from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/I/GPI/GPI.cif
> clipper spotlight #1.2
> clipper isolate #1.2.2/A maskRadius 4.0 focus false
> isolde sim start #1.2/A
Sim termination reason: None
ISOLDE: stopped sim
> isolde stepto #1.2/A
> isolde sim start #1.2/A
Sim termination reason: None
ISOLDE: stopped sim
> volume #1.1.1.1 level 0.1312
> close #1
> open /Users/eruboldi/Downloads/cryosparc_P2_J139_003_volume_map_sharp.mrc
Opened cryosparc_P2_J139_003_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 0.573, shown at level 0.0261, step 2, values float32
> volume #1 step 1
> volume #3 step 1
> volume #2 step 1
> volume #1 level 0.1934
> volume #1 level 0.06975
> surface dust #1 size 5.73
> volume #1 level 0.1134
> hide #!1 models
> show #!2 models
> show #!3 models
> volume #3 level 0.05586
> volume #2 level 0.0561
> hide #!3 models
> hide #!17 models
> volume #2 level 0.1215
> volume #2 level 0.06512
> volume #3 level 0.0514
> surface dust #2 size 5.73
> surface dust #3 size 5.73
> hide #!2 models
> volume #3 level 0.067
> open "/Users/eruboldi/Downloads/GlcNPI (1).pdb"
Must specify one map, got 0
> fitmap #1 inMap #3
Fit map cryosparc_P2_J139_003_volume_map_sharp.mrc in map
cryosparc_P2_J150_003_volume_map_sharp.mrc using 121529 points
correlation = 0.3597, correlation about mean = 0.1048, overlap = 940.5
steps = 112, shift = 2.81, angle = 7.29 degrees
Position of cryosparc_P2_J139_003_volume_map_sharp.mrc (#1) relative to
cryosparc_P2_J150_003_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99993782 0.01094420 -0.00214093 -2.32279855
-0.01112700 0.99192459 -0.12633999 19.70974441
0.00074095 0.12635595 0.99198469 -19.43107805
Axis 0.99614301 -0.01136052 -0.08700602
Axis point 0.00000000 163.59177387 145.47294829
Rotation angle (degrees) 7.28686300
Shift along axis -0.84713172
> select add #4
36 atoms, 37 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,-16.137,0,1,0,-3.5943,0,0,1,-90.621
Must specify one map, got 0
> fitmap #4 inMap #3
Fit molecule GlcNPI (1).pdb (#4) to map
cryosparc_P2_J150_003_volume_map_sharp.mrc (#3) using 36 atoms
average map value = 0, steps = 24
shifted from previous position = 0
rotated from previous position = 0 degrees
atoms outside contour = 36, contour level = 0.067
Position of GlcNPI (1).pdb (#4) relative to
cryosparc_P2_J150_003_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 -16.13710131
0.00000000 1.00000000 0.00000000 -3.59431574
0.00000000 0.00000000 1.00000000 -90.62087500
Axis 0.00000000 0.00000000 1.00000000
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -90.62087500
> view matrix models #4,1,0,0,-46.737,0,1,0,-18.322,0,0,1,-196.93
> view matrix models #4,1,0,0,-50.746,0,1,0,-10.37,0,0,1,-235.09
> hide #!3 models
> show #4
> hide #4 models
> show #4 models
> view matrix models #4,1,0,0,334.86,0,1,0,176.62,0,0,1,370.33
> view matrix models #4,1,0,0,241.14,0,1,0,130.68,0,0,1,224.78
> view matrix models #4,1,0,0,219.34,0,1,0,120.93,0,0,1,187.92
> view matrix models #4,1,0,0,201.32,0,1,0,111.95,0,0,1,160.36
> show #!3 models
> view matrix models #4,1,0,0,169.72,0,1,0,93.483,0,0,1,120.88
> view matrix models #4,1,0,0,176.43,0,1,0,107.85,0,0,1,148.48
> view matrix models #4,1,0,0,174.74,0,1,0,128.54,0,0,1,147.18
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.24463,-0.95711,-0.15524,172.71,0.95859,-0.26281,0.10973,129.66,-0.14582,-0.12196,0.98176,146.94
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.24463,-0.95711,-0.15524,158.04,0.95859,-0.26281,0.10973,110.96,-0.14582,-0.12196,0.98176,150.23
> view matrix models
> #4,-0.24463,-0.95711,-0.15524,157.14,0.95859,-0.26281,0.10973,131.27,-0.14582,-0.12196,0.98176,140.44
> view matrix models
> #4,-0.24463,-0.95711,-0.15524,144.9,0.95859,-0.26281,0.10973,125.34,-0.14582,-0.12196,0.98176,147.63
> view matrix models
> #4,-0.24463,-0.95711,-0.15524,142.19,0.95859,-0.26281,0.10973,125.44,-0.14582,-0.12196,0.98176,144.61
> view matrix models
> #4,-0.24463,-0.95711,-0.15524,144.52,0.95859,-0.26281,0.10973,130.68,-0.14582,-0.12196,0.98176,146.53
> ui tool show "Side View"
> view matrix models
> #4,-0.24463,-0.95711,-0.15524,143.76,0.95859,-0.26281,0.10973,132.67,-0.14582,-0.12196,0.98176,142.37
> view matrix models
> #4,-0.24463,-0.95711,-0.15524,137.8,0.95859,-0.26281,0.10973,131.05,-0.14582,-0.12196,0.98176,144.6
> view matrix models
> #4,-0.24463,-0.95711,-0.15524,137.5,0.95859,-0.26281,0.10973,130.46,-0.14582,-0.12196,0.98176,146.77
> color #3 #b2ffff9c models
> view matrix models
> #4,-0.24463,-0.95711,-0.15524,137.82,0.95859,-0.26281,0.10973,130.93,-0.14582,-0.12196,0.98176,145.89
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.75914,0.29407,-0.58072,139.13,0.57924,0.10183,0.80877,131.03,0.29697,-0.95034,-0.093038,145.48
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.75914,0.29407,-0.58072,138.18,0.57924,0.10183,0.80877,129.63,0.29697,-0.95034,-0.093038,146.38
> fitmap #4 inMap #3
Fit molecule GlcNPI (1).pdb (#4) to map
cryosparc_P2_J150_003_volume_map_sharp.mrc (#3) using 36 atoms
average map value = 0.1488, steps = 188
shifted from previous position = 3.3
rotated from previous position = 63 degrees
atoms outside contour = 11, contour level = 0.067
Position of GlcNPI (1).pdb (#4) relative to
cryosparc_P2_J150_003_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.79152332 -0.53345755 -0.29818430 138.23983655
0.60333437 0.60436263 0.52032053 126.43059174
-0.09735747 -0.59175068 0.80022038 145.23569780
Axis -0.69378145 -0.12528868 0.70920381
Axis point -36.03152662 261.84496038 0.00000000
Rotation angle (degrees) 53.26940734
Shift along axis -8.74684571
> view matrix models
> #4,0.79152,-0.53346,-0.29818,139.79,0.60333,0.60436,0.52032,128.3,-0.097357,-0.59175,0.80022,143.63
> view matrix models
> #4,0.79152,-0.53346,-0.29818,140.15,0.60333,0.60436,0.52032,128.54,-0.097357,-0.59175,0.80022,144.05
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.71056,-0.68075,-0.17799,140.1,0.66874,0.57468,0.47173,128.58,-0.21884,-0.45423,0.86359,143.96
> view matrix models
> #4,-0.32514,0.034933,0.94502,139.71,0.7444,-0.60686,0.27855,128.28,0.58323,0.79404,0.17131,144.79
> view matrix models
> #4,-0.20326,-0.44435,0.87249,139.72,0.97907,-0.10186,0.17621,128.63,0.010569,0.89004,0.45575,144.25
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.20326,-0.44435,0.87249,140.1,0.97907,-0.10186,0.17621,129.02,0.010569,0.89004,0.45575,147.14
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.69,0.57723,-0.4367,140.53,0.47331,0.096637,0.87558,128.92,0.54761,-0.81084,-0.20653,146.99
> fitmap #4 inMap #3
Fit molecule GlcNPI (1).pdb (#4) to map
cryosparc_P2_J150_003_volume_map_sharp.mrc (#3) using 36 atoms
average map value = 0.1008, steps = 116
shifted from previous position = 2.78
rotated from previous position = 8.74 degrees
atoms outside contour = 14, contour level = 0.067
Position of GlcNPI (1).pdb (#4) relative to
cryosparc_P2_J150_003_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.58368143 0.64451198 -0.49388290 138.36249757
0.49279263 0.20224269 0.84631751 130.36763214
0.64534597 -0.73736166 -0.19956545 145.93899156
Axis -0.80933839 -0.58220230 -0.07753609
Axis point 0.00000000 80.77525529 59.13256761
Rotation angle (degrees) 101.93610009
Shift along axis -199.19795571
> hide #4 models
> select subtract #4
Nothing selected
===== 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
Failed to send bug report. Error while sending follows:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/bug_reporter/tool.py", line 264, in submit
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST,
BUG_SELECTOR, fields, timeout=10, ssl=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/webservices/post_form.py", line 45, in
post_multipart_formdata
return r.status, r.msg, r.getheaders(), r.read()
^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 489, in read
s = self._safe_read(self.length)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 640, in _safe_read
raise IncompleteRead(data, amt-len(data))
http.client.IncompleteRead: IncompleteRead(666 bytes read, 6446 more expected)
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 Pro
Model Identifier: Mac14,7
Model Number: Z16U000NJD/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 13822.61.10
OS Loader Version: 13822.61.10
Software:
System Software Overview:
System Version: macOS 26.2 (25C56)
Kernel Version: Darwin 25.2.0
Time since boot: 147 days, 17 hours, 40 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 Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
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-Clipper: 0.26.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ISOLDE: 1.11.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
narwhals: 2.22.1
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 2.4.6
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
plotly: 6.7.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pyKVFinder: 0.9.2
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
tomlkit: 0.15.0
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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